[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/22507097/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/22595606/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=126, common to both=126
[1] "Reduce the number of clustering variables from 697 to 658."
[1] 658 126
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           100             26 
  KRAS MUTATED KRAS WILD-TYPE 
           100             26 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            81             45 
  TP53 MUTATED TP53 WILD-TYPE 
            81             45 
[1] "MAMLD1 MUTATION ANALYSIS"
[1] 3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
              28               98 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
              28               98 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              27               99 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              27               99 
[1] "CD99L2 MUTATION ANALYSIS"
[1] 3
  CD99L2 MUTATED CD99L2 WILD-TYPE 
              20              106 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
              20              106 
[1] "IPP MUTATION ANALYSIS"
[1] 3
  IPP MUTATED IPP WILD-TYPE 
           20           106 
  IPP MUTATED IPP WILD-TYPE 
           20           106 
[1] "IRS1 MUTATION ANALYSIS"
[1] 3
  IRS1 MUTATED IRS1 WILD-TYPE 
            20            106 
  IRS1 MUTATED IRS1 WILD-TYPE 
            20            106 
[1] "C19ORF55 MUTATION ANALYSIS"
[1] 3
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                16                110 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                16                110 
[1] "C15ORF24 MUTATION ANALYSIS"
[1] 3
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
                15                111 
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
                15                111 
[1] "QRICH1 MUTATION ANALYSIS"
[1] 3
  QRICH1 MUTATED QRICH1 WILD-TYPE 
              14              112 
  QRICH1 MUTATED QRICH1 WILD-TYPE 
              14              112 
[1] "IFT46 MUTATION ANALYSIS"
[1] 3
  IFT46 MUTATED IFT46 WILD-TYPE 
             13             113 
  IFT46 MUTATED IFT46 WILD-TYPE 
             13             113 
[1] "ARHGAP18 MUTATION ANALYSIS"
[1] 3
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                12                114 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                12                114 
[1] "EME2 MUTATION ANALYSIS"
[1] 3
  EME2 MUTATED EME2 WILD-TYPE 
            11            115 
  EME2 MUTATED EME2 WILD-TYPE 
            11            115 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             100 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             100 
[1] "NPNT MUTATION ANALYSIS"
[1] 3
  NPNT MUTATED NPNT WILD-TYPE 
            12            114 
  NPNT MUTATED NPNT WILD-TYPE 
            12            114 
[1] "TNFSF9 MUTATION ANALYSIS"
[1] 3
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
              12              114 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
              12              114 
[1] "SRP14 MUTATION ANALYSIS"
[1] 3
  SRP14 MUTATED SRP14 WILD-TYPE 
              9             117 
  SRP14 MUTATED SRP14 WILD-TYPE 
              9             117 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              17              109 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              17              109 
[1] "ERF MUTATION ANALYSIS"
[1] 3
  ERF MUTATED ERF WILD-TYPE 
           13           113 
  ERF MUTATED ERF WILD-TYPE 
           13           113 
[1] "MED9 MUTATION ANALYSIS"
[1] 3
  MED9 MUTATED MED9 WILD-TYPE 
             7            119 
  MED9 MUTATED MED9 WILD-TYPE 
             7            119 
[1] "BHLHB9 MUTATION ANALYSIS"
[1] 3
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
              12              114 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
              12              114 
[1] "ZNF185 MUTATION ANALYSIS"
[1] 3
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              116 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              116 
[1] "IRX4 MUTATION ANALYSIS"
[1] 3
  IRX4 MUTATED IRX4 WILD-TYPE 
            10            116 
  IRX4 MUTATED IRX4 WILD-TYPE 
            10            116 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             13             113 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             13             113 
[1] "EDC4 MUTATION ANALYSIS"
[1] 3
  EDC4 MUTATED EDC4 WILD-TYPE 
            16            110 
  EDC4 MUTATED EDC4 WILD-TYPE 
            16            110 
[1] "CCDC135 MUTATION ANALYSIS"
[1] 3
  CCDC135 MUTATED CCDC135 WILD-TYPE 
               13               113 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
               13               113 
[1] "APP MUTATION ANALYSIS"
[1] 3
  APP MUTATED APP WILD-TYPE 
           12           114 
  APP MUTATED APP WILD-TYPE 
           12           114 
[1] "TMC4 MUTATION ANALYSIS"
[1] 3
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            106 
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            106 
[1] "PHF13 MUTATION ANALYSIS"
[1] 3
  PHF13 MUTATED PHF13 WILD-TYPE 
              9             117 
  PHF13 MUTATED PHF13 WILD-TYPE 
              9             117 
[1] "B4GALT2 MUTATION ANALYSIS"
[1] 3
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
               10               116 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
               10               116 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               6              120 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               6              120 
[1] "YIPF2 MUTATION ANALYSIS"
[1] 3
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             11             115 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             11             115 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
             12             114 
  MED15 MUTATED MED15 WILD-TYPE 
             12             114 
[1] "MBD3 MUTATION ANALYSIS"
[1] 3
  MBD3 MUTATED MBD3 WILD-TYPE 
             9            117 
  MBD3 MUTATED MBD3 WILD-TYPE 
             9            117 
[1] "WWTR1 MUTATION ANALYSIS"
[1] 3
  WWTR1 MUTATED WWTR1 WILD-TYPE 
             12             114 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
             12             114 
[1] "FAM63B MUTATION ANALYSIS"
[1] 3
  FAM63B MUTATED FAM63B WILD-TYPE 
              11              115 
  FAM63B MUTATED FAM63B WILD-TYPE 
              11              115 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                13                113 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                13                113 
[1] "ERCC3 MUTATION ANALYSIS"
[1] 3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              9             117 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              9             117 
[1] "MYH10 MUTATION ANALYSIS"
[1] 3
  MYH10 MUTATED MYH10 WILD-TYPE 
             14             112 
  MYH10 MUTATED MYH10 WILD-TYPE 
             14             112 
[1] "ZMYM5 MUTATION ANALYSIS"
[1] 3
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
             13             113 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
             13             113 
[1] "CDCA8 MUTATION ANALYSIS"
[1] 3
  CDCA8 MUTATED CDCA8 WILD-TYPE 
              9             117 
  CDCA8 MUTATED CDCA8 WILD-TYPE 
              9             117 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
            11            115 
  PAK1 MUTATED PAK1 WILD-TYPE 
            11            115 
[1] "WRN MUTATION ANALYSIS"
[1] 3
  WRN MUTATED WRN WILD-TYPE 
           15           111 
  WRN MUTATED WRN WILD-TYPE 
           15           111 
[1] "CLOCK MUTATION ANALYSIS"
[1] 3
  CLOCK MUTATED CLOCK WILD-TYPE 
             12             114 
  CLOCK MUTATED CLOCK WILD-TYPE 
             12             114 
[1] "TMEM175 MUTATION ANALYSIS"
[1] 3
  TMEM175 MUTATED TMEM175 WILD-TYPE 
               13               113 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
               13               113 
[1] "THBS4 MUTATION ANALYSIS"
[1] 3
  THBS4 MUTATED THBS4 WILD-TYPE 
             16             110 
  THBS4 MUTATED THBS4 WILD-TYPE 
             16             110 
[1] "TMED10 MUTATION ANALYSIS"
[1] 3
  TMED10 MUTATED TMED10 WILD-TYPE 
               8              118 
  TMED10 MUTATED TMED10 WILD-TYPE 
               8              118 
[1] "NFIL3 MUTATION ANALYSIS"
[1] 3
  NFIL3 MUTATED NFIL3 WILD-TYPE 
             10             116 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
             10             116 
[1] "RGPD5 MUTATION ANALYSIS"
[1] 3
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              6             120 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              6             120 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            118 
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            118 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
             13             113 
  MED12 MUTATED MED12 WILD-TYPE 
             13             113 
[1] "SYT15 MUTATION ANALYSIS"
[1] 3
  SYT15 MUTATED SYT15 WILD-TYPE 
             11             115 
  SYT15 MUTATED SYT15 WILD-TYPE 
             11             115 
[1] "OTUD4 MUTATION ANALYSIS"
[1] 3
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             18             108 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             18             108 
[1] "KIAA1949 MUTATION ANALYSIS"
[1] 3
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                10                116 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                10                116 
[1] "OR10A7 MUTATION ANALYSIS"
[1] 3
  OR10A7 MUTATED OR10A7 WILD-TYPE 
              12              114 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
              12              114 
[1] "SYNGAP1 MUTATION ANALYSIS"
[1] 3
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
               15               111 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
               15               111 
[1] "TOX4 MUTATION ANALYSIS"
[1] 3
  TOX4 MUTATED TOX4 WILD-TYPE 
             9            117 
  TOX4 MUTATED TOX4 WILD-TYPE 
             9            117 
[1] "CUL4B MUTATION ANALYSIS"
[1] 3
  CUL4B MUTATED CUL4B WILD-TYPE 
             13             113 
  CUL4B MUTATED CUL4B WILD-TYPE 
             13             113 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
             13             113 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
             13             113 
[1] "OTOF MUTATION ANALYSIS"
[1] 3
  OTOF MUTATED OTOF WILD-TYPE 
            18            108 
  OTOF MUTATED OTOF WILD-TYPE 
            18            108 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
            10            116 
  SMG7 MUTATED SMG7 WILD-TYPE 
            10            116 
[1] "SLC6A9 MUTATION ANALYSIS"
[1] 3
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
              10              116 
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
              10              116 
[1] "INTS7 MUTATION ANALYSIS"
[1] 3
  INTS7 MUTATED INTS7 WILD-TYPE 
              9             117 
  INTS7 MUTATED INTS7 WILD-TYPE 
              9             117 
[1] "PASD1 MUTATION ANALYSIS"
[1] 3
  PASD1 MUTATED PASD1 WILD-TYPE 
             12             114 
  PASD1 MUTATED PASD1 WILD-TYPE 
             12             114 
[1] "BRDT MUTATION ANALYSIS"
[1] 3
  BRDT MUTATED BRDT WILD-TYPE 
            11            115 
  BRDT MUTATED BRDT WILD-TYPE 
            11            115 
[1] "CDH3 MUTATION ANALYSIS"
[1] 3
  CDH3 MUTATED CDH3 WILD-TYPE 
             7            119 
  CDH3 MUTATED CDH3 WILD-TYPE 
             7            119 
[1] "CTAGE5 MUTATION ANALYSIS"
[1] 3
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
               8              118 
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
               8              118 
[1] "C6ORF165 MUTATION ANALYSIS"
[1] 3
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 9                117 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 9                117 
[1] "POP5 MUTATION ANALYSIS"
[1] 3
  POP5 MUTATED POP5 WILD-TYPE 
             6            120 
  POP5 MUTATED POP5 WILD-TYPE 
             6            120 
[1] "CEL MUTATION ANALYSIS"
[1] 3
  CEL MUTATED CEL WILD-TYPE 
            7           119 
  CEL MUTATED CEL WILD-TYPE 
            7           119 
[1] "EIF3C MUTATION ANALYSIS"
[1] 3
  EIF3C MUTATED EIF3C WILD-TYPE 
              9             117 
  EIF3C MUTATED EIF3C WILD-TYPE 
              9             117 
[1] "NR4A3 MUTATION ANALYSIS"
[1] 3
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              7             119 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              7             119 
[1] "DPYS MUTATION ANALYSIS"
[1] 3
  DPYS MUTATED DPYS WILD-TYPE 
            11            115 
  DPYS MUTATED DPYS WILD-TYPE 
            11            115 
[1] "LRIG1 MUTATION ANALYSIS"
[1] 3
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             11             115 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             11             115 
[1] "EPS8L3 MUTATION ANALYSIS"
[1] 3
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               8              118 
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               8              118 
[1] "RIOK1 MUTATION ANALYSIS"
[1] 3
  RIOK1 MUTATED RIOK1 WILD-TYPE 
              8             118 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
              8             118 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             11             115 
  RBM10 MUTATED RBM10 WILD-TYPE 
             11             115 
[1] "USP40 MUTATION ANALYSIS"
[1] 3
  USP40 MUTATED USP40 WILD-TYPE 
             10             116 
  USP40 MUTATED USP40 WILD-TYPE 
             10             116 
[1] "NAPSA MUTATION ANALYSIS"
[1] 3
  NAPSA MUTATED NAPSA WILD-TYPE 
              8             118 
  NAPSA MUTATED NAPSA WILD-TYPE 
              8             118 
[1] "GPR25 MUTATION ANALYSIS"
[1] 3
  GPR25 MUTATED GPR25 WILD-TYPE 
              5             121 
  GPR25 MUTATED GPR25 WILD-TYPE 
              5             121 
[1] "SETD1A MUTATION ANALYSIS"
[1] 3
  SETD1A MUTATED SETD1A WILD-TYPE 
              11              115 
  SETD1A MUTATED SETD1A WILD-TYPE 
              11              115 
[1] "SEC63 MUTATION ANALYSIS"
[1] 3
  SEC63 MUTATED SEC63 WILD-TYPE 
              8             118 
  SEC63 MUTATED SEC63 WILD-TYPE 
              8             118 
[1] "GAS2L2 MUTATION ANALYSIS"
[1] 3
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
              12              114 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
              12              114 
[1] "PHF8 MUTATION ANALYSIS"
[1] 3
  PHF8 MUTATED PHF8 WILD-TYPE 
            11            115 
  PHF8 MUTATED PHF8 WILD-TYPE 
            11            115 
[1] "SLC39A5 MUTATION ANALYSIS"
[1] 3
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                8               118 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                8               118 
[1] "FAM82A2 MUTATION ANALYSIS"
[1] 3
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
                8               118 
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
                8               118 
[1] "CHGA MUTATION ANALYSIS"
[1] 3
  CHGA MUTATED CHGA WILD-TYPE 
            11            115 
  CHGA MUTATED CHGA WILD-TYPE 
            11            115 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
             7            119 
  EGR1 MUTATED EGR1 WILD-TYPE 
             7            119 
[1] "OLIG3 MUTATION ANALYSIS"
[1] 3
  OLIG3 MUTATED OLIG3 WILD-TYPE 
             10             116 
  OLIG3 MUTATED OLIG3 WILD-TYPE 
             10             116 
[1] "C14ORF49 MUTATION ANALYSIS"
[1] 3
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 8                118 
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 8                118 
[1] "TOB1 MUTATION ANALYSIS"
[1] 3
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            120 
  TOB1 MUTATED TOB1 WILD-TYPE 
             6            120 
[1] "MEPCE MUTATION ANALYSIS"
[1] 3
  MEPCE MUTATED MEPCE WILD-TYPE 
             10             116 
  MEPCE MUTATED MEPCE WILD-TYPE 
             10             116 
[1] "TXLNG MUTATION ANALYSIS"
[1] 3
  TXLNG MUTATED TXLNG WILD-TYPE 
              7             119 
  TXLNG MUTATED TXLNG WILD-TYPE 
              7             119 
[1] "TTK MUTATION ANALYSIS"
[1] 3
  TTK MUTATED TTK WILD-TYPE 
           12           114 
  TTK MUTATED TTK WILD-TYPE 
           12           114 
[1] "TMCO1 MUTATION ANALYSIS"
[1] 3
  TMCO1 MUTATED TMCO1 WILD-TYPE 
              8             118 
  TMCO1 MUTATED TMCO1 WILD-TYPE 
              8             118 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              117 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              117 
[1] "PTPRF MUTATION ANALYSIS"
[1] 3
  PTPRF MUTATED PTPRF WILD-TYPE 
             13             113 
  PTPRF MUTATED PTPRF WILD-TYPE 
             13             113 
[1] "YTHDF1 MUTATION ANALYSIS"
[1] 3
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               8              118 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               8              118 
[1] "AAMP MUTATION ANALYSIS"
[1] 3
  AAMP MUTATED AAMP WILD-TYPE 
             6            120 
  AAMP MUTATED AAMP WILD-TYPE 
             6            120 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
             6            120 
  RAI1 MUTATED RAI1 WILD-TYPE 
             6            120 
[1] "PDZD7 MUTATION ANALYSIS"
[1] 3
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              7             119 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              7             119 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          12          114 
  F8 MUTATED F8 WILD-TYPE 
          12          114 
[1] "CACNA1D MUTATION ANALYSIS"
[1] 3
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               16               110 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               16               110 
[1] "IFNGR2 MUTATION ANALYSIS"
[1] 3
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               7              119 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               7              119 
[1] "ALS2CR11 MUTATION ANALYSIS"
[1] 3
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 8                118 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 8                118 
[1] "OSBPL1A MUTATION ANALYSIS"
[1] 3
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                9               117 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                9               117 
[1] "SLC24A1 MUTATION ANALYSIS"
[1] 3
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                6               120 
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                6               120 
[1] "PDZD2 MUTATION ANALYSIS"
[1] 3
  PDZD2 MUTATED PDZD2 WILD-TYPE 
             13             113 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
             13             113 
[1] "CIR1 MUTATION ANALYSIS"
[1] 3
  CIR1 MUTATED CIR1 WILD-TYPE 
             5            121 
  CIR1 MUTATED CIR1 WILD-TYPE 
             5            121 
[1] "ZNF184 MUTATION ANALYSIS"
[1] 3
  ZNF184 MUTATED ZNF184 WILD-TYPE 
              10              116 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
              10              116 
[1] "RBM15B MUTATION ANALYSIS"
[1] 3
  RBM15B MUTATED RBM15B WILD-TYPE 
               7              119 
  RBM15B MUTATED RBM15B WILD-TYPE 
               7              119 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            17            109 
  ATRX MUTATED ATRX WILD-TYPE 
            17            109 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             11             115 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             11             115 
[1] "APOBEC4 MUTATION ANALYSIS"
[1] 3
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                6               120 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                6               120 
[1] "ST6GALNAC5 MUTATION ANALYSIS"
[1] 3
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                  12                  114 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                  12                  114 
[1] "OFD1 MUTATION ANALYSIS"
[1] 3
  OFD1 MUTATED OFD1 WILD-TYPE 
             7            119 
  OFD1 MUTATED OFD1 WILD-TYPE 
             7            119 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               8              118 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               8              118 
[1] "AFTPH MUTATION ANALYSIS"
[1] 3
  AFTPH MUTATED AFTPH WILD-TYPE 
              9             117 
  AFTPH MUTATED AFTPH WILD-TYPE 
              9             117 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                5               121 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                5               121 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             117 
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             117 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              6             120 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              6             120 
[1] "HSD17B7 MUTATION ANALYSIS"
[1] 3
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                8               118 
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                8               118 
[1] "HTATSF1 MUTATION ANALYSIS"
[1] 3
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
                9               117 
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
                9               117 
[1] "PRDM8 MUTATION ANALYSIS"
[1] 3
  PRDM8 MUTATED PRDM8 WILD-TYPE 
              8             118 
  PRDM8 MUTATED PRDM8 WILD-TYPE 
              8             118 
[1] "TIGD6 MUTATION ANALYSIS"
[1] 3
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              7             119 
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              7             119 
[1] "CLCC1 MUTATION ANALYSIS"
[1] 3
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              6             120 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              6             120 
[1] "MKL1 MUTATION ANALYSIS"
[1] 3
  MKL1 MUTATED MKL1 WILD-TYPE 
             7            119 
  MKL1 MUTATED MKL1 WILD-TYPE 
             7            119 
[1] "SFRS2IP MUTATION ANALYSIS"
[1] 3
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               11               115 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               11               115 
[1] "PAK3 MUTATION ANALYSIS"
[1] 3
  PAK3 MUTATED PAK3 WILD-TYPE 
            12            114 
  PAK3 MUTATED PAK3 WILD-TYPE 
            12            114 
[1] "RTKN2 MUTATION ANALYSIS"
[1] 3
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              8             118 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              8             118 
[1] "TEX2 MUTATION ANALYSIS"
[1] 3
  TEX2 MUTATED TEX2 WILD-TYPE 
             9            117 
  TEX2 MUTATED TEX2 WILD-TYPE 
             9            117 
[1] "TMEM41A MUTATION ANALYSIS"
[1] 3
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                6               120 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                6               120 
[1] "DHX57 MUTATION ANALYSIS"
[1] 3
  DHX57 MUTATED DHX57 WILD-TYPE 
             11             115 
  DHX57 MUTATED DHX57 WILD-TYPE 
             11             115 
[1] "UHRF1BP1 MUTATION ANALYSIS"
[1] 3
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 7                119 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 7                119 
[1] "NEDD4L MUTATION ANALYSIS"
[1] 3
  NEDD4L MUTATED NEDD4L WILD-TYPE 
              10              116 
  NEDD4L MUTATED NEDD4L WILD-TYPE 
              10              116 
[1] "SMCR7 MUTATION ANALYSIS"
[1] 3
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              7             119 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              7             119 
[1] "PUM2 MUTATION ANALYSIS"
[1] 3
  PUM2 MUTATED PUM2 WILD-TYPE 
             7            119 
  PUM2 MUTATED PUM2 WILD-TYPE 
             7            119 
[1] "IL1R2 MUTATION ANALYSIS"
[1] 3
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              6             120 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              6             120 
[1] "SLC22A9 MUTATION ANALYSIS"
[1] 3
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               118 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               118 
[1] "MAGEA10 MUTATION ANALYSIS"
[1] 3
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                6               120 
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                6               120 
[1] "PTPLAD2 MUTATION ANALYSIS"
[1] 3
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
                6               120 
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
                6               120 
[1] "HERC5 MUTATION ANALYSIS"
[1] 3
  HERC5 MUTATED HERC5 WILD-TYPE 
              6             120 
  HERC5 MUTATED HERC5 WILD-TYPE 
              6             120 
[1] "WDR67 MUTATION ANALYSIS"
[1] 3
  WDR67 MUTATED WDR67 WILD-TYPE 
              5             121 
  WDR67 MUTATED WDR67 WILD-TYPE 
              5             121 
[1] "TMEM40 MUTATION ANALYSIS"
[1] 3
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               6              120 
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               6              120 
[1] "UNC5A MUTATION ANALYSIS"
[1] 3
  UNC5A MUTATED UNC5A WILD-TYPE 
              8             118 
  UNC5A MUTATED UNC5A WILD-TYPE 
              8             118 
[1] "AARS2 MUTATION ANALYSIS"
[1] 3
  AARS2 MUTATED AARS2 WILD-TYPE 
              7             119 
  AARS2 MUTATED AARS2 WILD-TYPE 
              7             119 
[1] "PDILT MUTATION ANALYSIS"
[1] 3
  PDILT MUTATED PDILT WILD-TYPE 
              9             117 
  PDILT MUTATED PDILT WILD-TYPE 
              9             117 
[1] "PTPN21 MUTATION ANALYSIS"
[1] 3
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               8              118 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               8              118 
[1] "HIBCH MUTATION ANALYSIS"
[1] 3
  HIBCH MUTATED HIBCH WILD-TYPE 
              5             121 
  HIBCH MUTATED HIBCH WILD-TYPE 
              5             121 
[1] "C16ORF79 MUTATION ANALYSIS"
[1] 3
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 5                121 
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 5                121 
[1] "KIAA0430 MUTATION ANALYSIS"
[1] 3
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 9                117 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 9                117 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
             6            120 
  NOX5 MUTATED NOX5 WILD-TYPE 
             6            120 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            5           121 
  NF2 MUTATED NF2 WILD-TYPE 
            5           121 
[1] "EPHB6 MUTATION ANALYSIS"
[1] 3
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              7             119 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              7             119 
[1] "PRMT8 MUTATION ANALYSIS"
[1] 3
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              8             118 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              8             118 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               9              117 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               9              117 
[1] "ZC3H4 MUTATION ANALYSIS"
[1] 3
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              8             118 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              8             118 
[1] "NRD1 MUTATION ANALYSIS"
[1] 3
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            117 
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            117 
[1] "ZNF552 MUTATION ANALYSIS"
[1] 3
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               6              120 
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               6              120 
[1] "BCAS1 MUTATION ANALYSIS"
[1] 3
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              5             121 
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              5             121 
[1] "SERTAD1 MUTATION ANALYSIS"
[1] 3
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
                6               120 
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
                6               120 
[1] "GLCCI1 MUTATION ANALYSIS"
[1] 3
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
               6              120 
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
               6              120 
[1] "WASF3 MUTATION ANALYSIS"
[1] 3
  WASF3 MUTATED WASF3 WILD-TYPE 
              8             118 
  WASF3 MUTATED WASF3 WILD-TYPE 
              8             118 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             4            122 
  WDR5 MUTATED WDR5 WILD-TYPE 
             4            122 
[1] "FGF10 MUTATION ANALYSIS"
[1] 3
  FGF10 MUTATED FGF10 WILD-TYPE 
              6             120 
  FGF10 MUTATED FGF10 WILD-TYPE 
              6             120 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
                4               122 
  FAM155B MUTATED FAM155B WILD-TYPE 
                4               122 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
              6             120 
  RBM12 MUTATED RBM12 WILD-TYPE 
              6             120 
[1] "ZNF337 MUTATION ANALYSIS"
[1] 3
  ZNF337 MUTATED ZNF337 WILD-TYPE 
              10              116 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
              10              116 
[1] "C16ORF46 MUTATION ANALYSIS"
[1] 3
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 4                122 
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 4                122 
[1] "TAOK2 MUTATION ANALYSIS"
[1] 3
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              8             118 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              8             118 
[1] "DHX9 MUTATION ANALYSIS"
[1] 3
  DHX9 MUTATED DHX9 WILD-TYPE 
             7            119 
  DHX9 MUTATED DHX9 WILD-TYPE 
             7            119 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               8              118 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               8              118 
[1] "SLITRK5 MUTATION ANALYSIS"
[1] 3
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
               15               111 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
               15               111 
[1] "KIAA0802 MUTATION ANALYSIS"
[1] 3
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
                 5                121 
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
                 5                121 
[1] "CTRL MUTATION ANALYSIS"
[1] 3
  CTRL MUTATED CTRL WILD-TYPE 
             5            121 
  CTRL MUTATED CTRL WILD-TYPE 
             5            121 
[1] "DHX36 MUTATION ANALYSIS"
[1] 3
  DHX36 MUTATED DHX36 WILD-TYPE 
             10             116 
  DHX36 MUTATED DHX36 WILD-TYPE 
             10             116 
[1] "GTF3C3 MUTATION ANALYSIS"
[1] 3
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               5              121 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               5              121 
[1] "OTX1 MUTATION ANALYSIS"
[1] 3
  OTX1 MUTATED OTX1 WILD-TYPE 
             7            119 
  OTX1 MUTATED OTX1 WILD-TYPE 
             7            119 
[1] "MTMR15 MUTATION ANALYSIS"
[1] 3
  MTMR15 MUTATED MTMR15 WILD-TYPE 
               8              118 
  MTMR15 MUTATED MTMR15 WILD-TYPE 
               8              118 
[1] "IYD MUTATION ANALYSIS"
[1] 3
  IYD MUTATED IYD WILD-TYPE 
            6           120 
  IYD MUTATED IYD WILD-TYPE 
            6           120 
[1] "GTF2F1 MUTATION ANALYSIS"
[1] 3
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               5              121 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               5              121 
[1] "DIDO1 MUTATION ANALYSIS"
[1] 3
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             14             112 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             14             112 
[1] "GNL3L MUTATION ANALYSIS"
[1] 3
  GNL3L MUTATED GNL3L WILD-TYPE 
              5             121 
  GNL3L MUTATED GNL3L WILD-TYPE 
              5             121 
[1] "ZC3H7B MUTATION ANALYSIS"
[1] 3
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
               7              119 
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
               7              119 
[1] "COL4A4 MUTATION ANALYSIS"
[1] 3
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               9              117 
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               9              117 
[1] "SYCP2 MUTATION ANALYSIS"
[1] 3
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              8             118 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              8             118 
[1] "CNKSR2 MUTATION ANALYSIS"
[1] 3
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
              11              115 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
              11              115 
[1] "OR5A1 MUTATION ANALYSIS"
[1] 3
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              5             121 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              5             121 
[1] "OSBPL3 MUTATION ANALYSIS"
[1] 3
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
               8              118 
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
               8              118 
[1] "HSP90AB1 MUTATION ANALYSIS"
[1] 3
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 5                121 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 5                121 
[1] "PLAUR MUTATION ANALYSIS"
[1] 3
  PLAUR MUTATED PLAUR WILD-TYPE 
              4             122 
  PLAUR MUTATED PLAUR WILD-TYPE 
              4             122 
[1] "GPC2 MUTATION ANALYSIS"
[1] 3
  GPC2 MUTATED GPC2 WILD-TYPE 
             5            121 
  GPC2 MUTATED GPC2 WILD-TYPE 
             5            121 
[1] "ACBD3 MUTATION ANALYSIS"
[1] 3
  ACBD3 MUTATED ACBD3 WILD-TYPE 
              4             122 
  ACBD3 MUTATED ACBD3 WILD-TYPE 
              4             122 
[1] "PURB MUTATION ANALYSIS"
[1] 3
  PURB MUTATED PURB WILD-TYPE 
             4            122 
  PURB MUTATED PURB WILD-TYPE 
             4            122 
[1] "ABCC2 MUTATION ANALYSIS"
[1] 3
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              6             120 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              6             120 
[1] "KRT73 MUTATION ANALYSIS"
[1] 3
  KRT73 MUTATED KRT73 WILD-TYPE 
              5             121 
  KRT73 MUTATED KRT73 WILD-TYPE 
              5             121 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              7             119 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              7             119 
[1] "MAGEC1 MUTATION ANALYSIS"
[1] 3
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              21              105 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              21              105 
[1] "ZNF609 MUTATION ANALYSIS"
[1] 3
  ZNF609 MUTATED ZNF609 WILD-TYPE 
               4              122 
  ZNF609 MUTATED ZNF609 WILD-TYPE 
               4              122 
[1] "ATP4A MUTATION ANALYSIS"
[1] 3
  ATP4A MUTATED ATP4A WILD-TYPE 
             10             116 
  ATP4A MUTATED ATP4A WILD-TYPE 
             10             116 
[1] "TRPV2 MUTATION ANALYSIS"
[1] 3
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              7             119 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              7             119 
[1] "N4BP2 MUTATION ANALYSIS"
[1] 3
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              6             120 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              6             120 
[1] "HMMR MUTATION ANALYSIS"
[1] 3
  HMMR MUTATED HMMR WILD-TYPE 
             6            120 
  HMMR MUTATED HMMR WILD-TYPE 
             6            120 
[1] "CSNK1G3 MUTATION ANALYSIS"
[1] 3
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                5               121 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                5               121 
[1] "ATP13A3 MUTATION ANALYSIS"
[1] 3
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                5               121 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                5               121 
[1] "ZNF626 MUTATION ANALYSIS"
[1] 3
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              10              116 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              10              116 
[1] "LIMD1 MUTATION ANALYSIS"
[1] 3
  LIMD1 MUTATED LIMD1 WILD-TYPE 
              8             118 
  LIMD1 MUTATED LIMD1 WILD-TYPE 
              8             118 
[1] "ESCO2 MUTATION ANALYSIS"
[1] 3
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              4             122 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              4             122 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4             122 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4             122 
[1] "TFIP11 MUTATION ANALYSIS"
[1] 3
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               6              120 
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               6              120 
[1] "PVRL1 MUTATION ANALYSIS"
[1] 3
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              8             118 
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              8             118 
[1] "DIAPH3 MUTATION ANALYSIS"
[1] 3
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               7              119 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               7              119 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            118 
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            118 
[1] "USP4 MUTATION ANALYSIS"
[1] 3
  USP4 MUTATED USP4 WILD-TYPE 
             7            119 
  USP4 MUTATED USP4 WILD-TYPE 
             7            119 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              118 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              118 
[1] "ZMYND8 MUTATION ANALYSIS"
[1] 3
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               8              118 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               8              118 
[1] "ATG2B MUTATION ANALYSIS"
[1] 3
  ATG2B MUTATED ATG2B WILD-TYPE 
              9             117 
  ATG2B MUTATED ATG2B WILD-TYPE 
              9             117 
[1] "CDH10 MUTATION ANALYSIS"
[1] 3
  CDH10 MUTATED CDH10 WILD-TYPE 
             13             113 
  CDH10 MUTATED CDH10 WILD-TYPE 
             13             113 
[1] "OXR1 MUTATION ANALYSIS"
[1] 3
  OXR1 MUTATED OXR1 WILD-TYPE 
             5            121 
  OXR1 MUTATED OXR1 WILD-TYPE 
             5            121 
[1] "SEC31A MUTATION ANALYSIS"
[1] 3
  SEC31A MUTATED SEC31A WILD-TYPE 
               6              120 
  SEC31A MUTATED SEC31A WILD-TYPE 
               6              120 
[1] "NDEL1 MUTATION ANALYSIS"
[1] 3
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              5             121 
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              5             121 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               10               116 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               10               116 
[1] "HIRA MUTATION ANALYSIS"
[1] 3
  HIRA MUTATED HIRA WILD-TYPE 
             5            121 
  HIRA MUTATED HIRA WILD-TYPE 
             5            121 
[1] "XRCC2 MUTATION ANALYSIS"
[1] 3
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              4             122 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              4             122 
[1] "APEX1 MUTATION ANALYSIS"
[1] 3
  APEX1 MUTATED APEX1 WILD-TYPE 
              4             122 
  APEX1 MUTATED APEX1 WILD-TYPE 
              4             122 
[1] "TMEM90B MUTATION ANALYSIS"
[1] 3
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                6               120 
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                6               120 
[1] "RAB11FIP1 MUTATION ANALYSIS"
[1] 3
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  7                 119 
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  7                 119 
[1] "MPP6 MUTATION ANALYSIS"
[1] 3
  MPP6 MUTATED MPP6 WILD-TYPE 
             5            121 
  MPP6 MUTATED MPP6 WILD-TYPE 
             5            121 
[1] "KIAA2018 MUTATION ANALYSIS"
[1] 3
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 8                118 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 8                118 
[1] "CEP72 MUTATION ANALYSIS"
[1] 3
  CEP72 MUTATED CEP72 WILD-TYPE 
              6             120 
  CEP72 MUTATED CEP72 WILD-TYPE 
              6             120 
[1] "AJAP1 MUTATION ANALYSIS"
[1] 3
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              8             118 
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              8             118 
[1] "GABBR1 MUTATION ANALYSIS"
[1] 3
  GABBR1 MUTATED GABBR1 WILD-TYPE 
              10              116 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
              10              116 
[1] "PAMR1 MUTATION ANALYSIS"
[1] 3
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              7             119 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              7             119 
[1] "GRHPR MUTATION ANALYSIS"
[1] 3
  GRHPR MUTATED GRHPR WILD-TYPE 
              5             121 
  GRHPR MUTATED GRHPR WILD-TYPE 
              5             121 
[1] "CYP20A1 MUTATION ANALYSIS"
[1] 3
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                6               120 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                6               120 
[1] "ARMCX3 MUTATION ANALYSIS"
[1] 3
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               5              121 
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               5              121 
[1] "MED23 MUTATION ANALYSIS"
[1] 3
  MED23 MUTATED MED23 WILD-TYPE 
              6             120 
  MED23 MUTATED MED23 WILD-TYPE 
              6             120 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
           8          118 
  AR MUTATED AR WILD-TYPE 
           8          118 
[1] "NKTR MUTATION ANALYSIS"
[1] 3
  NKTR MUTATED NKTR WILD-TYPE 
             6            120 
  NKTR MUTATED NKTR WILD-TYPE 
             6            120 
[1] "VDAC1 MUTATION ANALYSIS"
[1] 3
  VDAC1 MUTATED VDAC1 WILD-TYPE 
              5             121 
  VDAC1 MUTATED VDAC1 WILD-TYPE 
              5             121 
[1] "RIT1 MUTATION ANALYSIS"
[1] 3
  RIT1 MUTATED RIT1 WILD-TYPE 
             4            122 
  RIT1 MUTATED RIT1 WILD-TYPE 
             4            122 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
              21              105 
  FAM47C MUTATED FAM47C WILD-TYPE 
              21              105 
[1] "SEC62 MUTATION ANALYSIS"
[1] 3
  SEC62 MUTATED SEC62 WILD-TYPE 
              5             121 
  SEC62 MUTATED SEC62 WILD-TYPE 
              5             121 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             120 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             120 
[1] "PLXNA3 MUTATION ANALYSIS"
[1] 3
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               7              119 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               7              119 
[1] "ACCN2 MUTATION ANALYSIS"
[1] 3
  ACCN2 MUTATED ACCN2 WILD-TYPE 
              6             120 
  ACCN2 MUTATED ACCN2 WILD-TYPE 
              6             120 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
              5             121 
  RGS22 MUTATED RGS22 WILD-TYPE 
              5             121 
[1] "FRG1 MUTATION ANALYSIS"
[1] 3
  FRG1 MUTATED FRG1 WILD-TYPE 
             7            119 
  FRG1 MUTATED FRG1 WILD-TYPE 
             7            119 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6               120 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6               120 
[1] "CR1L MUTATION ANALYSIS"
[1] 3
  CR1L MUTATED CR1L WILD-TYPE 
             5            121 
  CR1L MUTATED CR1L WILD-TYPE 
             5            121 
[1] "HDLBP MUTATION ANALYSIS"
[1] 3
  HDLBP MUTATED HDLBP WILD-TYPE 
              8             118 
  HDLBP MUTATED HDLBP WILD-TYPE 
              8             118 
[1] "KBTBD4 MUTATION ANALYSIS"
[1] 3
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               4              122 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               4              122 
[1] "SBSN MUTATION ANALYSIS"
[1] 3
  SBSN MUTATED SBSN WILD-TYPE 
             5            121 
  SBSN MUTATED SBSN WILD-TYPE 
             5            121 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4             122 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4             122 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               7              119 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               7              119 
[1] "PHIP MUTATION ANALYSIS"
[1] 3
  PHIP MUTATED PHIP WILD-TYPE 
             7            119 
  PHIP MUTATED PHIP WILD-TYPE 
             7            119 
[1] "FOXJ2 MUTATION ANALYSIS"
[1] 3
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              5             121 
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              5             121 
[1] "KIF3C MUTATION ANALYSIS"
[1] 3
  KIF3C MUTATED KIF3C WILD-TYPE 
              4             122 
  KIF3C MUTATED KIF3C WILD-TYPE 
              4             122 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               9              117 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               9              117 
[1] "NAGPA MUTATION ANALYSIS"
[1] 3
  NAGPA MUTATED NAGPA WILD-TYPE 
              5             121 
  NAGPA MUTATED NAGPA WILD-TYPE 
              5             121 
[1] "CLIP1 MUTATION ANALYSIS"
[1] 3
  CLIP1 MUTATED CLIP1 WILD-TYPE 
              6             120 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
              6             120 
[1] "FNDC7 MUTATION ANALYSIS"
[1] 3
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              4             122 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              4             122 
[1] "MOGS MUTATION ANALYSIS"
[1] 3
  MOGS MUTATED MOGS WILD-TYPE 
             5            121 
  MOGS MUTATED MOGS WILD-TYPE 
             5            121 
[1] "BCL3 MUTATION ANALYSIS"
[1] 3
  BCL3 MUTATED BCL3 WILD-TYPE 
             5            121 
  BCL3 MUTATED BCL3 WILD-TYPE 
             5            121 
[1] "MED12L MUTATION ANALYSIS"
[1] 3
  MED12L MUTATED MED12L WILD-TYPE 
              13              113 
  MED12L MUTATED MED12L WILD-TYPE 
              13              113 
[1] "EXOC4 MUTATION ANALYSIS"
[1] 3
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              7             119 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              7             119 
[1] "MARCH7 MUTATION ANALYSIS"
[1] 3
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               4              122 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               4              122 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              6             120 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              6             120 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              117 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              117 
[1] "IFFO1 MUTATION ANALYSIS"
[1] 3
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              5             121 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              5             121 
[1] "ARHGEF7 MUTATION ANALYSIS"
[1] 3
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
                6               120 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
                6               120 
[1] "ZNF878 MUTATION ANALYSIS"
[1] 3
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               8              118 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               8              118 
[1] "AFF4 MUTATION ANALYSIS"
[1] 3
  AFF4 MUTATED AFF4 WILD-TYPE 
             4            122 
  AFF4 MUTATED AFF4 WILD-TYPE 
             4            122 
[1] "ZNF493 MUTATION ANALYSIS"
[1] 3
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               9              117 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               9              117 
[1] "HMGB1 MUTATION ANALYSIS"
[1] 3
  HMGB1 MUTATED HMGB1 WILD-TYPE 
              5             121 
  HMGB1 MUTATED HMGB1 WILD-TYPE 
              5             121 
[1] "NKAP MUTATION ANALYSIS"
[1] 3
  NKAP MUTATED NKAP WILD-TYPE 
             4            122 
  NKAP MUTATED NKAP WILD-TYPE 
             4            122 
[1] "ZFP36 MUTATION ANALYSIS"
[1] 3
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              4             122 
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              4             122 
[1] "GIT1 MUTATION ANALYSIS"
[1] 3
  GIT1 MUTATED GIT1 WILD-TYPE 
             5            121 
  GIT1 MUTATED GIT1 WILD-TYPE 
             5            121 
[1] "RUNX1T1 MUTATION ANALYSIS"
[1] 3
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
                5               121 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
                5               121 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             14             112 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             14             112 
[1] "AP2A2 MUTATION ANALYSIS"
[1] 3
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              5             121 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              5             121 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
              5             121 
  EIF5B MUTATED EIF5B WILD-TYPE 
              5             121 
[1] "WHSC1L1 MUTATION ANALYSIS"
[1] 3
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                6               120 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                6               120 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              7             119 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              7             119 
[1] "E2F8 MUTATION ANALYSIS"
[1] 3
  E2F8 MUTATED E2F8 WILD-TYPE 
             4            122 
  E2F8 MUTATED E2F8 WILD-TYPE 
             4            122 
[1] "SPRR4 MUTATION ANALYSIS"
[1] 3
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              4             122 
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              4             122 
[1] "ZMIZ2 MUTATION ANALYSIS"
[1] 3
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              6             120 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              6             120 
[1] "OR5H1 MUTATION ANALYSIS"
[1] 3
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              7             119 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              7             119 
[1] "SMYD5 MUTATION ANALYSIS"
[1] 3
  SMYD5 MUTATED SMYD5 WILD-TYPE 
              5             121 
  SMYD5 MUTATED SMYD5 WILD-TYPE 
              5             121 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              3             123 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              3             123 
[1] "C7ORF16 MUTATION ANALYSIS"
[1] 3
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
                4               122 
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
                4               122 
[1] "DOCK6 MUTATION ANALYSIS"
[1] 3
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              5             121 
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              5             121 
[1] "OR10A2 MUTATION ANALYSIS"
[1] 3
  OR10A2 MUTATED OR10A2 WILD-TYPE 
               4              122 
  OR10A2 MUTATED OR10A2 WILD-TYPE 
               4              122 
[1] "KDM2A MUTATION ANALYSIS"
[1] 3
  KDM2A MUTATED KDM2A WILD-TYPE 
              5             121 
  KDM2A MUTATED KDM2A WILD-TYPE 
              5             121 
[1] "RBM45 MUTATION ANALYSIS"
[1] 3
  RBM45 MUTATED RBM45 WILD-TYPE 
              5             121 
  RBM45 MUTATED RBM45 WILD-TYPE 
              5             121 
[1] "PHRF1 MUTATION ANALYSIS"
[1] 3
  PHRF1 MUTATED PHRF1 WILD-TYPE 
              4             122 
  PHRF1 MUTATED PHRF1 WILD-TYPE 
              4             122 
[1] "KCND3 MUTATION ANALYSIS"
[1] 3
  KCND3 MUTATED KCND3 WILD-TYPE 
              5             121 
  KCND3 MUTATED KCND3 WILD-TYPE 
              5             121 
[1] "CD1D MUTATION ANALYSIS"
[1] 3
  CD1D MUTATED CD1D WILD-TYPE 
             6            120 
  CD1D MUTATED CD1D WILD-TYPE 
             6            120 
[1] "PHF21A MUTATION ANALYSIS"
[1] 3
  PHF21A MUTATED PHF21A WILD-TYPE 
               4              122 
  PHF21A MUTATED PHF21A WILD-TYPE 
               4              122 
[1] "STEAP2 MUTATION ANALYSIS"
[1] 3
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               5              121 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               5              121 
[1] "SALL1 MUTATION ANALYSIS"
[1] 3
  SALL1 MUTATED SALL1 WILD-TYPE 
             10             116 
  SALL1 MUTATED SALL1 WILD-TYPE 
             10             116 
[1] "DSTN MUTATION ANALYSIS"
[1] 3
  DSTN MUTATED DSTN WILD-TYPE 
             3            123 
  DSTN MUTATED DSTN WILD-TYPE 
             3            123 
[1] "C6ORF154 MUTATION ANALYSIS"
[1] 3
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 4                122 
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 4                122 
[1] "TDRD6 MUTATION ANALYSIS"
[1] 3
  TDRD6 MUTATED TDRD6 WILD-TYPE 
              8             118 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
              8             118 
[1] "SIGLEC11 MUTATION ANALYSIS"
[1] 3
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 5                121 
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 5                121 
[1] "UGP2 MUTATION ANALYSIS"
[1] 3
  UGP2 MUTATED UGP2 WILD-TYPE 
             5            121 
  UGP2 MUTATED UGP2 WILD-TYPE 
             5            121 
[1] "SCD MUTATION ANALYSIS"
[1] 3
  SCD MUTATED SCD WILD-TYPE 
            4           122 
  SCD MUTATED SCD WILD-TYPE 
            4           122 
[1] "PANK2 MUTATION ANALYSIS"
[1] 3
  PANK2 MUTATED PANK2 WILD-TYPE 
              4             122 
  PANK2 MUTATED PANK2 WILD-TYPE 
              4             122 
[1] "GOLGA6B MUTATION ANALYSIS"
[1] 3
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                6               120 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                6               120 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
              9             117 
  MKI67 MUTATED MKI67 WILD-TYPE 
              9             117 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              4             122 
  STK19 MUTATED STK19 WILD-TYPE 
              4             122 
[1] "SPANXN3 MUTATION ANALYSIS"
[1] 3
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                5               121 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                5               121 
[1] "RTEL1 MUTATION ANALYSIS"
[1] 3
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              6             120 
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              6             120 
[1] "NWD1 MUTATION ANALYSIS"
[1] 3
  NWD1 MUTATED NWD1 WILD-TYPE 
             8            118 
  NWD1 MUTATED NWD1 WILD-TYPE 
             8            118 
[1] "NBPF1 MUTATION ANALYSIS"
[1] 3
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              5             121 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              5             121 
[1] "PPP1R10 MUTATION ANALYSIS"
[1] 3
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                4               122 
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                4               122 
[1] "DDX50 MUTATION ANALYSIS"
[1] 3
  DDX50 MUTATED DDX50 WILD-TYPE 
              5             121 
  DDX50 MUTATED DDX50 WILD-TYPE 
              5             121 
[1] "HOXA1 MUTATION ANALYSIS"
[1] 3
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              4             122 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              4             122 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               6              120 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               6              120 
[1] "XPA MUTATION ANALYSIS"
[1] 3
  XPA MUTATED XPA WILD-TYPE 
            3           123 
  XPA MUTATED XPA WILD-TYPE 
            3           123 
[1] "FADS2 MUTATION ANALYSIS"
[1] 3
  FADS2 MUTATED FADS2 WILD-TYPE 
              4             122 
  FADS2 MUTATED FADS2 WILD-TYPE 
              4             122 
[1] "SYT2 MUTATION ANALYSIS"
[1] 3
  SYT2 MUTATED SYT2 WILD-TYPE 
             4            122 
  SYT2 MUTATED SYT2 WILD-TYPE 
             4            122 
[1] "RBM33 MUTATION ANALYSIS"
[1] 3
  RBM33 MUTATED RBM33 WILD-TYPE 
              6             120 
  RBM33 MUTATED RBM33 WILD-TYPE 
              6             120 
[1] "ESD MUTATION ANALYSIS"
[1] 3
  ESD MUTATED ESD WILD-TYPE 
            5           121 
  ESD MUTATED ESD WILD-TYPE 
            5           121 
[1] "RANBP2 MUTATION ANALYSIS"
[1] 3
  RANBP2 MUTATED RANBP2 WILD-TYPE 
              14              112 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
              14              112 
[1] "ABCB4 MUTATION ANALYSIS"
[1] 3
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              5             121 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              5             121 
[1] "FHL3 MUTATION ANALYSIS"
[1] 3
  FHL3 MUTATED FHL3 WILD-TYPE 
             4            122 
  FHL3 MUTATED FHL3 WILD-TYPE 
             4            122 
[1] "NAP1L3 MUTATION ANALYSIS"
[1] 3
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               4              122 
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               4              122 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             9            117 
  GNAS MUTATED GNAS WILD-TYPE 
             9            117 
[1] "PARP14 MUTATION ANALYSIS"
[1] 3
  PARP14 MUTATED PARP14 WILD-TYPE 
               5              121 
  PARP14 MUTATED PARP14 WILD-TYPE 
               5              121 
[1] "SLCO1B3 MUTATION ANALYSIS"
[1] 3
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
                7               119 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
                7               119 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
              7             119 
  BCL9L MUTATED BCL9L WILD-TYPE 
              7             119 
[1] "ZNF428 MUTATION ANALYSIS"
[1] 3
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               3              123 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               3              123 
[1] "ARFGAP3 MUTATION ANALYSIS"
[1] 3
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                4               122 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                4               122 
[1] "SALL2 MUTATION ANALYSIS"
[1] 3
  SALL2 MUTATED SALL2 WILD-TYPE 
              5             121 
  SALL2 MUTATED SALL2 WILD-TYPE 
              5             121 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
              5             121 
  BMP2K MUTATED BMP2K WILD-TYPE 
              5             121 
[1] "RAI2 MUTATION ANALYSIS"
[1] 3
  RAI2 MUTATED RAI2 WILD-TYPE 
             4            122 
  RAI2 MUTATED RAI2 WILD-TYPE 
             4            122 
[1] "COL27A1 MUTATION ANALYSIS"
[1] 3
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                4               122 
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                4               122 
[1] "CCPG1 MUTATION ANALYSIS"
[1] 3
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              5             121 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              5             121 
[1] "TERF1 MUTATION ANALYSIS"
[1] 3
  TERF1 MUTATED TERF1 WILD-TYPE 
              3             123 
  TERF1 MUTATED TERF1 WILD-TYPE 
              3             123 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 5                121 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 5                121 
[1] "ZMYM4 MUTATION ANALYSIS"
[1] 3
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              4             122 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              4             122 
[1] "TSPYL6 MUTATION ANALYSIS"
[1] 3
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               4              122 
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               4              122 
[1] "SULT1C3 MUTATION ANALYSIS"
[1] 3
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                4               122 
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                4               122 
[1] "SH3PXD2A MUTATION ANALYSIS"
[1] 3
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
                 7                119 
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
                 7                119 
[1] "ZSWIM4 MUTATION ANALYSIS"
[1] 3
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
               5              121 
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
               5              121 
[1] "CCR3 MUTATION ANALYSIS"
[1] 3
  CCR3 MUTATED CCR3 WILD-TYPE 
             4            122 
  CCR3 MUTATED CCR3 WILD-TYPE 
             4            122 
[1] "CPLX3 MUTATION ANALYSIS"
[1] 3
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              4             122 
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              4             122 
[1] "RAD17 MUTATION ANALYSIS"
[1] 3
  RAD17 MUTATED RAD17 WILD-TYPE 
              5             121 
  RAD17 MUTATED RAD17 WILD-TYPE 
              5             121 
[1] "RANBP9 MUTATION ANALYSIS"
[1] 3
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               5              121 
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               5              121 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5              121 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5              121 
[1] "CD86 MUTATION ANALYSIS"
[1] 3
  CD86 MUTATED CD86 WILD-TYPE 
             4            122 
  CD86 MUTATED CD86 WILD-TYPE 
             4            122 
[1] "OR1N2 MUTATION ANALYSIS"
[1] 3
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              6             120 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              6             120 
[1] "KIAA0408 MUTATION ANALYSIS"
[1] 3
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                 6                120 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                 6                120 
[1] "GPRIN2 MUTATION ANALYSIS"
[1] 3
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               4              122 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               4              122 
[1] "HSP90AA1 MUTATION ANALYSIS"
[1] 3
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 4                122 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 4                122 
[1] "SHPRH MUTATION ANALYSIS"
[1] 3
  SHPRH MUTATED SHPRH WILD-TYPE 
              5             121 
  SHPRH MUTATED SHPRH WILD-TYPE 
              5             121 
[1] "CCKAR MUTATION ANALYSIS"
[1] 3
  CCKAR MUTATED CCKAR WILD-TYPE 
              4             122 
  CCKAR MUTATED CCKAR WILD-TYPE 
              4             122 
[1] "CHRNA9 MUTATION ANALYSIS"
[1] 3
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              122 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              122 
[1] "SH2D2A MUTATION ANALYSIS"
[1] 3
  SH2D2A MUTATED SH2D2A WILD-TYPE 
               5              121 
  SH2D2A MUTATED SH2D2A WILD-TYPE 
               5              121 
[1] "SLC9A11 MUTATION ANALYSIS"
[1] 3
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                5               121 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                5               121 
[1] "P2RY1 MUTATION ANALYSIS"
[1] 3
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              6             120 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              6             120 
[1] "SCYL3 MUTATION ANALYSIS"
[1] 3
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              4             122 
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              4             122 
[1] "INTS5 MUTATION ANALYSIS"
[1] 3
  INTS5 MUTATED INTS5 WILD-TYPE 
              3             123 
  INTS5 MUTATED INTS5 WILD-TYPE 
              3             123 
[1] "DAAM1 MUTATION ANALYSIS"
[1] 3
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             120 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             120 
[1] "RERE MUTATION ANALYSIS"
[1] 3
  RERE MUTATED RERE WILD-TYPE 
             6            120 
  RERE MUTATED RERE WILD-TYPE 
             6            120 
[1] "CUX2 MUTATION ANALYSIS"
[1] 3
  CUX2 MUTATED CUX2 WILD-TYPE 
             5            121 
  CUX2 MUTATED CUX2 WILD-TYPE 
             5            121 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            11            115 
  RPTN MUTATED RPTN WILD-TYPE 
            11            115 
[1] "HIST1H2BJ MUTATION ANALYSIS"
[1] 3
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  4                 122 
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  4                 122 
[1] "SLCO2A1 MUTATION ANALYSIS"
[1] 3
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                4               122 
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                4               122 
[1] "TULP1 MUTATION ANALYSIS"
[1] 3
  TULP1 MUTATED TULP1 WILD-TYPE 
              3             123 
  TULP1 MUTATED TULP1 WILD-TYPE 
              3             123 
[1] "C14ORF21 MUTATION ANALYSIS"
[1] 3
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 6                120 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 6                120 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
             4            122 
  PPIG MUTATED PPIG WILD-TYPE 
             4            122 
[1] "SLC39A4 MUTATION ANALYSIS"
[1] 3
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                4               122 
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                4               122 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             122 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             122 
[1] "FCGBP MUTATION ANALYSIS"
[1] 3
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             114 
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             114 
[1] "MAMSTR MUTATION ANALYSIS"
[1] 3
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               3              123 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               3              123 
[1] "OR2T33 MUTATION ANALYSIS"
[1] 3
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               4              122 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               4              122 
[1] "KCNB1 MUTATION ANALYSIS"
[1] 3
  KCNB1 MUTATED KCNB1 WILD-TYPE 
              5             121 
  KCNB1 MUTATED KCNB1 WILD-TYPE 
              5             121 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
             10             116 
  RREB1 MUTATED RREB1 WILD-TYPE 
             10             116 
[1] "CANT1 MUTATION ANALYSIS"
[1] 3
  CANT1 MUTATED CANT1 WILD-TYPE 
              3             123 
  CANT1 MUTATED CANT1 WILD-TYPE 
              3             123 
[1] "SMARCA2 MUTATION ANALYSIS"
[1] 3
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4               122 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4               122 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              122 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              122 
[1] "PPP2R5C MUTATION ANALYSIS"
[1] 3
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
                5               121 
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
                5               121 
[1] "COPA MUTATION ANALYSIS"
[1] 3
  COPA MUTATED COPA WILD-TYPE 
             5            121 
  COPA MUTATED COPA WILD-TYPE 
             5            121 
[1] "RCOR1 MUTATION ANALYSIS"
[1] 3
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              5             121 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              5             121 
[1] "PTCD1 MUTATION ANALYSIS"
[1] 3
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              3             123 
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              3             123 
[1] "SOS1 MUTATION ANALYSIS"
[1] 3
  SOS1 MUTATED SOS1 WILD-TYPE 
             5            121 
  SOS1 MUTATED SOS1 WILD-TYPE 
             5            121 
[1] "IPO4 MUTATION ANALYSIS"
[1] 3
  IPO4 MUTATED IPO4 WILD-TYPE 
             3            123 
  IPO4 MUTATED IPO4 WILD-TYPE 
             3            123 
[1] "KCNA4 MUTATION ANALYSIS"
[1] 3
  KCNA4 MUTATED KCNA4 WILD-TYPE 
             10             116 
  KCNA4 MUTATED KCNA4 WILD-TYPE 
             10             116 
[1] "ZNF644 MUTATION ANALYSIS"
[1] 3
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               5              121 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               5              121 
[1] "TEP1 MUTATION ANALYSIS"
[1] 3
  TEP1 MUTATED TEP1 WILD-TYPE 
             9            117 
  TEP1 MUTATED TEP1 WILD-TYPE 
             9            117 
[1] "TMEM184A MUTATION ANALYSIS"
[1] 3
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 4                122 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 4                122 
[1] "NBPF9 MUTATION ANALYSIS"
[1] 3
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              8             118 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              8             118 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 7                119 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 7                119 
[1] "MAML3 MUTATION ANALYSIS"
[1] 3
  MAML3 MUTATED MAML3 WILD-TYPE 
              7             119 
  MAML3 MUTATED MAML3 WILD-TYPE 
              7             119 
[1] "NBPF3 MUTATION ANALYSIS"
[1] 3
  NBPF3 MUTATED NBPF3 WILD-TYPE 
             12             114 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
             12             114 
[1] "TRAF3IP2 MUTATION ANALYSIS"
[1] 3
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 4                122 
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 4                122 
[1] "SMARCC2 MUTATION ANALYSIS"
[1] 3
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                5               121 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                5               121 
[1] "DNAH5 MUTATION ANALYSIS"
[1] 3
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             11             115 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             11             115 
[1] "C18ORF19 MUTATION ANALYSIS"
[1] 3
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 3                123 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 3                123 
[1] "KIF20B MUTATION ANALYSIS"
[1] 3
  KIF20B MUTATED KIF20B WILD-TYPE 
               5              121 
  KIF20B MUTATED KIF20B WILD-TYPE 
               5              121 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             119 
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             119 
[1] "PRG4 MUTATION ANALYSIS"
[1] 3
  PRG4 MUTATED PRG4 WILD-TYPE 
            12            114 
  PRG4 MUTATED PRG4 WILD-TYPE 
            12            114 
[1] "PHF14 MUTATION ANALYSIS"
[1] 3
  PHF14 MUTATED PHF14 WILD-TYPE 
              3             123 
  PHF14 MUTATED PHF14 WILD-TYPE 
              3             123 
[1] "RASGRF2 MUTATION ANALYSIS"
[1] 3
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                6               120 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                6               120 
[1] "PNMAL1 MUTATION ANALYSIS"
[1] 3
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               4              122 
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               4              122 
[1] "FOXP2 MUTATION ANALYSIS"
[1] 3
  FOXP2 MUTATED FOXP2 WILD-TYPE 
             10             116 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
             10             116 
[1] "CGREF1 MUTATION ANALYSIS"
[1] 3
  CGREF1 MUTATED CGREF1 WILD-TYPE 
               6              120 
  CGREF1 MUTATED CGREF1 WILD-TYPE 
               6              120 
[1] "ZNF780A MUTATION ANALYSIS"
[1] 3
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                7               119 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                7               119 
[1] "ADC MUTATION ANALYSIS"
[1] 3
  ADC MUTATED ADC WILD-TYPE 
            3           123 
  ADC MUTATED ADC WILD-TYPE 
            3           123 
[1] "FHDC1 MUTATION ANALYSIS"
[1] 3
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              6             120 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              6             120 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               9              117 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               9              117 
[1] "OR2J2 MUTATION ANALYSIS"
[1] 3
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              4             122 
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              4             122 
[1] "PLD2 MUTATION ANALYSIS"
[1] 3
  PLD2 MUTATED PLD2 WILD-TYPE 
             3            123 
  PLD2 MUTATED PLD2 WILD-TYPE 
             3            123 
[1] "SYCP1 MUTATION ANALYSIS"
[1] 3
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              5             121 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              5             121 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              7             119 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              7             119 
[1] "KRTAP5-3 MUTATION ANALYSIS"
[1] 3
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 7                119 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 7                119 
[1] "SSBP3 MUTATION ANALYSIS"
[1] 3
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             123 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             123 
[1] "ZNF347 MUTATION ANALYSIS"
[1] 3
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               5              121 
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               5              121 
[1] "IPO13 MUTATION ANALYSIS"
[1] 3
  IPO13 MUTATED IPO13 WILD-TYPE 
              4             122 
  IPO13 MUTATED IPO13 WILD-TYPE 
              4             122 
[1] "ACSM4 MUTATION ANALYSIS"
[1] 3
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              4             122 
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              4             122 
[1] "SPAG17 MUTATION ANALYSIS"
[1] 3
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               8              118 
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               8              118 
[1] "OGFOD1 MUTATION ANALYSIS"
[1] 3
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               3              123 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               3              123 
[1] "ZADH2 MUTATION ANALYSIS"
[1] 3
  ZADH2 MUTATED ZADH2 WILD-TYPE 
              3             123 
  ZADH2 MUTATED ZADH2 WILD-TYPE 
              3             123 
[1] "G2E3 MUTATION ANALYSIS"
[1] 3
  G2E3 MUTATED G2E3 WILD-TYPE 
             4            122 
  G2E3 MUTATED G2E3 WILD-TYPE 
             4            122 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              7             119 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              7             119 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              5             121 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              5             121 
[1] "EAF2 MUTATION ANALYSIS"
[1] 3
  EAF2 MUTATED EAF2 WILD-TYPE 
             3            123 
  EAF2 MUTATED EAF2 WILD-TYPE 
             3            123 
[1] "REPS1 MUTATION ANALYSIS"
[1] 3
  REPS1 MUTATED REPS1 WILD-TYPE 
              4             122 
  REPS1 MUTATED REPS1 WILD-TYPE 
              4             122 
[1] "ZNF43 MUTATION ANALYSIS"
[1] 3
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              7             119 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              7             119 
[1] "PRPF4 MUTATION ANALYSIS"
[1] 3
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              3             123 
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              3             123 
[1] "CMTM1 MUTATION ANALYSIS"
[1] 3
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              3             123 
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              3             123 
[1] "L1CAM MUTATION ANALYSIS"
[1] 3
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             120 
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             120 
[1] "MMP14 MUTATION ANALYSIS"
[1] 3
  MMP14 MUTATED MMP14 WILD-TYPE 
              4             122 
  MMP14 MUTATED MMP14 WILD-TYPE 
              4             122 
[1] "CENPF MUTATION ANALYSIS"
[1] 3
  CENPF MUTATED CENPF WILD-TYPE 
              5             121 
  CENPF MUTATED CENPF WILD-TYPE 
              5             121 
[1] "AMAC1L2 MUTATION ANALYSIS"
[1] 3
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                6               120 
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                6               120 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 5                121 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 5                121 
[1] "ERBB2IP MUTATION ANALYSIS"
[1] 3
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                5               121 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                5               121 
[1] "PRF1 MUTATION ANALYSIS"
[1] 3
  PRF1 MUTATED PRF1 WILD-TYPE 
             6            120 
  PRF1 MUTATED PRF1 WILD-TYPE 
             6            120 
[1] "WNT2 MUTATION ANALYSIS"
[1] 3
  WNT2 MUTATED WNT2 WILD-TYPE 
             6            120 
  WNT2 MUTATED WNT2 WILD-TYPE 
             6            120 
[1] "R3HDM1 MUTATION ANALYSIS"
[1] 3
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               5              121 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               5              121 
[1] "THRA MUTATION ANALYSIS"
[1] 3
  THRA MUTATED THRA WILD-TYPE 
             4            122 
  THRA MUTATED THRA WILD-TYPE 
             4            122 
[1] "MGAT2 MUTATION ANALYSIS"
[1] 3
  MGAT2 MUTATED MGAT2 WILD-TYPE 
              4             122 
  MGAT2 MUTATED MGAT2 WILD-TYPE 
              4             122 
[1] "HMX2 MUTATION ANALYSIS"
[1] 3
  HMX2 MUTATED HMX2 WILD-TYPE 
             4            122 
  HMX2 MUTATED HMX2 WILD-TYPE 
             4            122 
[1] "KRTAP4-8 MUTATION ANALYSIS"
[1] 3
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 5                121 
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 5                121 
[1] "TBC1D1 MUTATION ANALYSIS"
[1] 3
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               4              122 
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               4              122 
[1] "MTR MUTATION ANALYSIS"
[1] 3
  MTR MUTATED MTR WILD-TYPE 
            7           119 
  MTR MUTATED MTR WILD-TYPE 
            7           119 
[1] "CCDC103 MUTATION ANALYSIS"
[1] 3
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                3               123 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                3               123 
[1] "RBBP8 MUTATION ANALYSIS"
[1] 3
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              5             121 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              5             121 
[1] "FAM102A MUTATION ANALYSIS"
[1] 3
  FAM102A MUTATED FAM102A WILD-TYPE 
                4               122 
  FAM102A MUTATED FAM102A WILD-TYPE 
                4               122 
[1] "FAM18A MUTATION ANALYSIS"
[1] 3
  FAM18A MUTATED FAM18A WILD-TYPE 
               3              123 
  FAM18A MUTATED FAM18A WILD-TYPE 
               3              123 
[1] "AMAC1 MUTATION ANALYSIS"
[1] 3
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              7             119 
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              7             119 
[1] "NFATC2 MUTATION ANALYSIS"
[1] 3
  NFATC2 MUTATED NFATC2 WILD-TYPE 
               6              120 
  NFATC2 MUTATED NFATC2 WILD-TYPE 
               6              120 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              121 
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              121 
[1] "PCLO MUTATION ANALYSIS"
[1] 3
  PCLO MUTATED PCLO WILD-TYPE 
             8            118 
  PCLO MUTATED PCLO WILD-TYPE 
             8            118 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              3             123 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              3             123 
[1] "POM121 MUTATION ANALYSIS"
[1] 3
  POM121 MUTATED POM121 WILD-TYPE 
               5              121 
  POM121 MUTATED POM121 WILD-TYPE 
               5              121 
[1] "HIST1H2BK MUTATION ANALYSIS"
[1] 3
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  4                 122 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  4                 122 
[1] "ZHX3 MUTATION ANALYSIS"
[1] 3
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             7            119 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             7            119 
[1] "RGPD3 MUTATION ANALYSIS"
[1] 3
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              8             118 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              8             118 
[1] "ZNF554 MUTATION ANALYSIS"
[1] 3
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               3              123 
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               3              123 
[1] "RETN MUTATION ANALYSIS"
[1] 3
  RETN MUTATED RETN WILD-TYPE 
             3            123 
  RETN MUTATED RETN WILD-TYPE 
             3            123 
[1] "RSC1A1 MUTATION ANALYSIS"
[1] 3
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               3              123 
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               3              123 
[1] "RYR2 MUTATION ANALYSIS"
[1] 3
  RYR2 MUTATED RYR2 WILD-TYPE 
            14            112 
  RYR2 MUTATED RYR2 WILD-TYPE 
            14            112 
[1] "HNRNPCL1 MUTATION ANALYSIS"
[1] 3
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 6                120 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 6                120 
[1] "SEPHS2 MUTATION ANALYSIS"
[1] 3
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              121 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              121 
[1] "KIAA0020 MUTATION ANALYSIS"
[1] 3
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 3                123 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 3                123 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               3              123 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               3              123 
[1] "CCDC158 MUTATION ANALYSIS"
[1] 3
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                4               122 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                4               122 
[1] "FTH1 MUTATION ANALYSIS"
[1] 3
  FTH1 MUTATED FTH1 WILD-TYPE 
             3            123 
  FTH1 MUTATED FTH1 WILD-TYPE 
             3            123 
[1] "BCKDHA MUTATION ANALYSIS"
[1] 3
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               3              123 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               3              123 
[1] "SLC34A2 MUTATION ANALYSIS"
[1] 3
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                5               121 
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                5               121 
[1] "RAB11FIP5 MUTATION ANALYSIS"
[1] 3
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  3                 123 
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  3                 123 
[1] "ATP6V1A MUTATION ANALYSIS"
[1] 3
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                3               123 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                3               123 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               123 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               123 
[1] "GIGYF1 MUTATION ANALYSIS"
[1] 3
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               3              123 
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               3              123 
[1] "EPB41L4B MUTATION ANALYSIS"
[1] 3
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 4                122 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 4                122 
[1] "EPHX1 MUTATION ANALYSIS"
[1] 3
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              4             122 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              4             122 
[1] "LUZP1 MUTATION ANALYSIS"
[1] 3
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              3             123 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              3             123 
[1] "ZHX1 MUTATION ANALYSIS"
[1] 3
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             3            123 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             3            123 
[1] "GNAL MUTATION ANALYSIS"
[1] 3
  GNAL MUTATED GNAL WILD-TYPE 
             3            123 
  GNAL MUTATED GNAL WILD-TYPE 
             3            123 
[1] "DOCK10 MUTATION ANALYSIS"
[1] 3
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               6              120 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               6              120 
[1] "CDC25A MUTATION ANALYSIS"
[1] 3
  CDC25A MUTATED CDC25A WILD-TYPE 
               3              123 
  CDC25A MUTATED CDC25A WILD-TYPE 
               3              123 
[1] "VPS24 MUTATION ANALYSIS"
[1] 3
  VPS24 MUTATED VPS24 WILD-TYPE 
              3             123 
  VPS24 MUTATED VPS24 WILD-TYPE 
              3             123 
[1] "F5 MUTATION ANALYSIS"
[1] 3
  F5 MUTATED F5 WILD-TYPE 
          11          115 
  F5 MUTATED F5 WILD-TYPE 
          11          115 
[1] "AFF2 MUTATION ANALYSIS"
[1] 3
  AFF2 MUTATED AFF2 WILD-TYPE 
             6            120 
  AFF2 MUTATED AFF2 WILD-TYPE 
             6            120 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             10             116 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             10             116 
[1] "RNF168 MUTATION ANALYSIS"
[1] 3
  RNF168 MUTATED RNF168 WILD-TYPE 
               4              122 
  RNF168 MUTATED RNF168 WILD-TYPE 
               4              122 
[1] "TGFBI MUTATION ANALYSIS"
[1] 3
  TGFBI MUTATED TGFBI WILD-TYPE 
              6             120 
  TGFBI MUTATED TGFBI WILD-TYPE 
              6             120 
[1] "KLK13 MUTATION ANALYSIS"
[1] 3
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             121 
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             121 
[1] "ASS1 MUTATION ANALYSIS"
[1] 3
  ASS1 MUTATED ASS1 WILD-TYPE 
             4            122 
  ASS1 MUTATED ASS1 WILD-TYPE 
             4            122 
[1] "FOXD4 MUTATION ANALYSIS"
[1] 3
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              6             120 
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              6             120 
[1] "PVRL4 MUTATION ANALYSIS"
[1] 3
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              3             123 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              3             123 
[1] "NBEA MUTATION ANALYSIS"
[1] 3
  NBEA MUTATED NBEA WILD-TYPE 
             3            123 
  NBEA MUTATED NBEA WILD-TYPE 
             3            123 
[1] "ZNF737 MUTATION ANALYSIS"
[1] 3
  ZNF737 MUTATED ZNF737 WILD-TYPE 
               5              121 
  ZNF737 MUTATED ZNF737 WILD-TYPE 
               5              121 
[1] "CPVL MUTATION ANALYSIS"
[1] 3
  CPVL MUTATED CPVL WILD-TYPE 
             3            123 
  CPVL MUTATED CPVL WILD-TYPE 
             3            123 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             121 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             121 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              4             122 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4             122 
[1] "BCL11A MUTATION ANALYSIS"
[1] 3
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              120 
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              120 
[1] "ZNF207 MUTATION ANALYSIS"
[1] 3
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               4              122 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               4              122 
[1] "CCDC55 MUTATION ANALYSIS"
[1] 3
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               3              123 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               3              123 
[1] "ORAI3 MUTATION ANALYSIS"
[1] 3
  ORAI3 MUTATED ORAI3 WILD-TYPE 
              3             123 
  ORAI3 MUTATED ORAI3 WILD-TYPE 
              3             123 
[1] "LAMA1 MUTATION ANALYSIS"
[1] 3
  LAMA1 MUTATED LAMA1 WILD-TYPE 
              8             118 
  LAMA1 MUTATED LAMA1 WILD-TYPE 
              8             118 
[1] "AFAP1L2 MUTATION ANALYSIS"
[1] 3
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                4               122 
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                4               122 
[1] "ATXN2L MUTATION ANALYSIS"
[1] 3
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               4              122 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               4              122 
[1] "BECN1 MUTATION ANALYSIS"
[1] 3
  BECN1 MUTATED BECN1 WILD-TYPE 
              3             123 
  BECN1 MUTATED BECN1 WILD-TYPE 
              3             123 
[1] "MAP3K7 MUTATION ANALYSIS"
[1] 3
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               4              122 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               4              122 
[1] "HVCN1 MUTATION ANALYSIS"
[1] 3
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              4             122 
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              4             122 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               5              121 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               5              121 
[1] "ENPP7 MUTATION ANALYSIS"
[1] 3
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              6             120 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              6             120 
[1] "UNC5D MUTATION ANALYSIS"
[1] 3
  UNC5D MUTATED UNC5D WILD-TYPE 
              4             122 
  UNC5D MUTATED UNC5D WILD-TYPE 
              4             122 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
             4            122 
  TTF1 MUTATED TTF1 WILD-TYPE 
             4            122 
[1] "CD93 MUTATION ANALYSIS"
[1] 3
  CD93 MUTATED CD93 WILD-TYPE 
             5            121 
  CD93 MUTATED CD93 WILD-TYPE 
             5            121 
[1] "CEACAM8 MUTATION ANALYSIS"
[1] 3
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
                3               123 
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
                3               123 
[1] "PARP1 MUTATION ANALYSIS"
[1] 3
  PARP1 MUTATED PARP1 WILD-TYPE 
              4             122 
  PARP1 MUTATED PARP1 WILD-TYPE 
              4             122 
[1] "CRNN MUTATION ANALYSIS"
[1] 3
  CRNN MUTATED CRNN WILD-TYPE 
            10            116 
  CRNN MUTATED CRNN WILD-TYPE 
            10            116 
[1] "ZNF254 MUTATION ANALYSIS"
[1] 3
  ZNF254 MUTATED ZNF254 WILD-TYPE 
               5              121 
  ZNF254 MUTATED ZNF254 WILD-TYPE 
               5              121 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               3              123 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               3              123 
[1] "DRD5 MUTATION ANALYSIS"
[1] 3
  DRD5 MUTATED DRD5 WILD-TYPE 
             4            122 
  DRD5 MUTATED DRD5 WILD-TYPE 
             4            122 
[1] "MKI67IP MUTATION ANALYSIS"
[1] 3
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                4               122 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                4               122 
[1] "SYNPO2L MUTATION ANALYSIS"
[1] 3
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
                6               120 
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
                6               120 
[1] "PROX1 MUTATION ANALYSIS"
[1] 3
  PROX1 MUTATED PROX1 WILD-TYPE 
              4             122 
  PROX1 MUTATED PROX1 WILD-TYPE 
              4             122 
[1] "KLK15 MUTATION ANALYSIS"
[1] 3
  KLK15 MUTATED KLK15 WILD-TYPE 
              6             120 
  KLK15 MUTATED KLK15 WILD-TYPE 
              6             120 
[1] "C14ORF115 MUTATION ANALYSIS"
[1] 3
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  3                 123 
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  3                 123 
[1] "SNIP1 MUTATION ANALYSIS"
[1] 3
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              3             123 
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              3             123 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               4              122 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               4              122 
[1] "RBM16 MUTATION ANALYSIS"
[1] 3
  RBM16 MUTATED RBM16 WILD-TYPE 
              4             122 
  RBM16 MUTATED RBM16 WILD-TYPE 
              4             122 
[1] "PHACTR2 MUTATION ANALYSIS"
[1] 3
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                3               123 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                3               123 
[1] "TLR1 MUTATION ANALYSIS"
[1] 3
  TLR1 MUTATED TLR1 WILD-TYPE 
             4            122 
  TLR1 MUTATED TLR1 WILD-TYPE 
             4            122 
[1] "OR6C74 MUTATION ANALYSIS"
[1] 3
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               3              123 
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               3              123 
[1] "ROBO3 MUTATION ANALYSIS"
[1] 3
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              7             119 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              7             119 
[1] "SLC45A4 MUTATION ANALYSIS"
[1] 3
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                6               120 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                6               120 
[1] "COQ9 MUTATION ANALYSIS"
[1] 3
  COQ9 MUTATED COQ9 WILD-TYPE 
             3            123 
  COQ9 MUTATED COQ9 WILD-TYPE 
             3            123 
[1] "CLCN3 MUTATION ANALYSIS"
[1] 3
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              3             123 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              3             123 
[1] "SFRS11 MUTATION ANALYSIS"
[1] 3
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               3              123 
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               3              123 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                123 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                123 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
              5             121 
  PRKCD MUTATED PRKCD WILD-TYPE 
              5             121 
[1] "ATP2B2 MUTATION ANALYSIS"
[1] 3
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               5              121 
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               5              121 
[1] "RASAL1 MUTATION ANALYSIS"
[1] 3
  RASAL1 MUTATED RASAL1 WILD-TYPE 
               3              123 
  RASAL1 MUTATED RASAL1 WILD-TYPE 
               3              123 
[1] "NPIP MUTATION ANALYSIS"
[1] 3
  NPIP MUTATED NPIP WILD-TYPE 
             3            123 
  NPIP MUTATED NPIP WILD-TYPE 
             3            123 
[1] "DISP1 MUTATION ANALYSIS"
[1] 3
  DISP1 MUTATED DISP1 WILD-TYPE 
              9             117 
  DISP1 MUTATED DISP1 WILD-TYPE 
              9             117 
[1] "CD14 MUTATION ANALYSIS"
[1] 3
  CD14 MUTATED CD14 WILD-TYPE 
             3            123 
  CD14 MUTATED CD14 WILD-TYPE 
             3            123 
[1] "TATDN2 MUTATION ANALYSIS"
[1] 3
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               4              122 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               4              122 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               9              117 
  ARID1A MUTATED ARID1A WILD-TYPE 
               9              117 
[1] "ZC3H11A MUTATION ANALYSIS"
[1] 3
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               121 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               121 
[1] "ANKRD49 MUTATION ANALYSIS"
[1] 3
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               123 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               123 
[1] "NDUFV2 MUTATION ANALYSIS"
[1] 3
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              123 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              123 
[1] "PPP1R12C MUTATION ANALYSIS"
[1] 3
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 4                122 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 4                122 
[1] "CCDC74A MUTATION ANALYSIS"
[1] 3
  CCDC74A MUTATED CCDC74A WILD-TYPE 
                4               122 
  CCDC74A MUTATED CCDC74A WILD-TYPE 
                4               122 
[1] "C3ORF15 MUTATION ANALYSIS"
[1] 3
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                4               122 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                4               122 
[1] "DCX MUTATION ANALYSIS"
[1] 3
  DCX MUTATED DCX WILD-TYPE 
            3           123 
  DCX MUTATED DCX WILD-TYPE 
            3           123 
[1] "HMGCR MUTATION ANALYSIS"
[1] 3
  HMGCR MUTATED HMGCR WILD-TYPE 
              6             120 
  HMGCR MUTATED HMGCR WILD-TYPE 
              6             120 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              5             121 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              5             121 
[1] "FZD7 MUTATION ANALYSIS"
[1] 3
  FZD7 MUTATED FZD7 WILD-TYPE 
             4            122 
  FZD7 MUTATED FZD7 WILD-TYPE 
             4            122 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               6              120 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               6              120 
[1] "LRRC41 MUTATION ANALYSIS"
[1] 3
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               3              123 
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               3              123 
[1] "STAG3 MUTATION ANALYSIS"
[1] 3
  STAG3 MUTATED STAG3 WILD-TYPE 
              5             121 
  STAG3 MUTATED STAG3 WILD-TYPE 
              5             121 
[1] "PSME4 MUTATION ANALYSIS"
[1] 3
  PSME4 MUTATED PSME4 WILD-TYPE 
              5             121 
  PSME4 MUTATED PSME4 WILD-TYPE 
              5             121 
[1] "LILRA2 MUTATION ANALYSIS"
[1] 3
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               5              121 
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               5              121 
[1] "ATP2C2 MUTATION ANALYSIS"
[1] 3
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              122 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              122 
[1] "KIAA1211 MUTATION ANALYSIS"
[1] 3
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 5                121 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 5                121 
[1] "LPIN3 MUTATION ANALYSIS"
[1] 3
  LPIN3 MUTATED LPIN3 WILD-TYPE 
              4             122 
  LPIN3 MUTATED LPIN3 WILD-TYPE 
              4             122 
[1] "WDR8 MUTATION ANALYSIS"
[1] 3
  WDR8 MUTATED WDR8 WILD-TYPE 
             4            122 
  WDR8 MUTATED WDR8 WILD-TYPE 
             4            122 
[1] "ASH1L MUTATION ANALYSIS"
[1] 3
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             120 
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             120 
[1] "SPINT1 MUTATION ANALYSIS"
[1] 3
  SPINT1 MUTATED SPINT1 WILD-TYPE 
               3              123 
  SPINT1 MUTATED SPINT1 WILD-TYPE 
               3              123 
[1] "SARS2 MUTATION ANALYSIS"
[1] 3
  SARS2 MUTATED SARS2 WILD-TYPE 
              4             122 
  SARS2 MUTATED SARS2 WILD-TYPE 
              4             122 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              8             118 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              8             118 
[1] "XIRP2 MUTATION ANALYSIS"
[1] 3
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              6             120 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              6             120 
[1] "SLC4A5 MUTATION ANALYSIS"
[1] 3
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               4              122 
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               4              122 
[1] "BTN2A2 MUTATION ANALYSIS"
[1] 3
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              123 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              123 
[1] "SV2A MUTATION ANALYSIS"
[1] 3
  SV2A MUTATED SV2A WILD-TYPE 
             4            122 
  SV2A MUTATED SV2A WILD-TYPE 
             4            122 
[1] "MORC3 MUTATION ANALYSIS"
[1] 3
  MORC3 MUTATED MORC3 WILD-TYPE 
              3             123 
  MORC3 MUTATED MORC3 WILD-TYPE 
              3             123 
[1] "HABP4 MUTATION ANALYSIS"
[1] 3
  HABP4 MUTATED HABP4 WILD-TYPE 
              4             122 
  HABP4 MUTATED HABP4 WILD-TYPE 
              4             122 
[1] "SLC5A3 MUTATION ANALYSIS"
[1] 3
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               4              122 
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               4              122 
[1] "TGOLN2 MUTATION ANALYSIS"
[1] 3
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              123 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              123 
[1] "HIST1H1E MUTATION ANALYSIS"
[1] 3
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 3                123 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 3                123 
[1] "APOA1BP MUTATION ANALYSIS"
[1] 3
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                4               122 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                4               122 
[1] "AKNAD1 MUTATION ANALYSIS"
[1] 3
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               3              123 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               3              123 
[1] "MMP9 MUTATION ANALYSIS"
[1] 3
  MMP9 MUTATED MMP9 WILD-TYPE 
             3            123 
  MMP9 MUTATED MMP9 WILD-TYPE 
             3            123 
[1] "SCAND3 MUTATION ANALYSIS"
[1] 3
  SCAND3 MUTATED SCAND3 WILD-TYPE 
               5              121 
  SCAND3 MUTATED SCAND3 WILD-TYPE 
               5              121 
[1] "RNGTT MUTATION ANALYSIS"
[1] 3
  RNGTT MUTATED RNGTT WILD-TYPE 
              3             123 
  RNGTT MUTATED RNGTT WILD-TYPE 
              3             123 
[1] "C1QTNF7 MUTATION ANALYSIS"
[1] 3
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                4               122 
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                4               122 
[1] "CHMP2A MUTATION ANALYSIS"
[1] 3
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               4              122 
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               4              122 
[1] "ATP6V0A4 MUTATION ANALYSIS"
[1] 3
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 6                120 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 6                120 
[1] "FANCD2 MUTATION ANALYSIS"
[1] 3
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              119 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              119 
[1] "ZCCHC11 MUTATION ANALYSIS"
[1] 3
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                8               118 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                8               118 
[1] "GRM1 MUTATION ANALYSIS"
[1] 3
  GRM1 MUTATED GRM1 WILD-TYPE 
             8            118 
  GRM1 MUTATED GRM1 WILD-TYPE 
             8            118 
[1] "TNFRSF11A MUTATION ANALYSIS"
[1] 3
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  4                 122 
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  4                 122 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 7                119 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 7                119 
[1] "SNX32 MUTATION ANALYSIS"
[1] 3
  SNX32 MUTATED SNX32 WILD-TYPE 
              4             122 
  SNX32 MUTATED SNX32 WILD-TYPE 
              4             122 
[1] "BRF1 MUTATION ANALYSIS"
[1] 3
  BRF1 MUTATED BRF1 WILD-TYPE 
             4            122 
  BRF1 MUTATED BRF1 WILD-TYPE 
             4            122 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
             9            117 
  TPTE MUTATED TPTE WILD-TYPE 
             9            117 
[1] "EXOSC10 MUTATION ANALYSIS"
[1] 3
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                3               123 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                3               123 
[1] "DUSP13 MUTATION ANALYSIS"
[1] 3
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               3              123 
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               3              123 
[1] "C1ORF110 MUTATION ANALYSIS"
[1] 3
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 4                122 
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 4                122 
[1] "PCOLCE2 MUTATION ANALYSIS"
[1] 3
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                3               123 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                3               123 
[1] "FLVCR1 MUTATION ANALYSIS"
[1] 3
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              123 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              123 
[1] "EXOSC5 MUTATION ANALYSIS"
[1] 3
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               4              122 
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               4              122 
[1] "PDXDC1 MUTATION ANALYSIS"
[1] 3
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              123 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              123 
[1] "C11ORF63 MUTATION ANALYSIS"
[1] 3
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 3                123 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 3                123 
[1] "FAM71F1 MUTATION ANALYSIS"
[1] 3
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
                3               123 
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
                3               123 
[1] "UBE2Q1 MUTATION ANALYSIS"
[1] 3
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               3              123 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               3              123 
[1] "GALNT10 MUTATION ANALYSIS"
[1] 3
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                5               121 
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                5               121 
[1] "PPL MUTATION ANALYSIS"
[1] 3
  PPL MUTATED PPL WILD-TYPE 
            4           122 
  PPL MUTATED PPL WILD-TYPE 
            4           122 
[1] "CDC42BPG MUTATION ANALYSIS"
[1] 3
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 5                121 
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 5                121 
[1] "THBS1 MUTATION ANALYSIS"
[1] 3
  THBS1 MUTATED THBS1 WILD-TYPE 
              7             119 
  THBS1 MUTATED THBS1 WILD-TYPE 
              7             119 
[1] "LAMA3 MUTATION ANALYSIS"
[1] 3
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              4             122 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              4             122 
[1] "DYRK4 MUTATION ANALYSIS"
[1] 3
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              3             123 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              3             123 
[1] "HNRNPH1 MUTATION ANALYSIS"
[1] 3
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                4               122 
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                4               122 
[1] "UGT1A10 MUTATION ANALYSIS"
[1] 3
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
                4               122 
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
                4               122 
[1] "TEKT4 MUTATION ANALYSIS"
[1] 3
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             120 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             120 
[1] "PHTF2 MUTATION ANALYSIS"
[1] 3
  PHTF2 MUTATED PHTF2 WILD-TYPE 
              4             122 
  PHTF2 MUTATED PHTF2 WILD-TYPE 
              4             122 
[1] "CDC6 MUTATION ANALYSIS"
[1] 3
  CDC6 MUTATED CDC6 WILD-TYPE 
             3            123 
  CDC6 MUTATED CDC6 WILD-TYPE 
             3            123 
[1] "PRKDC MUTATION ANALYSIS"
[1] 3
  PRKDC MUTATED PRKDC WILD-TYPE 
              3             123 
  PRKDC MUTATED PRKDC WILD-TYPE 
              3             123 
[1] "KDM6B MUTATION ANALYSIS"
[1] 3
  KDM6B MUTATED KDM6B WILD-TYPE 
              6             120 
  KDM6B MUTATED KDM6B WILD-TYPE 
              6             120 
[1] "LRRCC1 MUTATION ANALYSIS"
[1] 3
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               5              121 
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               5              121 
[1] "ZNF285 MUTATION ANALYSIS"
[1] 3
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               4              122 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               4              122 
[1] "RPS6KA5 MUTATION ANALYSIS"
[1] 3
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                4               122 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                4               122 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
              3             123 
  ASB11 MUTATED ASB11 WILD-TYPE 
              3             123 
[1] "CCT8 MUTATION ANALYSIS"
[1] 3
  CCT8 MUTATED CCT8 WILD-TYPE 
             4            122 
  CCT8 MUTATED CCT8 WILD-TYPE 
             4            122 
[1] "PSMB4 MUTATION ANALYSIS"
[1] 3
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             122 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             122 
[1] "SIGLEC7 MUTATION ANALYSIS"
[1] 3
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                3               123 
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                3               123 
[1] "ATP2B3 MUTATION ANALYSIS"
[1] 3
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
               3              123 
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
               3              123 
[1] "CCDC130 MUTATION ANALYSIS"
[1] 3
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                4               122 
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                4               122 
[1] "BAT2 MUTATION ANALYSIS"
[1] 3
  BAT2 MUTATED BAT2 WILD-TYPE 
             6            120 
  BAT2 MUTATED BAT2 WILD-TYPE 
             6            120 
[1] "STARD3 MUTATION ANALYSIS"
[1] 3
  STARD3 MUTATED STARD3 WILD-TYPE 
               3              123 
  STARD3 MUTATED STARD3 WILD-TYPE 
               3              123 
[1] "C16ORF70 MUTATION ANALYSIS"
[1] 3
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 4                122 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 4                122 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5             121 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5             121 
[1] "LATS1 MUTATION ANALYSIS"
[1] 3
  LATS1 MUTATED LATS1 WILD-TYPE 
              5             121 
  LATS1 MUTATED LATS1 WILD-TYPE 
              5             121 
[1] "LARP1B MUTATION ANALYSIS"
[1] 3
  LARP1B MUTATED LARP1B WILD-TYPE 
               3              123 
  LARP1B MUTATED LARP1B WILD-TYPE 
               3              123 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               6              120 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               6              120 
[1] "PHKA2 MUTATION ANALYSIS"
[1] 3
  PHKA2 MUTATED PHKA2 WILD-TYPE 
              6             120 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
              6             120 
[1] "ABCC3 MUTATION ANALYSIS"
[1] 3
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              3             123 
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              3             123 
[1] "CPNE2 MUTATION ANALYSIS"
[1] 3
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             123 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             123 
[1] "MICALCL MUTATION ANALYSIS"
[1] 3
  MICALCL MUTATED MICALCL WILD-TYPE 
                4               122 
  MICALCL MUTATED MICALCL WILD-TYPE 
                4               122 
[1] "SPAG9 MUTATION ANALYSIS"
[1] 3
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              4             122 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              4             122 
[1] "SLITRK3 MUTATION ANALYSIS"
[1] 3
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
                4               122 
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
                4               122 
[1] "HIST1H2BE MUTATION ANALYSIS"
[1] 3
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
                  3                 123 
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
                  3                 123 
[1] "NGF MUTATION ANALYSIS"
[1] 3
  NGF MUTATED NGF WILD-TYPE 
            4           122 
  NGF MUTATED NGF WILD-TYPE 
            4           122 
[1] "EHMT2 MUTATION ANALYSIS"
[1] 3
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              3             123 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              3             123 
[1] "PLEKHG2 MUTATION ANALYSIS"
[1] 3
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
                5               121 
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
                5               121 
[1] "SRFBP1 MUTATION ANALYSIS"
[1] 3
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              123 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              123 
[1] "TSC22D1 MUTATION ANALYSIS"
[1] 3
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3               123 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3               123 
[1] "EEF2 MUTATION ANALYSIS"
[1] 3
  EEF2 MUTATED EEF2 WILD-TYPE 
             4            122 
  EEF2 MUTATED EEF2 WILD-TYPE 
             4            122 
[1] "E2F7 MUTATION ANALYSIS"
[1] 3
  E2F7 MUTATED E2F7 WILD-TYPE 
             3            123 
  E2F7 MUTATED E2F7 WILD-TYPE 
             3            123 
[1] "NR2C1 MUTATION ANALYSIS"
[1] 3
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              3             123 
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              3             123 
[1] "ASPM MUTATION ANALYSIS"
[1] 3
  ASPM MUTATED ASPM WILD-TYPE 
             9            117 
  ASPM MUTATED ASPM WILD-TYPE 
             9            117 
[1] "CCDC108 MUTATION ANALYSIS"
[1] 3
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                3               123 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                3               123 
[1] "PDGFRB MUTATION ANALYSIS"
[1] 3
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               4              122 
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               4              122 
[1] "TWISTNB MUTATION ANALYSIS"
[1] 3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3               123 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3               123 
[1] "GRIN3B MUTATION ANALYSIS"
[1] 3
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               4              122 
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               4              122 
[1] "ENTPD2 MUTATION ANALYSIS"
[1] 3
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              122 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              122 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
              4             122 
  STK11 MUTATED STK11 WILD-TYPE 
              4             122 
[1] "LBR MUTATION ANALYSIS"
[1] 3
  LBR MUTATED LBR WILD-TYPE 
            4           122 
  LBR MUTATED LBR WILD-TYPE 
            4           122 
[1] "AKD1 MUTATION ANALYSIS"
[1] 3
  AKD1 MUTATED AKD1 WILD-TYPE 
             3            123 
  AKD1 MUTATED AKD1 WILD-TYPE 
             3            123 
[1] "GABRD MUTATION ANALYSIS"
[1] 3
  GABRD MUTATED GABRD WILD-TYPE 
              4             122 
  GABRD MUTATED GABRD WILD-TYPE 
              4             122 
[1] "CEACAM5 MUTATION ANALYSIS"
[1] 3
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                4               122 
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                4               122 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_PACK_YEARS_SMOKED"            
[15] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 126 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 126 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RESIDUAL_TUMOR"                "NUMBER_OF_LYMPH_NODES"        
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=43, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 5 17 99  3 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    5    17   102 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 5 17 99  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    5    17   102 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=23, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=23, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   45 54
  KRAS WILD-TYPE 18  8
  KRAS MUTATED KRAS WILD-TYPE 
            99             26 
  KRAS MUTATED KRAS WILD-TYPE 
            54              8 
$`KRAS MUTATED`
TCGA-2J-AABR TCGA-2J-AABT TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q 
       14.40        10.49         7.66         8.02        15.78         1.08 
TCGA-IB-A5SS TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 
       15.12        17.26        16.37         2.17        23.97         9.63 
TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
        2.63        20.61        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        15.06        34.09        10.13        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        3.12        17.00        16.37        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        17.49        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        10.85         0.23        19.82        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       36.69        41.33        12.00        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40         8.05         7.56 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A779 
       10.29         8.78         3.12        15.32         9.40        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
        0.39        13.81        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

$`KRAS WILD-TYPE`
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-LB-A7SX TCGA-US-A77E TCGA-2J-AABA 
       58.98        60.95        90.12        12.92        14.14        19.96 
TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       15.22        45.47        63.85        50.70        32.81        36.26 
TCGA-3A-A9J0 TCGA-F2-7273 TCGA-FB-A78T TCGA-FB-AAPP TCGA-HZ-7918 TCGA-IB-8126 
       24.43        19.46        12.33        15.95        31.86        15.19 
TCGA-IB-A5SQ TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-RL-AAAS TCGA-US-A776 
        7.20        13.28        12.46        13.68         0.30        39.98 
TCGA-US-A77J TCGA-XD-AAUH 
       18.67        12.99 

  KRAS MUTATED KRAS WILD-TYPE 
          0.23           0.30 
  KRAS MUTATED KRAS WILD-TYPE 
         75.12          90.12 
  KRAS MUTATED KRAS WILD-TYPE 
        14.470         19.065 
[1] "0.2 - 75.1 (14.5)" "0.3 - 90.1 (19.1)"
[1] "hr=" "2.6"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KRAS MUTATED         0        3        6        17        68         3
  KRAS WILD-TYPE       1        0        6         2        14         1
                vv
clus             STAGE IV
  KRAS MUTATED          3
  KRAS WILD-TYPE        0
D1V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              0              1
  STAGE IA             3              0
  STAGE IB             6              6
  STAGE IIA           17              2
  STAGE IIB           68             14
  STAGE III            3              1
  STAGE IV             3              0
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  KRAS MUTATED    4 11    85
  KRAS WILD-TYPE  1  6    17
D1V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               4              1
  T2              11              6
  T3+T4           85             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  KRAS MUTATED   26 74
  KRAS WILD-TYPE  9 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     26   74
  KRAS WILD-TYPE    9   15
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           26              9
  1           74             15
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  KRAS MUTATED   47  3
  KRAS WILD-TYPE 10  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     47    3
  KRAS WILD-TYPE   10    0
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           47             10
  1            3              0
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  KRAS MUTATED   39 61
  KRAS WILD-TYPE 12 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     39   61
  KRAS WILD-TYPE   12   14
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           39             12
  MALE             61             14
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus              0  1
  KRAS MUTATED   69 24
  KRAS WILD-TYPE 19  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     69   24
  KRAS WILD-TYPE   19    6
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            69             19
  YES           24              6
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRAS MUTATED                                    89
  KRAS WILD-TYPE                                  16
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRAS MUTATED                                      10
  KRAS WILD-TYPE                                     8
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRAS MUTATED                                                  0
  KRAS WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  KRAS MUTATED                                     0
  KRAS WILD-TYPE                                   1
D1V9, multiclass
                                                  clus
vv                                                 KRAS MUTATED KRAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        89             16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      10              8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   61 29  3  2
  KRAS WILD-TYPE 19  6  1  0
D1V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           61             19
  R1           29              6
  R2            3              1
  RX            2              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       6                         2    91
  KRAS WILD-TYPE     0                         3    23
D1V14, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                6              0
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               91             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"
D1V15, binary
                cls
clus              0  1
  KRAS MUTATED    5 68
  KRAS WILD-TYPE  0 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5   68
  KRAS WILD-TYPE    0   23
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                5              0
  NOT HISPANIC OR LATINO           68             23
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   36 45
  TP53 WILD-TYPE 27 17
  TP53 MUTATED TP53 WILD-TYPE 
            81             44 
  TP53 MUTATED TP53 WILD-TYPE 
            45             17 
$`TP53 MUTATED`
TCGA-2J-AABR TCGA-2J-AABT TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS 
       14.40        10.49         8.02        15.78         1.08        15.12 
TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 
       12.92        17.26        16.37         2.17        23.97         9.63 
TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
        2.63        20.61        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
        9.60        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       34.09        10.13        24.43         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       12.33        37.15         7.50        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5926 
        5.03         1.02        24.36         2.01         5.10        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 
       22.06         8.28        30.25        17.49        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-A5SO 
       10.13         5.26        10.85        19.82        36.69        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUN 
       15.85        20.88        21.90         1.35        15.88         4.73 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-OE-A75W 
       14.17         6.02         7.40         8.05        10.29         8.78 
TCGA-RB-AA9M TCGA-US-A779 TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        9.40        16.80        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        12.76        15.35 

$`TP53 WILD-TYPE`
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-US-A77E TCGA-2J-AABA 
       58.98        60.95        90.12         7.66        14.14        19.96 
TCGA-2J-AABE TCGA-2J-AABP TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IO TCGA-3A-A9IR 
       22.22        15.22        45.47        43.50        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-FB-AAPP 
       32.81        36.26        75.12        71.74        19.46        15.95 
TCGA-FB-AAPU TCGA-FZ-5922 TCGA-FZ-5923 TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-A8P1 
       12.53        36.20        20.35        32.15        31.86         0.23 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-A7LX TCGA-IB-AAUM 
       19.82        41.33        15.19         7.20         8.22         0.26 
TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-Q3-A5QY 
        7.86        11.11        13.28         7.56        12.46        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J 
        3.12        15.32         0.30        39.98         0.39        18.67 
TCGA-YB-A89D TCGA-YY-A8LH 
       11.51        66.28 

  TP53 MUTATED TP53 WILD-TYPE 
          1.02           0.23 
  TP53 MUTATED TP53 WILD-TYPE 
         42.31          90.12 
  TP53 MUTATED TP53 WILD-TYPE 
        14.400         19.065 
[1] "1.0 - 42.3 (14.4)" "0.2 - 90.1 (19.1)"
[1] "hr=" "2.2"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TP53 MUTATED         0        3        4        13        56         3
  TP53 WILD-TYPE       1        0        8         6        26         1
                vv
clus             STAGE IV
  TP53 MUTATED          2
  TP53 WILD-TYPE        1
D2V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              0              1
  STAGE IA             3              0
  STAGE IB             4              8
  STAGE IIA           13              6
  STAGE IIB           56             26
  STAGE III            3              1
  STAGE IV             2              1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TP53 MUTATED    4  9    68
  TP53 WILD-TYPE  1  8    34
D2V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               4              1
  T2               9              8
  T3+T4           68             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                cls
clus              0  1
  TP53 MUTATED   21 60
  TP53 WILD-TYPE 14 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     21   60
  TP53 WILD-TYPE   14   29
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           21             14
  1           60             29
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus              0  1
  TP53 MUTATED   39  2
  TP53 WILD-TYPE 18  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     39    2
  TP53 WILD-TYPE   18    1
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           39             18
  1            2              1
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus              0  1
  TP53 MUTATED   33 48
  TP53 WILD-TYPE 18 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     33   48
  TP53 WILD-TYPE   18   27
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           33             18
  MALE             48             27
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED   58 19
  TP53 WILD-TYPE 30 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     58   19
  TP53 WILD-TYPE   30   11
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            58             30
  YES           19             11
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TP53 MUTATED                                    72
  TP53 WILD-TYPE                                  33
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TP53 MUTATED                                       8
  TP53 WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TP53 MUTATED                                                  0
  TP53 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TP53 MUTATED                                     0
  TP53 WILD-TYPE                                   1
D2V9, multiclass
                                                  clus
vv                                                 TP53 MUTATED TP53 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        72             33
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       8             10
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   47 26  4  1
  TP53 WILD-TYPE 33  9  0  1
D2V12, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           47             33
  R1           26              9
  R2            4              0
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       4                         2    74
  TP53 WILD-TYPE     2                         3    40
D2V14, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                4              2
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               74             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                cls
clus              0  1
  TP53 MUTATED    4 52
  TP53 WILD-TYPE  1 39
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   52
  TP53 WILD-TYPE    1   39
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4              1
  NOT HISPANIC OR LATINO           52             39
[1] 2 2
[1] FALSE

Clustering(3) Variable = MAMLD1 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  MAMLD1 MUTATED   15 13
  MAMLD1 WILD-TYPE 48 49
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
              28               97 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
              13               49 
$`MAMLD1 MUTATED`
TCGA-2J-AABT TCGA-3A-A9IL TCGA-US-A77E TCGA-2J-AAB6 TCGA-2J-AABA TCGA-2J-AABK 
       10.49        90.12        14.14         9.63        19.96        15.91 
TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IV TCGA-F2-7273 
       22.49        12.95         9.60        45.47        36.26        19.46 
TCGA-F2-A7TX TCGA-FB-AAPP TCGA-FB-AAPU TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
        3.12        15.95        12.53        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SP TCGA-OE-A75W TCGA-Q3-A5QY 
       17.49        10.85        19.82        15.85         8.78        13.68 
TCGA-Q3-AA2A TCGA-XD-AAUG TCGA-YB-A89D TCGA-YH-A8SY 
        3.12        13.81        11.51        12.76 

$`MAMLD1 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        58.98        60.95         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
        1.08        15.12        12.92        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH 
       23.97         2.63        20.61        22.22        22.72        42.31 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       75.12        71.74        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       32.15        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH 
       18.67        12.99        12.03        31.27        23.67        66.28 
TCGA-Z5-AAPL 
       15.35 

  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
            3.12             0.23 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
           90.12            75.12 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
          13.975           15.320 
[1] "3.1 - 90.1 (14.0)" "0.2 - 75.1 (15.3)"
[1] "hr=" "1"  
D3V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAMLD1 MUTATED         1        0        2         6        16         2
  MAMLD1 WILD-TYPE       0        3       10        13        66         2
                  vv
clus               STAGE IV
  MAMLD1 MUTATED          1
  MAMLD1 WILD-TYPE        2
D3V3, multiclass
           clus
vv          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              6               13
  STAGE IIB             16               66
  STAGE III              2                2
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MAMLD1 MUTATED    1  2    25
  MAMLD1 WILD-TYPE  4 15    77
D3V4, multiclass
       clus
vv      MAMLD1 MUTATED MAMLD1 WILD-TYPE
  T1                 1                4
  T2                 2               15
  T3+T4             25               77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    8 19
  MAMLD1 WILD-TYPE 27 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      8   19
  MAMLD1 WILD-TYPE   27   70
   clus
vv  MAMLD1 MUTATED MAMLD1 WILD-TYPE
  0              8               27
  1             19               70
[1] 2 2
[1] FALSE
D3V6, binary
                  cls
clus                0  1
  MAMLD1 MUTATED   10  1
  MAMLD1 WILD-TYPE 47  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED     10    1
  MAMLD1 WILD-TYPE   47    2
   clus
vv  MAMLD1 MUTATED MAMLD1 WILD-TYPE
  0             10               47
  1              1                2
[1] 2 2
[1] FALSE
D3V7, binary
                  cls
clus                0  1
  MAMLD1 MUTATED   10 18
  MAMLD1 WILD-TYPE 41 57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED     10   18
  MAMLD1 WILD-TYPE   41   57
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  FEMALE             10               41
  MALE               18               57
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                0  1
  MAMLD1 MUTATED   21  6
  MAMLD1 WILD-TYPE 67 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED     21    6
  MAMLD1 WILD-TYPE   67   24
     clus
vv    MAMLD1 MUTATED MAMLD1 WILD-TYPE
  NO              21               67
  YES              6               24
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAMLD1 MUTATED                                    21
  MAMLD1 WILD-TYPE                                  84
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAMLD1 MUTATED                                       6
  MAMLD1 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAMLD1 MUTATED                                                  0
  MAMLD1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAMLD1 MUTATED                                     0
  MAMLD1 WILD-TYPE                                   1
D3V9, multiclass
                                                  clus
vv                                                 MAMLD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MAMLD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            84
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
                  vv
clus               R0 R1 R2 RX
  MAMLD1 MUTATED   13  9  3  2
  MAMLD1 WILD-TYPE 67 26  1  0
D3V12, multiclass
    clus
vv   MAMLD1 MUTATED MAMLD1 WILD-TYPE
  R0             13               67
  R1              9               26
  R2              3                1
  RX              2                0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMLD1 MUTATED       4                         1    23
  MAMLD1 WILD-TYPE     2                         4    91
D3V14, multiclass
                           clus
vv                          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  ASIAN                                  4                2
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                 23               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    0 15
  MAMLD1 WILD-TYPE  5 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      0   15
  MAMLD1 WILD-TYPE    5   76
                        clus
vv                       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             15               76
[1] 2 2
[1] FALSE

Clustering(4) Variable = CDKN2A MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED   13 13
  CDKN2A WILD-TYPE 50 49
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26               99 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              13               49 
$`CDKN2A MUTATED`
TCGA-IB-A5SS TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2L-AAQE 
       15.12         2.63        22.72        42.31        15.91        22.49 
TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       12.95        43.50         7.36        33.57        15.06        34.09 
TCGA-3E-AAAY TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAQ2 TCGA-FZ-5920 TCGA-HV-A7OL 
       75.12        17.00        12.33         5.03         2.01         8.28 
TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-OE-A75W TCGA-RB-AA9M 
        5.26        19.82         1.35        15.88         8.78         9.40 
TCGA-US-A77G TCGA-YB-A89D 
        0.39        11.51 

$`CDKN2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       22.22        14.47        15.22         9.11        21.44         4.70 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IO 
        3.39         9.60        45.47        20.84        24.26        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       50.70        32.81        36.26        10.13        24.43        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       19.46         3.12        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         1.02        24.36 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP 
        5.10        36.20        20.35        17.79        22.06        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.39             0.23 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           75.12            90.12 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          14.005           15.350 
[1] "0.4 - 75.1 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D4V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDKN2A MUTATED         0        2        0         4        19         1
  CDKN2A WILD-TYPE       1        1       12        15        63         3
                  vv
clus               STAGE IV
  CDKN2A MUTATED          1
  CDKN2A WILD-TYPE        2
D4V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                0                1
  STAGE IA               2                1
  STAGE IB               0               12
  STAGE IIA              4               15
  STAGE IIB             19               63
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CDKN2A MUTATED    3  1    23
  CDKN2A WILD-TYPE  2 16    79
D4V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T1                 3                2
  T2                 1               16
  T3+T4             23               79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                  cls
clus                0  1
  CDKN2A MUTATED    8 19
  CDKN2A WILD-TYPE 27 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8   19
  CDKN2A WILD-TYPE   27   70
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0              8               27
  1             19               70
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                0  1
  CDKN2A MUTATED   11  1
  CDKN2A WILD-TYPE 46  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    1
  CDKN2A WILD-TYPE   46    2
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             11               46
  1              1                2
[1] 2 2
[1] FALSE
D4V7, binary
                  cls
clus                0  1
  CDKN2A MUTATED    7 20
  CDKN2A WILD-TYPE 44 55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      7   20
  CDKN2A WILD-TYPE   44   55
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              7               44
  MALE               20               55
[1] 2 2
[1] FALSE
D4V8, binary
                  cls
clus                0  1
  CDKN2A MUTATED   18  7
  CDKN2A WILD-TYPE 70 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     18    7
  CDKN2A WILD-TYPE   70   23
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              18               70
  YES              7               23
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDKN2A MUTATED                                    25
  CDKN2A WILD-TYPE                                  80
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDKN2A MUTATED                                       2
  CDKN2A WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDKN2A MUTATED                                                  0
  CDKN2A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDKN2A MUTATED                                     0
  CDKN2A WILD-TYPE                                   1
D4V9, multiclass
                                                  clus
vv                                                 CDKN2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CDKN2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            80
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
                  vv
clus               R0 R1 R2 RX
  CDKN2A MUTATED   18  7  1  0
  CDKN2A WILD-TYPE 62 28  3  2
D4V12, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             18               62
  R1              7               28
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       1                         2    24
  CDKN2A WILD-TYPE     5                         3    90
D4V14, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                 24               90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                  cls
clus                0  1
  CDKN2A MUTATED    0 20
  CDKN2A WILD-TYPE  5 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   20
  CDKN2A WILD-TYPE    5   71
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             20               71
[1] 2 2
[1] FALSE

Clustering(5) Variable = CD99L2 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  CD99L2 MUTATED   10 10
  CD99L2 WILD-TYPE 53 52
  CD99L2 MUTATED CD99L2 WILD-TYPE 
              20              105 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
              10               52 
$`CD99L2 MUTATED`
TCGA-2J-AABR TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABU TCGA-2L-AAQJ TCGA-3A-A9I9 
       14.40        23.97         9.63         9.11        12.95        20.84 
TCGA-3A-A9IB TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-HV-AA8V TCGA-HZ-8637 TCGA-HZ-A77O 
        7.36        15.55         1.02        30.25        17.00         5.26 
TCGA-HZ-A77P TCGA-IB-A6UF TCGA-IB-AAUM TCGA-Q3-A5QY TCGA-US-A779 TCGA-XD-AAUG 
       10.85        21.90         0.26        13.68        16.80        13.81 
TCGA-XN-A8T3 TCGA-YY-A8LH 
       31.27        66.28 

$`CD99L2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       16.37         2.17         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV 
       22.72        42.31        15.91        14.47        15.22        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
        4.70        22.49         3.39         9.60        45.47        43.50 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.13         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG 
       15.19        12.00        15.85         7.20        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       39.98         0.39        18.67        12.99        12.03        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76        15.35 

  CD99L2 MUTATED CD99L2 WILD-TYPE 
            0.26             0.23 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
           66.28            90.12 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
          14.105           15.320 
[1] "0.3 - 66.3 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D5V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CD99L2 MUTATED         0        0        1         4        13         1
  CD99L2 WILD-TYPE       1        3       11        15        69         3
                  vv
clus               STAGE IV
  CD99L2 MUTATED          1
  CD99L2 WILD-TYPE        2
D5V3, multiclass
           clus
vv          CD99L2 MUTATED CD99L2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              4               15
  STAGE IIB             13               69
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CD99L2 MUTATED    0  4    16
  CD99L2 WILD-TYPE  5 13    86
D5V4, multiclass
       clus
vv      CD99L2 MUTATED CD99L2 WILD-TYPE
  T1                 0                5
  T2                 4               13
  T3+T4             16               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                  cls
clus                0  1
  CD99L2 MUTATED    6 14
  CD99L2 WILD-TYPE 29 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      6   14
  CD99L2 WILD-TYPE   29   75
   clus
vv  CD99L2 MUTATED CD99L2 WILD-TYPE
  0              6               29
  1             14               75
[1] 2 2
[1] FALSE
D5V6, binary
                  cls
clus                0  1
  CD99L2 MUTATED    7  1
  CD99L2 WILD-TYPE 50  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      7    1
  CD99L2 WILD-TYPE   50    2
   clus
vv  CD99L2 MUTATED CD99L2 WILD-TYPE
  0              7               50
  1              1                2
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                0  1
  CD99L2 MUTATED    9 11
  CD99L2 WILD-TYPE 42 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      9   11
  CD99L2 WILD-TYPE   42   64
        clus
vv       CD99L2 MUTATED CD99L2 WILD-TYPE
  FEMALE              9               42
  MALE               11               64
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus                0  1
  CD99L2 MUTATED   15  4
  CD99L2 WILD-TYPE 73 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED     15    4
  CD99L2 WILD-TYPE   73   26
     clus
vv    CD99L2 MUTATED CD99L2 WILD-TYPE
  NO              15               73
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD99L2 MUTATED                                    18
  CD99L2 WILD-TYPE                                  87
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD99L2 MUTATED                                       2
  CD99L2 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD99L2 MUTATED                                                  0
  CD99L2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CD99L2 MUTATED                                     0
  CD99L2 WILD-TYPE                                   1
D5V9, multiclass
                                                  clus
vv                                                 CD99L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CD99L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            87
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
                  vv
clus               R0 R1 R2 RX
  CD99L2 MUTATED   16  3  1  0
  CD99L2 WILD-TYPE 64 32  3  2
D5V12, multiclass
    clus
vv   CD99L2 MUTATED CD99L2 WILD-TYPE
  R0             16               64
  R1              3               32
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD99L2 MUTATED       1                         0    19
  CD99L2 WILD-TYPE     5                         5    95
D5V14, multiclass
                           clus
vv                          CD99L2 MUTATED CD99L2 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 19               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                  cls
clus                0  1
  CD99L2 MUTATED    2 12
  CD99L2 WILD-TYPE  3 79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      2   12
  CD99L2 WILD-TYPE    3   79
                        clus
vv                       CD99L2 MUTATED CD99L2 WILD-TYPE
  HISPANIC OR LATINO                  2                3
  NOT HISPANIC OR LATINO             12               79
[1] 2 2
[1] FALSE

Clustering(6) Variable = IPP MUTATION ANALYSIS
D6V1, survival
               sevent
clus2            0  1
  IPP MUTATED   11  9
  IPP WILD-TYPE 52 53
  IPP MUTATED IPP WILD-TYPE 
           20           105 
  IPP MUTATED IPP WILD-TYPE 
            9            53 
$`IPP MUTATED`
TCGA-3A-A9IJ TCGA-2J-AABE TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-F2-A7TX TCGA-FB-A5VM 
       60.95        22.22        12.95         7.36         3.12        16.37 
TCGA-FB-AAQ0 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-A7LX TCGA-IB-AAUP 
       15.55        32.15        19.82         7.20         8.22        14.17 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-US-A776 
        8.05        13.28        13.68         3.12         9.40        39.98 
TCGA-XD-AAUI TCGA-Z5-AAPL 
       12.03        15.35 

$`IPP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50        20.84        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A78T 
       24.43        75.12        71.74        19.46        17.00        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        23.54         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUW 
        4.73         7.86         6.02        11.11         7.40         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A779 
       12.46        10.29         8.78        15.32         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        13.81        12.99        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  IPP MUTATED IPP WILD-TYPE 
         3.12          0.23 
  IPP MUTATED IPP WILD-TYPE 
        60.95         90.12 
  IPP MUTATED IPP WILD-TYPE 
        13.48         15.78 
[1] "3.1 - 61.0 (13.5)" "0.2 - 90.1 (15.8)"
[1] "hr=" "1.1"
D6V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IPP MUTATED         0        0        4         4        11         1
  IPP WILD-TYPE       1        3        8        15        71         3
               vv
clus            STAGE IV
  IPP MUTATED          0
  IPP WILD-TYPE        3
D6V3, multiclass
           clus
vv          IPP MUTATED IPP WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            4             8
  STAGE IIA           4            15
  STAGE IIB          11            71
  STAGE III           1             3
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  IPP MUTATED    1  3    16
  IPP WILD-TYPE  4 14    86
D6V4, multiclass
       clus
vv      IPP MUTATED IPP WILD-TYPE
  T1              1             4
  T2              3            14
  T3+T4          16            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
               cls
clus             0  1
  IPP MUTATED    8 12
  IPP WILD-TYPE 27 77
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      8   12
  IPP WILD-TYPE   27   77
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0           8            27
  1          12            77
[1] 2 2
[1] FALSE
D6V6, binary
               cls
clus             0  1
  IPP MUTATED   10  0
  IPP WILD-TYPE 47  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED     10    0
  IPP WILD-TYPE   47    3
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0          10            47
  1           0             3
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus             0  1
  IPP MUTATED    7 13
  IPP WILD-TYPE 44 62
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      7   13
  IPP WILD-TYPE   44   62
        clus
vv       IPP MUTATED IPP WILD-TYPE
  FEMALE           7            44
  MALE            13            62
[1] 2 2
[1] FALSE
D6V8, binary
               cls
clus             0  1
  IPP MUTATED   17  3
  IPP WILD-TYPE 71 27
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED     17    3
  IPP WILD-TYPE   71   27
     clus
vv    IPP MUTATED IPP WILD-TYPE
  NO           17            71
  YES           3            27
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IPP MUTATED                                    17
  IPP WILD-TYPE                                  88
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IPP MUTATED                                       2
  IPP WILD-TYPE                                    16
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IPP MUTATED                                                  1
  IPP WILD-TYPE                                                0
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  IPP MUTATED                                     0
  IPP WILD-TYPE                                   1
D6V9, multiclass
                                                  clus
vv                                                 IPP MUTATED IPP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       17            88
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      2            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           1             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
               vv
clus            R0 R1 R2 RX
  IPP MUTATED   15  4  0  1
  IPP WILD-TYPE 65 31  4  1
D6V12, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  R0          15            65
  R1           4            31
  R2           0             4
  RX           1             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPP MUTATED       1                         0    19
  IPP WILD-TYPE     5                         5    95
D6V14, multiclass
                           clus
vv                          IPP MUTATED IPP WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                              19            95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
               cls
clus             0  1
  IPP MUTATED    0 16
  IPP WILD-TYPE  5 75
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      0   16
  IPP WILD-TYPE    5   75
                        clus
vv                       IPP MUTATED IPP WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          16            75
[1] 2 2
[1] FALSE

Clustering(7) Variable = IRS1 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  IRS1 MUTATED   12  8
  IRS1 WILD-TYPE 51 54
  IRS1 MUTATED IRS1 WILD-TYPE 
            20            105 
  IRS1 MUTATED IRS1 WILD-TYPE 
             8             54 
$`IRS1 MUTATED`
TCGA-2J-AABR TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABE TCGA-2J-AABH 
       14.40        14.14         2.17        23.97        22.22        42.31 
TCGA-3A-A9J0 TCGA-F2-7273 TCGA-FB-AAPQ TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-HV-AA8V 
       24.43        19.46        37.15        23.54         5.03        30.25 
TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-A5SP TCGA-Q3-A5QY TCGA-RB-AA9M 
       17.00         5.26        19.82        15.85        13.68         9.40 
TCGA-US-A77G TCGA-Z5-AAPL 
        0.39        15.35 

$`IRS1 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABK 
        9.63         2.63        20.61        19.96        22.72        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        10.13        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        15.95         7.50 
TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       12.53        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77P 
       32.15        17.49        31.86        20.19        10.13        10.85 
TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        8.78         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  IRS1 MUTATED IRS1 WILD-TYPE 
          0.39           0.23 
  IRS1 MUTATED IRS1 WILD-TYPE 
         42.31          90.12 
  IRS1 MUTATED IRS1 WILD-TYPE 
        16.425         15.120 
[1] "0.4 - 42.3 (16.4)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.4"
D7V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IRS1 MUTATED         0        0        0         5        14         0
  IRS1 WILD-TYPE       1        3       12        14        68         4
                vv
clus             STAGE IV
  IRS1 MUTATED          1
  IRS1 WILD-TYPE        2
D7V3, multiclass
           clus
vv          IRS1 MUTATED IRS1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            5             14
  STAGE IIB           14             68
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  IRS1 MUTATED    1  3    16
  IRS1 WILD-TYPE  4 14    86
D7V4, multiclass
       clus
vv      IRS1 MUTATED IRS1 WILD-TYPE
  T1               1              4
  T2               3             14
  T3+T4           16             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                cls
clus              0  1
  IRS1 MUTATED    6 14
  IRS1 WILD-TYPE 29 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      6   14
  IRS1 WILD-TYPE   29   75
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0            6             29
  1           14             75
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus              0  1
  IRS1 MUTATED    8  1
  IRS1 WILD-TYPE 49  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      8    1
  IRS1 WILD-TYPE   49    2
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0            8             49
  1            1              2
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus              0  1
  IRS1 MUTATED    5 15
  IRS1 WILD-TYPE 46 60
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      5   15
  IRS1 WILD-TYPE   46   60
        clus
vv       IRS1 MUTATED IRS1 WILD-TYPE
  FEMALE            5             46
  MALE             15             60
[1] 2 2
[1] FALSE
D7V8, binary
                cls
clus              0  1
  IRS1 MUTATED   16  4
  IRS1 WILD-TYPE 72 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED     16    4
  IRS1 WILD-TYPE   72   26
     clus
vv    IRS1 MUTATED IRS1 WILD-TYPE
  NO            16             72
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS1 MUTATED                                    15
  IRS1 WILD-TYPE                                  90
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS1 MUTATED                                       5
  IRS1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS1 MUTATED                                                  0
  IRS1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  IRS1 MUTATED                                     0
  IRS1 WILD-TYPE                                   1
D7V9, multiclass
                                                  clus
vv                                                 IRS1 MUTATED IRS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        15             90
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       5             13
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
                vv
clus             R0 R1 R2 RX
  IRS1 MUTATED   15  4  1  0
  IRS1 WILD-TYPE 65 31  3  2
D7V12, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  R0           15             65
  R1            4             31
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS1 MUTATED       1                         1    18
  IRS1 WILD-TYPE     5                         4    96
D7V14, multiclass
                           clus
vv                          IRS1 MUTATED IRS1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               18             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                cls
clus              0  1
  IRS1 MUTATED    1 12
  IRS1 WILD-TYPE  4 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      1   12
  IRS1 WILD-TYPE    4   79
                        clus
vv                       IRS1 MUTATED IRS1 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           12             79
[1] 2 2
[1] FALSE

Clustering(8) Variable = C19ORF55 MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                 0  1
  C19ORF55 MUTATED    9  7
  C19ORF55 WILD-TYPE 54 55
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                16                109 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 7                 55 
$`C19ORF55 MUTATED`
TCGA-LB-A7SX TCGA-2J-AAB4 TCGA-2J-AABF TCGA-2L-AAQI TCGA-3A-A9IU TCGA-3A-A9IV 
       12.92        23.97        22.72         3.39        15.06        36.26 
TCGA-FZ-5920 TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HZ-A77P TCGA-IB-7651 TCGA-US-A776 
        2.01        22.06        30.25        10.85        19.82        39.98 
TCGA-US-A779 TCGA-XD-AAUG TCGA-XN-A8T3 TCGA-Z5-AAPL 
       16.80        13.81        31.27        15.35 

$`C19ORF55 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.22        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        32.81        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03         1.02        24.36         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79         8.28        32.15        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A77G 
       13.68         3.12        15.32         9.40         0.30         0.39 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       18.67        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
              2.01               0.23 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
             39.98              90.12 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
             18.31              15.12 
[1] "2.0 - 40.0 (18.3)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.4"
D8V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C19ORF55 MUTATED         0        0        2         3        10         0
  C19ORF55 WILD-TYPE       1        3       10        16        72         4
                    vv
clus                 STAGE IV
  C19ORF55 MUTATED          1
  C19ORF55 WILD-TYPE        2
D8V3, multiclass
           clus
vv          C19ORF55 MUTATED C19ORF55 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 2                 10
  STAGE IIA                3                 16
  STAGE IIB               10                 72
  STAGE III                0                  4
  STAGE IV                 1                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C19ORF55 MUTATED    0  3    13
  C19ORF55 WILD-TYPE  5 14    89
D8V4, multiclass
       clus
vv      C19ORF55 MUTATED C19ORF55 WILD-TYPE
  T1                   0                  5
  T2                   3                 14
  T3+T4               13                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    5 11
  C19ORF55 WILD-TYPE 30 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      5   11
  C19ORF55 WILD-TYPE   30   78
   clus
vv  C19ORF55 MUTATED C19ORF55 WILD-TYPE
  0                5                 30
  1               11                 78
[1] 2 2
[1] FALSE
D8V6, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    6  1
  C19ORF55 WILD-TYPE 51  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      6    1
  C19ORF55 WILD-TYPE   51    2
   clus
vv  C19ORF55 MUTATED C19ORF55 WILD-TYPE
  0                6                 51
  1                1                  2
[1] 2 2
[1] FALSE
D8V7, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    6 10
  C19ORF55 WILD-TYPE 45 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      6   10
  C19ORF55 WILD-TYPE   45   65
        clus
vv       C19ORF55 MUTATED C19ORF55 WILD-TYPE
  FEMALE                6                 45
  MALE                 10                 65
[1] 2 2
[1] FALSE
D8V8, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED   13  2
  C19ORF55 WILD-TYPE 75 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED     13    2
  C19ORF55 WILD-TYPE   75   28
     clus
vv    C19ORF55 MUTATED C19ORF55 WILD-TYPE
  NO                13                 75
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C19ORF55 MUTATED                                    11
  C19ORF55 WILD-TYPE                                  94
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C19ORF55 MUTATED                                       4
  C19ORF55 WILD-TYPE                                    14
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C19ORF55 MUTATED                                                  1
  C19ORF55 WILD-TYPE                                                0
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C19ORF55 MUTATED                                     0
  C19ORF55 WILD-TYPE                                   1
D8V9, multiclass
                                                  clus
vv                                                 C19ORF55 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C19ORF55 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
                    vv
clus                 R0 R1 R2 RX
  C19ORF55 MUTATED   11  4  1  0
  C19ORF55 WILD-TYPE 69 31  3  2
D8V12, multiclass
    clus
vv   C19ORF55 MUTATED C19ORF55 WILD-TYPE
  R0               11                 69
  R1                4                 31
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C19ORF55 MUTATED       1                         2    13
  C19ORF55 WILD-TYPE     5                         3   101
D8V14, multiclass
                           clus
vv                          C19ORF55 MUTATED C19ORF55 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                   13                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    1 11
  C19ORF55 WILD-TYPE  4 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      1   11
  C19ORF55 WILD-TYPE    4   80
                        clus
vv                       C19ORF55 MUTATED C19ORF55 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               11                 80
[1] 2 2
[1] FALSE

Clustering(9) Variable = C15ORF24 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                 0  1
  C15ORF24 MUTATED    7  7
  C15ORF24 WILD-TYPE 56 55
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
                14                111 
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
                 7                 55 
$`C15ORF24 MUTATED`
TCGA-LB-A7SX TCGA-2J-AAB4 TCGA-2J-AABA TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       12.92        23.97        19.96        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-3A-A9IU TCGA-3E-AAAY TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A6UG 
        9.11        15.06        75.12        19.82        15.19         1.35 
TCGA-Q3-A5QY TCGA-XD-AAUI 
       13.68        12.03 

$`C15ORF24 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
       16.37         2.17         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       22.72        42.31        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        32.81        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
              1.35               0.23 
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
             75.12              90.12 
  C15ORF24 MUTATED C15ORF24 WILD-TYPE 
            15.125             15.350 
[1] "1.4 - 75.1 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D9V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C15ORF24 MUTATED         0        0        0         0        14         1
  C15ORF24 WILD-TYPE       1        3       12        19        68         3
                    vv
clus                 STAGE IV
  C15ORF24 MUTATED          0
  C15ORF24 WILD-TYPE        3
D9V3, multiclass
           clus
vv          C15ORF24 MUTATED C15ORF24 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB               14                 68
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C15ORF24 MUTATED    0  1    14
  C15ORF24 WILD-TYPE  5 16    88
D9V4, multiclass
       clus
vv      C15ORF24 MUTATED C15ORF24 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4               14                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                    cls
clus                  0  1
  C15ORF24 MUTATED    0 15
  C15ORF24 WILD-TYPE 35 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF24 MUTATED      0   15
  C15ORF24 WILD-TYPE   35   74
   clus
vv  C15ORF24 MUTATED C15ORF24 WILD-TYPE
  0                0                 35
  1               15                 74
[1] 2 2
[1] FALSE
D9V6, binary
                    cls
clus                  0  1
  C15ORF24 MUTATED    9  0
  C15ORF24 WILD-TYPE 48  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF24 MUTATED      9    0
  C15ORF24 WILD-TYPE   48    3
   clus
vv  C15ORF24 MUTATED C15ORF24 WILD-TYPE
  0                9                 48
  1                0                  3
[1] 2 2
[1] FALSE
D9V7, binary
                    cls
clus                  0  1
  C15ORF24 MUTATED    5 10
  C15ORF24 WILD-TYPE 46 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF24 MUTATED      5   10
  C15ORF24 WILD-TYPE   46   65
        clus
vv       C15ORF24 MUTATED C15ORF24 WILD-TYPE
  FEMALE                5                 46
  MALE                 10                 65
[1] 2 2
[1] FALSE
D9V8, binary
                    cls
clus                  0  1
  C15ORF24 MUTATED   12  2
  C15ORF24 WILD-TYPE 76 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF24 MUTATED     12    2
  C15ORF24 WILD-TYPE   76   28
     clus
vv    C15ORF24 MUTATED C15ORF24 WILD-TYPE
  NO                12                 76
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C15ORF24 MUTATED                                    13
  C15ORF24 WILD-TYPE                                  92
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C15ORF24 MUTATED                                       1
  C15ORF24 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C15ORF24 MUTATED                                                  0
  C15ORF24 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C15ORF24 MUTATED                                     1
  C15ORF24 WILD-TYPE                                   0
D9V9, multiclass
                                                  clus
vv                                                 C15ORF24 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 C15ORF24 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              92
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
                    vv
clus                 R0 R1 R2 RX
  C15ORF24 MUTATED    8  6  0  0
  C15ORF24 WILD-TYPE 72 29  4  2
D9V12, multiclass
    clus
vv   C15ORF24 MUTATED C15ORF24 WILD-TYPE
  R0                8                 72
  R1                6                 29
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF24 MUTATED       0                         1    14
  C15ORF24 WILD-TYPE     6                         4   100
D9V14, multiclass
                           clus
vv                          C15ORF24 MUTATED C15ORF24 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                   14                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                    cls
clus                  0  1
  C15ORF24 MUTATED    0  9
  C15ORF24 WILD-TYPE  5 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF24 MUTATED      0    9
  C15ORF24 WILD-TYPE    5   82
                        clus
vv                       C15ORF24 MUTATED C15ORF24 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                9                 82
[1] 2 2
[1] FALSE

Clustering(10) Variable = QRICH1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  QRICH1 MUTATED    7  7
  QRICH1 WILD-TYPE 56 55
  QRICH1 MUTATED QRICH1 WILD-TYPE 
              14              111 
  QRICH1 MUTATED QRICH1 WILD-TYPE 
               7               55 
$`QRICH1 MUTATED`
TCGA-2J-AABU TCGA-2L-AAQE TCGA-2L-AAQI TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-FB-AAQ3 
        9.11        22.49         3.39        15.06        24.43         1.02 
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5ST TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-XD-AAUI 
       10.85        19.82        20.88         3.12         9.40        12.03 
TCGA-YB-A89D TCGA-Z5-AAPL 
       11.51        15.35 

$`QRICH1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-2L-AAQL 
       14.47        15.22        21.44         4.70        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        32.81        36.26        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         4.04         5.03        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
       10.29         8.78        13.68        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.99        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       23.67        12.76        66.28 

  QRICH1 MUTATED QRICH1 WILD-TYPE 
            1.02             0.23 
  QRICH1 MUTATED QRICH1 WILD-TYPE 
           24.43            90.12 
  QRICH1 MUTATED QRICH1 WILD-TYPE 
           11.77            15.55 
[1] "1.0 - 24.4 (11.8)" "0.2 - 90.1 (15.6)"
[1] "hr=" "1.4"
D10V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  QRICH1 MUTATED         0        0        1         1        12         0
  QRICH1 WILD-TYPE       1        3       11        18        70         4
                  vv
clus               STAGE IV
  QRICH1 MUTATED          0
  QRICH1 WILD-TYPE        3
D10V3, multiclass
           clus
vv          QRICH1 MUTATED QRICH1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB             12               70
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  QRICH1 MUTATED    1  0    13
  QRICH1 WILD-TYPE  4 17    89
D10V4, multiclass
       clus
vv      QRICH1 MUTATED QRICH1 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4             13               89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                  cls
clus                0  1
  QRICH1 MUTATED    1 13
  QRICH1 WILD-TYPE 34 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH1 MUTATED      1   13
  QRICH1 WILD-TYPE   34   76
   clus
vv  QRICH1 MUTATED QRICH1 WILD-TYPE
  0              1               34
  1             13               76
[1] 2 2
[1] FALSE
D10V6, binary
                  cls
clus                0  1
  QRICH1 MUTATED    5  0
  QRICH1 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH1 MUTATED      5    0
  QRICH1 WILD-TYPE   52    3
   clus
vv  QRICH1 MUTATED QRICH1 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                0  1
  QRICH1 MUTATED    6  8
  QRICH1 WILD-TYPE 45 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH1 MUTATED      6    8
  QRICH1 WILD-TYPE   45   67
        clus
vv       QRICH1 MUTATED QRICH1 WILD-TYPE
  FEMALE              6               45
  MALE                8               67
[1] 2 2
[1] FALSE
D10V8, binary
                  cls
clus                0  1
  QRICH1 MUTATED   12  2
  QRICH1 WILD-TYPE 76 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH1 MUTATED     12    2
  QRICH1 WILD-TYPE   76   28
     clus
vv    QRICH1 MUTATED QRICH1 WILD-TYPE
  NO              12               76
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  QRICH1 MUTATED                                    13
  QRICH1 WILD-TYPE                                  92
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  QRICH1 MUTATED                                       1
  QRICH1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  QRICH1 MUTATED                                                  0
  QRICH1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  QRICH1 MUTATED                                     0
  QRICH1 WILD-TYPE                                   1
D10V9, multiclass
                                                  clus
vv                                                 QRICH1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 QRICH1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            92
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
[1] "Remove cluster labels:" "QRICH1 MUTATED"        
clus
  QRICH1 MUTATED QRICH1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-YY-A8LH 
"QRICH1 WILD-TYPE" 
D10V11, continuous
[1] "Remove cluster labels:" "QRICH1 MUTATED"        
clus
  QRICH1 MUTATED QRICH1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XN-A8T5       TCGA-YY-A8LH 
"QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" "QRICH1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  QRICH1 MUTATED   11  2  0  1
  QRICH1 WILD-TYPE 69 33  4  1
D10V12, multiclass
    clus
vv   QRICH1 MUTATED QRICH1 WILD-TYPE
  R0             11               69
  R1              2               33
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  QRICH1 MUTATED       0                         0    14
  QRICH1 WILD-TYPE     6                         5   100
D10V14, multiclass
                           clus
vv                          QRICH1 MUTATED QRICH1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 14              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                  cls
clus                0  1
  QRICH1 MUTATED    0 11
  QRICH1 WILD-TYPE  5 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH1 MUTATED      0   11
  QRICH1 WILD-TYPE    5   80
                        clus
vv                       QRICH1 MUTATED QRICH1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             11               80
[1] 2 2
[1] FALSE

Clustering(11) Variable = IFT46 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  IFT46 MUTATED    6  7
  IFT46 WILD-TYPE 57 55
  IFT46 MUTATED IFT46 WILD-TYPE 
             13             112 
  IFT46 MUTATED IFT46 WILD-TYPE 
              7              55 
$`IFT46 MUTATED`
TCGA-US-A77E TCGA-2L-AAQI TCGA-3A-A9IV TCGA-3E-AAAZ TCGA-F2-A8YN TCGA-FZ-5923 
       14.14         3.39        36.26        71.74        17.00        20.35 
TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A7LX TCGA-RL-AAAS 
        0.23        19.82        12.00        15.85         8.22         0.30 
TCGA-YH-A8SY 
       12.76 

$`IFT46 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM 
       10.13        24.43        75.12        19.46         3.12        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
        5.10        36.20        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26        10.85        19.82        36.69        41.33        15.19 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         9.40        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  IFT46 MUTATED IFT46 WILD-TYPE 
           0.23            0.26 
  IFT46 MUTATED IFT46 WILD-TYPE 
          71.74           90.12 
  IFT46 MUTATED IFT46 WILD-TYPE 
          14.14           15.27 
[1] "0.2 - 71.7 (14.1)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.2"
D11V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IFT46 MUTATED         0        0        3         3         5         1
  IFT46 WILD-TYPE       1        3        9        16        77         3
                 vv
clus              STAGE IV
  IFT46 MUTATED          1
  IFT46 WILD-TYPE        2
D11V3, multiclass
           clus
vv          IFT46 MUTATED IFT46 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              3               9
  STAGE IIA             3              16
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  IFT46 MUTATED    0  3    10
  IFT46 WILD-TYPE  5 14    92
D11V4, multiclass
       clus
vv      IFT46 MUTATED IFT46 WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                 cls
clus               0  1
  IFT46 MUTATED    6  7
  IFT46 WILD-TYPE 29 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      6    7
  IFT46 WILD-TYPE   29   82
   clus
vv  IFT46 MUTATED IFT46 WILD-TYPE
  0             6              29
  1             7              82
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus               0  1
  IFT46 MUTATED    5  1
  IFT46 WILD-TYPE 52  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      5    1
  IFT46 WILD-TYPE   52    2
   clus
vv  IFT46 MUTATED IFT46 WILD-TYPE
  0             5              52
  1             1               2
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus               0  1
  IFT46 MUTATED    4  9
  IFT46 WILD-TYPE 47 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      4    9
  IFT46 WILD-TYPE   47   66
        clus
vv       IFT46 MUTATED IFT46 WILD-TYPE
  FEMALE             4              47
  MALE               9              66
[1] 2 2
[1] FALSE
D11V8, binary
                 cls
clus               0  1
  IFT46 MUTATED   10  1
  IFT46 WILD-TYPE 78 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED     10    1
  IFT46 WILD-TYPE   78   29
     clus
vv    IFT46 MUTATED IFT46 WILD-TYPE
  NO             10              78
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IFT46 MUTATED                                    10
  IFT46 WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IFT46 MUTATED                                       2
  IFT46 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IFT46 MUTATED                                                  0
  IFT46 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  IFT46 MUTATED                                     0
  IFT46 WILD-TYPE                                   1
D11V9, multiclass
                                                  clus
vv                                                 IFT46 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 IFT46 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
[1] "Remove cluster labels:" "IFT46 MUTATED"         
clus
  IFT46 MUTATED IFT46 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-IB-7885      TCGA-IB-8126 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  IFT46 MUTATED    7  4  0  0
  IFT46 WILD-TYPE 73 31  4  2
D11V12, multiclass
    clus
vv   IFT46 MUTATED IFT46 WILD-TYPE
  R0             7              73
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFT46 MUTATED       0                         0    13
  IFT46 WILD-TYPE     6                         5   101
D11V14, multiclass
                           clus
vv                          IFT46 MUTATED IFT46 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                13             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                 cls
clus               0  1
  IFT46 MUTATED    1  9
  IFT46 WILD-TYPE  4 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      1    9
  IFT46 WILD-TYPE    4   82
                        clus
vv                       IFT46 MUTATED IFT46 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(12) Variable = ARHGAP18 MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                 0  1
  ARHGAP18 MUTATED    7  5
  ARHGAP18 WILD-TYPE 56 57
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                12                113 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 5                 57 
$`ARHGAP18 MUTATED`
TCGA-LB-A7SX TCGA-3A-A9IR TCGA-3A-A9J0 TCGA-F2-7273 TCGA-HV-A7OL TCGA-HV-AA8V 
       12.92        50.70        24.43        19.46         8.28        30.25 
TCGA-IB-8126 TCGA-IB-A5ST TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-LB-A9Q5 TCGA-YB-A89D 
       15.19        20.88         7.86         6.02        10.29        11.51 

$`ARHGAP18 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN 
       34.09        10.13        75.12        71.74         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG 
       41.33        12.00        15.85         7.20        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUR 
        8.22        15.88         0.26         4.73        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
              6.02               0.23 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             50.70              90.12 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
            14.055             15.320 
[1] "6.0 - 50.7 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D12V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ARHGAP18 MUTATED         0        0        1         1         9         1
  ARHGAP18 WILD-TYPE       1        3       11        18        73         3
                    vv
clus                 STAGE IV
  ARHGAP18 MUTATED          0
  ARHGAP18 WILD-TYPE        3
D12V3, multiclass
           clus
vv          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                9                 73
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  ARHGAP18 MUTATED    0  1    11
  ARHGAP18 WILD-TYPE  5 16    91
D12V4, multiclass
       clus
vv      ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4               11                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    2 10
  ARHGAP18 WILD-TYPE 33 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      2   10
  ARHGAP18 WILD-TYPE   33   79
   clus
vv  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  0                2                 33
  1               10                 79
[1] 2 2
[1] FALSE
D12V6, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    5  0
  ARHGAP18 WILD-TYPE 52  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      5    0
  ARHGAP18 WILD-TYPE   52    3
   clus
vv  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  0                5                 52
  1                0                  3
[1] 2 2
[1] FALSE
D12V7, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    6  6
  ARHGAP18 WILD-TYPE 45 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      6    6
  ARHGAP18 WILD-TYPE   45   69
        clus
vv       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  FEMALE                6                 45
  MALE                  6                 69
[1] 2 2
[1] FALSE
D12V8, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    9  3
  ARHGAP18 WILD-TYPE 79 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      9    3
  ARHGAP18 WILD-TYPE   79   27
     clus
vv    ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  NO                 9                 79
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARHGAP18 MUTATED                                    11
  ARHGAP18 WILD-TYPE                                  94
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARHGAP18 MUTATED                                       1
  ARHGAP18 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARHGAP18 MUTATED                                                  0
  ARHGAP18 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  ARHGAP18 MUTATED                                     0
  ARHGAP18 WILD-TYPE                                   1
D12V9, multiclass
                                                  clus
vv                                                 ARHGAP18 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 ARHGAP18 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
                    vv
clus                 R0 R1 R2 RX
  ARHGAP18 MUTATED    5  5  2  0
  ARHGAP18 WILD-TYPE 75 30  2  2
D12V12, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  R0                5                 75
  R1                5                 30
  R2                2                  2
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP18 MUTATED       2                         2     8
  ARHGAP18 WILD-TYPE     4                         3   106
D12V14, multiclass
                           clus
vv                          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                2                  3
  WHITE                                    8                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    0 10
  ARHGAP18 WILD-TYPE  5 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      0   10
  ARHGAP18 WILD-TYPE    5   81
                        clus
vv                       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               10                 81
[1] 2 2
[1] FALSE

Clustering(13) Variable = EME2 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2             0  1
  EME2 MUTATED    7  4
  EME2 WILD-TYPE 56 58
  EME2 MUTATED EME2 WILD-TYPE 
            11            114 
  EME2 MUTATED EME2 WILD-TYPE 
             4             58 
$`EME2 MUTATED`
TCGA-2J-AABE TCGA-3A-A9I9 TCGA-FB-AAQ1 TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-7885 
       22.22        20.84         4.04         8.28        19.82        41.33 
TCGA-IB-A5SO TCGA-IB-A7M4 TCGA-IB-AAUR TCGA-IB-AAUU TCGA-YB-A89D 
       12.00        15.88        11.11         8.05        11.51 

$`EME2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       36.69        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        6.02         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  EME2 MUTATED EME2 WILD-TYPE 
          4.04           0.23 
  EME2 MUTATED EME2 WILD-TYPE 
         41.33          90.12 
  EME2 MUTATED EME2 WILD-TYPE 
         12.00          15.27 
[1] "4.0 - 41.3 (12.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D13V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EME2 MUTATED         0        0        0         3         8         0
  EME2 WILD-TYPE       1        3       12        16        74         4
                vv
clus             STAGE IV
  EME2 MUTATED          0
  EME2 WILD-TYPE        3
D13V3, multiclass
           clus
vv          EME2 MUTATED EME2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            3             16
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  EME2 MUTATED    0  0    11
  EME2 WILD-TYPE  5 17    91
D13V4, multiclass
       clus
vv      EME2 MUTATED EME2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4           11             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                cls
clus              0  1
  EME2 MUTATED    3  8
  EME2 WILD-TYPE 32 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      3    8
  EME2 WILD-TYPE   32   81
   clus
vv  EME2 MUTATED EME2 WILD-TYPE
  0            3             32
  1            8             81
[1] 2 2
[1] FALSE
D13V6, binary
                cls
clus              0  1
  EME2 MUTATED    6  0
  EME2 WILD-TYPE 51  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      6    0
  EME2 WILD-TYPE   51    3
   clus
vv  EME2 MUTATED EME2 WILD-TYPE
  0            6             51
  1            0              3
[1] 2 2
[1] FALSE
D13V7, binary
                cls
clus              0  1
  EME2 MUTATED    2  9
  EME2 WILD-TYPE 49 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      2    9
  EME2 WILD-TYPE   49   66
        clus
vv       EME2 MUTATED EME2 WILD-TYPE
  FEMALE            2             49
  MALE              9             66
[1] 2 2
[1] FALSE
D13V8, binary
                cls
clus              0  1
  EME2 MUTATED    8  3
  EME2 WILD-TYPE 80 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      8    3
  EME2 WILD-TYPE   80   27
     clus
vv    EME2 MUTATED EME2 WILD-TYPE
  NO             8             80
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EME2 MUTATED                                    11
  EME2 WILD-TYPE                                  94
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EME2 MUTATED                                       0
  EME2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EME2 MUTATED                                                  0
  EME2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EME2 MUTATED                                     0
  EME2 WILD-TYPE                                   1
D13V9, multiclass
                                                  clus
vv                                                 EME2 MUTATED EME2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        11             94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
                vv
clus             R0 R1 R2 RX
  EME2 MUTATED    8  2  1  0
  EME2 WILD-TYPE 72 33  3  2
D13V12, multiclass
    clus
vv   EME2 MUTATED EME2 WILD-TYPE
  R0            8             72
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EME2 MUTATED       1                         0    10
  EME2 WILD-TYPE     5                         5   104
D13V14, multiclass
                           clus
vv                          EME2 MUTATED EME2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               10            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                cls
clus              0  1
  EME2 MUTATED    0  8
  EME2 WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      0    8
  EME2 WILD-TYPE    5   83
                        clus
vv                       EME2 MUTATED EME2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(14) Variable = SMAD4 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED   12 14
  SMAD4 WILD-TYPE 51 48
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26              99 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             14              48 
$`SMAD4 MUTATED`
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABA 
        8.02         1.08        15.12        23.97         2.63        19.96 
TCGA-2J-AABE TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3E-AAAZ TCGA-FB-A78T TCGA-FB-AAPQ 
       22.22        33.57        34.09        71.74        12.33        37.15 
TCGA-FB-AAQ3 TCGA-FZ-5923 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A8P1 
        1.02        20.35        30.25        17.49        20.19         0.23 
TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUR TCGA-LB-A9Q5 
       19.82        15.85         0.26         4.73        11.11        10.29 
TCGA-US-A77G TCGA-YB-A89D 
        0.39        11.51 

$`SMAD4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78        12.92        17.26        14.14        16.37         2.17 
TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
        9.63        20.61        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        75.12        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       16.37        15.95         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03        24.36         2.01         5.10        36.20 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-8637 
       17.79        22.06         8.28        32.15        31.86        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13         5.26        10.85        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS 
        8.22        15.88         7.86        14.17         6.02         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.23            0.30 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          71.74           90.12 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         15.485          15.220 
[1] "0.2 - 71.7 (15.5)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.2"
D14V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMAD4 MUTATED         0        3        2         3        17         0
  SMAD4 WILD-TYPE       1        0       10        16        65         4
                 vv
clus              STAGE IV
  SMAD4 MUTATED          1
  SMAD4 WILD-TYPE        2
D14V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              3               0
  STAGE IB              2              10
  STAGE IIA             3              16
  STAGE IIB            17              65
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SMAD4 MUTATED    3  5    18
  SMAD4 WILD-TYPE  2 12    84
D14V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                3               2
  T2                5              12
  T3+T4            18              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                 cls
clus               0  1
  SMAD4 MUTATED    8 18
  SMAD4 WILD-TYPE 27 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      8   18
  SMAD4 WILD-TYPE   27   71
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             8              27
  1            18              71
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus               0  1
  SMAD4 MUTATED   11  1
  SMAD4 WILD-TYPE 46  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     11    1
  SMAD4 WILD-TYPE   46    2
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            11              46
  1             1               2
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED    9 17
  SMAD4 WILD-TYPE 42 58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      9   17
  SMAD4 WILD-TYPE   42   58
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             9              42
  MALE              17              58
[1] 2 2
[1] FALSE
D14V8, binary
                 cls
clus               0  1
  SMAD4 MUTATED   18  4
  SMAD4 WILD-TYPE 70 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     18    4
  SMAD4 WILD-TYPE   70   26
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO             18              70
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMAD4 MUTATED                                    24
  SMAD4 WILD-TYPE                                  81
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMAD4 MUTATED                                       2
  SMAD4 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMAD4 MUTATED                                                  0
  SMAD4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMAD4 MUTATED                                     0
  SMAD4 WILD-TYPE                                   1
D14V9, multiclass
                                                  clus
vv                                                 SMAD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SMAD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           81
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
                 vv
clus              R0 R1 R2 RX
  SMAD4 MUTATED   18  5  2  0
  SMAD4 WILD-TYPE 62 30  2  2
D14V12, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            18              62
  R1             5              30
  R2             2               2
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       2                         0    24
  SMAD4 WILD-TYPE     4                         5    90
D14V14, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                24              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1 18
  SMAD4 WILD-TYPE  4 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1   18
  SMAD4 WILD-TYPE    4   73
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            18              73
[1] 2 2
[1] FALSE

Clustering(15) Variable = NPNT MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  NPNT MUTATED    7  5
  NPNT WILD-TYPE 56 57
  NPNT MUTATED NPNT WILD-TYPE 
            12            113 
  NPNT MUTATED NPNT WILD-TYPE 
             5             57 
$`NPNT MUTATED`
TCGA-2J-AABR TCGA-F2-A44G TCGA-LB-A7SX TCGA-3A-A9IH TCGA-3A-A9IV TCGA-FB-AAPS 
       14.40         7.66        12.92        33.57        36.26         7.50 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-A5SQ TCGA-IB-AAUV TCGA-Q3-A5QY TCGA-US-A77G 
        5.26         0.23         7.20        13.28        13.68         0.39 

$`NPNT WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       10.49        58.98        60.95        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
        1.08        15.12        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO 
       45.47        43.50        20.84         7.36        24.26        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.33        15.95        37.15        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  NPNT MUTATED NPNT WILD-TYPE 
          0.23           0.26 
  NPNT MUTATED NPNT WILD-TYPE 
         36.26          90.12 
  NPNT MUTATED NPNT WILD-TYPE 
         10.29          15.78 
[1] "0.2 - 36.3 (10.3)" "0.3 - 90.1 (15.8)"
[1] "hr=" "1.3"
D15V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NPNT MUTATED         0        1        3         1         7         0
  NPNT WILD-TYPE       1        2        9        18        75         4
                vv
clus             STAGE IV
  NPNT MUTATED          0
  NPNT WILD-TYPE        3
D15V3, multiclass
           clus
vv          NPNT MUTATED NPNT WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             3              9
  STAGE IIA            1             18
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NPNT MUTATED    1  5     6
  NPNT WILD-TYPE  4 12    96
D15V4, multiclass
       clus
vv      NPNT MUTATED NPNT WILD-TYPE
  T1               1              4
  T2               5             12
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                cls
clus              0  1
  NPNT MUTATED    5  7
  NPNT WILD-TYPE 30 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      5    7
  NPNT WILD-TYPE   30   82
   clus
vv  NPNT MUTATED NPNT WILD-TYPE
  0            5             30
  1            7             82
[1] 2 2
[1] FALSE
D15V6, binary
                cls
clus              0  1
  NPNT MUTATED    4  0
  NPNT WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      4    0
  NPNT WILD-TYPE   53    3
   clus
vv  NPNT MUTATED NPNT WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D15V7, binary
                cls
clus              0  1
  NPNT MUTATED    8  4
  NPNT WILD-TYPE 43 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      8    4
  NPNT WILD-TYPE   43   71
        clus
vv       NPNT MUTATED NPNT WILD-TYPE
  FEMALE            8             43
  MALE              4             71
[1] 2 2
[1] FALSE
D15V8, binary
                cls
clus              0  1
  NPNT MUTATED    9  2
  NPNT WILD-TYPE 79 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      9    2
  NPNT WILD-TYPE   79   28
     clus
vv    NPNT MUTATED NPNT WILD-TYPE
  NO             9             79
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NPNT MUTATED                                    11
  NPNT WILD-TYPE                                  94
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NPNT MUTATED                                       1
  NPNT WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NPNT MUTATED                                                  0
  NPNT WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NPNT MUTATED                                     0
  NPNT WILD-TYPE                                   1
D15V9, multiclass
                                                  clus
vv                                                 NPNT MUTATED NPNT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        11             94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
                vv
clus             R0 R1 R2 RX
  NPNT MUTATED   10  2  0  0
  NPNT WILD-TYPE 70 33  4  2
D15V12, multiclass
    clus
vv   NPNT MUTATED NPNT WILD-TYPE
  R0           10             70
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPNT MUTATED       0                         1    11
  NPNT WILD-TYPE     6                         4   103
D15V14, multiclass
                           clus
vv                          NPNT MUTATED NPNT WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               11            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                cls
clus              0  1
  NPNT MUTATED    0 11
  NPNT WILD-TYPE  5 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      0   11
  NPNT WILD-TYPE    5   80
                        clus
vv                       NPNT MUTATED NPNT WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           11             80
[1] 2 2
[1] FALSE

Clustering(16) Variable = TNFSF9 MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  TNFSF9 MUTATED    7  5
  TNFSF9 WILD-TYPE 56 57
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
              12              113 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               5               57 
$`TNFSF9 MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQE TCGA-F2-7273 TCGA-HV-A7OL TCGA-HZ-7925 TCGA-IB-7651 
       12.92        22.49        19.46         8.28        20.19        19.82 
TCGA-IB-AAUP TCGA-LB-A8F3 TCGA-RB-AA9M TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       14.17        12.46         9.40        31.27        23.67        12.76 

$`TNFSF9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 
       22.06        32.15        30.25        17.49        31.86        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        10.29         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        11.51        66.28        15.35 

  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
            8.28             0.23 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
           31.27            90.12 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
          16.815           15.220 
[1] "8.3 - 31.3 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D16V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TNFSF9 MUTATED         0        0        2         2         7         1
  TNFSF9 WILD-TYPE       1        3       10        17        75         3
                  vv
clus               STAGE IV
  TNFSF9 MUTATED          0
  TNFSF9 WILD-TYPE        3
D16V3, multiclass
           clus
vv          TNFSF9 MUTATED TNFSF9 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              2               17
  STAGE IIB              7               75
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TNFSF9 MUTATED    1  2     9
  TNFSF9 WILD-TYPE  4 15    93
D16V4, multiclass
       clus
vv      TNFSF9 MUTATED TNFSF9 WILD-TYPE
  T1                 1                4
  T2                 2               15
  T3+T4              9               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    4  8
  TNFSF9 WILD-TYPE 31 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      4    8
  TNFSF9 WILD-TYPE   31   81
   clus
vv  TNFSF9 MUTATED TNFSF9 WILD-TYPE
  0              4               31
  1              8               81
[1] 2 2
[1] FALSE
D16V6, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    6  0
  TNFSF9 WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      6    0
  TNFSF9 WILD-TYPE   51    3
   clus
vv  TNFSF9 MUTATED TNFSF9 WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D16V7, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    5  7
  TNFSF9 WILD-TYPE 46 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      5    7
  TNFSF9 WILD-TYPE   46   68
        clus
vv       TNFSF9 MUTATED TNFSF9 WILD-TYPE
  FEMALE              5               46
  MALE                7               68
[1] 2 2
[1] FALSE
D16V8, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    6  6
  TNFSF9 WILD-TYPE 82 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      6    6
  TNFSF9 WILD-TYPE   82   24
     clus
vv    TNFSF9 MUTATED TNFSF9 WILD-TYPE
  NO               6               82
  YES              6               24
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNFSF9 MUTATED                                    10
  TNFSF9 WILD-TYPE                                  95
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNFSF9 MUTATED                                       1
  TNFSF9 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNFSF9 MUTATED                                                  0
  TNFSF9 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TNFSF9 MUTATED                                     0
  TNFSF9 WILD-TYPE                                   1
D16V9, multiclass
                                                  clus
vv                                                 TNFSF9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TNFSF9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
                  vv
clus               R0 R1 R2 RX
  TNFSF9 MUTATED    5  5  1  0
  TNFSF9 WILD-TYPE 75 30  3  2
D16V12, multiclass
    clus
vv   TNFSF9 MUTATED TNFSF9 WILD-TYPE
  R0              5               75
  R1              5               30
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNFSF9 MUTATED       1                         3     8
  TNFSF9 WILD-TYPE     5                         2   106
D16V14, multiclass
                           clus
vv                          TNFSF9 MUTATED TNFSF9 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              3                2
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    2  8
  TNFSF9 WILD-TYPE  3 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      2    8
  TNFSF9 WILD-TYPE    3   83
                        clus
vv                       TNFSF9 MUTATED TNFSF9 WILD-TYPE
  HISPANIC OR LATINO                  2                3
  NOT HISPANIC OR LATINO              8               83
[1] 2 2
[1] FALSE

Clustering(17) Variable = SRP14 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2              0  1
  SRP14 MUTATED    5  4
  SRP14 WILD-TYPE 58 58
  SRP14 MUTATED SRP14 WILD-TYPE 
              9             116 
  SRP14 MUTATED SRP14 WILD-TYPE 
              4              58 
$`SRP14 MUTATED`
TCGA-2J-AABK TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-A6UG TCGA-IB-AAUQ 
       15.91        22.06        20.19        10.85         1.35         6.02 
TCGA-IB-AAUU TCGA-US-A776 TCGA-US-A77J 
        8.05        39.98        18.67 

$`SRP14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        4.73         7.86        14.17        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
       15.32         9.40         0.30        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SRP14 MUTATED SRP14 WILD-TYPE 
           1.35            0.23 
  SRP14 MUTATED SRP14 WILD-TYPE 
          39.98           90.12 
  SRP14 MUTATED SRP14 WILD-TYPE 
         15.910          15.205 
[1] "1.4 - 40.0 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D17V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SRP14 MUTATED         0        0        0         2         7         0
  SRP14 WILD-TYPE       1        3       12        17        75         4
                 vv
clus              STAGE IV
  SRP14 MUTATED          0
  SRP14 WILD-TYPE        3
D17V3, multiclass
           clus
vv          SRP14 MUTATED SRP14 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SRP14 MUTATED    0  0     9
  SRP14 WILD-TYPE  5 17    93
D17V4, multiclass
       clus
vv      SRP14 MUTATED SRP14 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                 cls
clus               0  1
  SRP14 MUTATED    2  7
  SRP14 WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      2    7
  SRP14 WILD-TYPE   33   82
   clus
vv  SRP14 MUTATED SRP14 WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D17V6, binary
                 cls
clus               0  1
  SRP14 MUTATED    4  0
  SRP14 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      4    0
  SRP14 WILD-TYPE   53    3
   clus
vv  SRP14 MUTATED SRP14 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus               0  1
  SRP14 MUTATED    1  8
  SRP14 WILD-TYPE 50 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      1    8
  SRP14 WILD-TYPE   50   67
        clus
vv       SRP14 MUTATED SRP14 WILD-TYPE
  FEMALE             1              50
  MALE               8              67
[1] 2 2
[1] FALSE
D17V8, binary
                 cls
clus               0  1
  SRP14 MUTATED    7  1
  SRP14 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      7    1
  SRP14 WILD-TYPE   81   29
     clus
vv    SRP14 MUTATED SRP14 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SRP14 MUTATED                                     6
  SRP14 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SRP14 MUTATED                                       2
  SRP14 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SRP14 MUTATED                                                  1
  SRP14 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SRP14 MUTATED                                     0
  SRP14 WILD-TYPE                                   1
D17V9, multiclass
                                                  clus
vv                                                 SRP14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SRP14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
                 vv
clus              R0 R1 R2 RX
  SRP14 MUTATED    6  3  0  0
  SRP14 WILD-TYPE 74 32  4  2
D17V12, multiclass
    clus
vv   SRP14 MUTATED SRP14 WILD-TYPE
  R0             6              74
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRP14 MUTATED       0                         0     9
  SRP14 WILD-TYPE     6                         5   105
D17V14, multiclass
                           clus
vv                          SRP14 MUTATED SRP14 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                 cls
clus               0  1
  SRP14 MUTATED    0  8
  SRP14 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      0    8
  SRP14 WILD-TYPE    5   83
                        clus
vv                       SRP14 MUTATED SRP14 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(18) Variable = SORBS2 MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2               0  1
  SORBS2 MUTATED    6 10
  SORBS2 WILD-TYPE 57 52
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              16              109 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
              10               52 
$`SORBS2 MUTATED`
TCGA-2L-AAQI TCGA-3A-A9IC TCGA-3A-A9IU TCGA-F2-A8YN TCGA-FB-AAPQ TCGA-FB-AAPU 
        3.39        24.26        15.06        17.00        37.15        12.53 
TCGA-FZ-5919 TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SQ TCGA-IB-A6UF 
       24.36        30.25        19.82        41.33         7.20        21.90 
TCGA-LB-A9Q5 TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-YB-A89D 
       10.29        15.32         0.30        11.51 

$`SORBS2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 
       16.37        12.33        15.95         7.50        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03         1.02         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        32.15        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46         8.78        13.68         3.12 
TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
            0.30             0.23 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           41.33            90.12 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           16.16            15.19 
[1] "0.3 - 41.3 (16.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D18V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SORBS2 MUTATED         0        0        2         2        13         0
  SORBS2 WILD-TYPE       1        3       10        17        69         4
                  vv
clus               STAGE IV
  SORBS2 MUTATED          0
  SORBS2 WILD-TYPE        3
D18V3, multiclass
           clus
vv          SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              2               17
  STAGE IIB             13               69
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SORBS2 MUTATED    0  2    15
  SORBS2 WILD-TYPE  5 15    87
D18V4, multiclass
       clus
vv      SORBS2 MUTATED SORBS2 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4             15               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                  cls
clus                0  1
  SORBS2 MUTATED    4 13
  SORBS2 WILD-TYPE 31 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      4   13
  SORBS2 WILD-TYPE   31   76
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              4               31
  1             13               76
[1] 2 2
[1] FALSE
D18V6, binary
                  cls
clus                0  1
  SORBS2 MUTATED    6  0
  SORBS2 WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      6    0
  SORBS2 WILD-TYPE   51    3
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                0  1
  SORBS2 MUTATED    9  8
  SORBS2 WILD-TYPE 42 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      9    8
  SORBS2 WILD-TYPE   42   67
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE              9               42
  MALE                8               67
[1] 2 2
[1] FALSE
D18V8, binary
                  cls
clus                0  1
  SORBS2 MUTATED   13  3
  SORBS2 WILD-TYPE 75 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED     13    3
  SORBS2 WILD-TYPE   75   27
     clus
vv    SORBS2 MUTATED SORBS2 WILD-TYPE
  NO              13               75
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORBS2 MUTATED                                    16
  SORBS2 WILD-TYPE                                  89
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORBS2 MUTATED                                       1
  SORBS2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORBS2 MUTATED                                                  0
  SORBS2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SORBS2 MUTATED                                     0
  SORBS2 WILD-TYPE                                   1
D18V9, multiclass
                                                  clus
vv                                                 SORBS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SORBS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            89
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
                  vv
clus               R0 R1 R2 RX
  SORBS2 MUTATED   11  4  1  0
  SORBS2 WILD-TYPE 69 31  3  2
D18V12, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  R0             11               69
  R1              4               31
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORBS2 MUTATED       2                         0    15
  SORBS2 WILD-TYPE     4                         5    99
D18V14, multiclass
                           clus
vv                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 15               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                  cls
clus                0  1
  SORBS2 MUTATED    0 15
  SORBS2 WILD-TYPE  5 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      0   15
  SORBS2 WILD-TYPE    5   76
                        clus
vv                       SORBS2 MUTATED SORBS2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             15               76
[1] 2 2
[1] FALSE

Clustering(19) Variable = ERF MUTATION ANALYSIS
D19V1, survival
               sevent
clus2            0  1
  ERF MUTATED    5  8
  ERF WILD-TYPE 58 54
  ERF MUTATED ERF WILD-TYPE 
           13           112 
  ERF MUTATED ERF WILD-TYPE 
            8            54 
$`ERF MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-F2-7273 
        9.63        15.22         9.11        12.95        43.50        19.46 
TCGA-FB-A5VM TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A6UF TCGA-IB-AAUN 
       16.37         8.28        19.82        15.19        21.90         4.73 
TCGA-OE-A75W 
        8.78 

$`ERF WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49         3.39         9.60        45.47 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       75.12        71.74         3.12        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ERF MUTATED ERF WILD-TYPE 
         4.73          0.23 
  ERF MUTATED ERF WILD-TYPE 
        43.50         90.12 
  ERF MUTATED ERF WILD-TYPE 
       15.190        15.335 
[1] "4.7 - 43.5 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D19V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ERF MUTATED         0        0        2         3         6         2
  ERF WILD-TYPE       1        3       10        16        76         2
               vv
clus            STAGE IV
  ERF MUTATED          0
  ERF WILD-TYPE        3
D19V3, multiclass
           clus
vv          ERF MUTATED ERF WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            2            10
  STAGE IIA           3            16
  STAGE IIB           6            76
  STAGE III           2             2
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  ERF MUTATED    0  2    11
  ERF WILD-TYPE  5 15    91
D19V4, multiclass
       clus
vv      ERF MUTATED ERF WILD-TYPE
  T1              0             5
  T2              2            15
  T3+T4          11            91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
               cls
clus             0  1
  ERF MUTATED    6  7
  ERF WILD-TYPE 29 82
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      6    7
  ERF WILD-TYPE   29   82
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0           6            29
  1           7            82
[1] 2 2
[1] FALSE
D19V6, binary
               cls
clus             0  1
  ERF MUTATED   10  0
  ERF WILD-TYPE 47  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     10    0
  ERF WILD-TYPE   47    3
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0          10            47
  1           0             3
[1] 2 2
[1] FALSE
D19V7, binary
               cls
clus             0  1
  ERF MUTATED    5  8
  ERF WILD-TYPE 46 67
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      5    8
  ERF WILD-TYPE   46   67
        clus
vv       ERF MUTATED ERF WILD-TYPE
  FEMALE           5            46
  MALE             8            67
[1] 2 2
[1] FALSE
D19V8, binary
               cls
clus             0  1
  ERF MUTATED   10  3
  ERF WILD-TYPE 78 27
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED     10    3
  ERF WILD-TYPE   78   27
     clus
vv    ERF MUTATED ERF WILD-TYPE
  NO           10            78
  YES           3            27
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ERF MUTATED                                    12
  ERF WILD-TYPE                                  93
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ERF MUTATED                                       0
  ERF WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ERF MUTATED                                                  0
  ERF WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  ERF MUTATED                                     1
  ERF WILD-TYPE                                   0
D19V9, multiclass
                                                  clus
vv                                                 ERF MUTATED ERF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       12            93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        1             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
               vv
clus            R0 R1 R2 RX
  ERF MUTATED    7  5  1  0
  ERF WILD-TYPE 73 30  3  2
D19V12, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  R0           7            73
  R1           5            30
  R2           1             3
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERF MUTATED       1                         2    10
  ERF WILD-TYPE     5                         3   104
D19V14, multiclass
                           clus
vv                          ERF MUTATED ERF WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           2             3
  WHITE                              10           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
               cls
clus             0  1
  ERF MUTATED    0  8
  ERF WILD-TYPE  5 83
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      0    8
  ERF WILD-TYPE    5   83
                        clus
vv                       ERF MUTATED ERF WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           8            83
[1] 2 2
[1] FALSE

Clustering(20) Variable = MED9 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  MED9 MUTATED    3  4
  MED9 WILD-TYPE 60 58
  MED9 MUTATED MED9 WILD-TYPE 
             7            118 
  MED9 MUTATED MED9 WILD-TYPE 
             4             58 
$`MED9 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABE TCGA-3A-A9IX TCGA-3E-AAAY TCGA-HZ-8637 TCGA-IB-7651 
        2.17        22.22        34.09        75.12        17.00        19.82 
TCGA-IB-A5SQ 
        7.20 

$`MED9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MED9 MUTATED MED9 WILD-TYPE 
          2.17           0.23 
  MED9 MUTATED MED9 WILD-TYPE 
         75.12          90.12 
  MED9 MUTATED MED9 WILD-TYPE 
        19.820         15.155 
[1] "2.2 - 75.1 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D20V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MED9 MUTATED         0        1        1         1         4         0
  MED9 WILD-TYPE       1        2       11        18        78         4
                vv
clus             STAGE IV
  MED9 MUTATED          0
  MED9 WILD-TYPE        3
D20V3, multiclass
           clus
vv          MED9 MUTATED MED9 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  MED9 MUTATED    1  1     5
  MED9 WILD-TYPE  4 16    97
D20V4, multiclass
       clus
vv      MED9 MUTATED MED9 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                cls
clus              0  1
  MED9 MUTATED    3  4
  MED9 WILD-TYPE 32 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      3    4
  MED9 WILD-TYPE   32   85
   clus
vv  MED9 MUTATED MED9 WILD-TYPE
  0            3             32
  1            4             85
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus              0  1
  MED9 MUTATED    4  0
  MED9 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      4    0
  MED9 WILD-TYPE   53    3
   clus
vv  MED9 MUTATED MED9 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus              0  1
  MED9 MUTATED    3  4
  MED9 WILD-TYPE 48 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      3    4
  MED9 WILD-TYPE   48   71
        clus
vv       MED9 MUTATED MED9 WILD-TYPE
  FEMALE            3             48
  MALE              4             71
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus              0  1
  MED9 MUTATED    4  3
  MED9 WILD-TYPE 84 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      4    3
  MED9 WILD-TYPE   84   27
     clus
vv    MED9 MUTATED MED9 WILD-TYPE
  NO             4             84
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED9 MUTATED                                     6
  MED9 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED9 MUTATED                                       1
  MED9 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED9 MUTATED                                                  0
  MED9 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MED9 MUTATED                                     0
  MED9 WILD-TYPE                                   1
D20V9, multiclass
                                                  clus
vv                                                 MED9 MUTATED MED9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
D20V11, continuous
                vv
clus             R0 R1 R2 RX
  MED9 MUTATED    6  0  0  0
  MED9 WILD-TYPE 74 35  4  2
D20V12, multiclass
    clus
vv   MED9 MUTATED MED9 WILD-TYPE
  R0            6             74
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED9 MUTATED       0                         0     7
  MED9 WILD-TYPE     6                         5   107
D20V14, multiclass
                           clus
vv                          MED9 MUTATED MED9 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
                cls
clus              0  1
  MED9 MUTATED    1  4
  MED9 WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      1    4
  MED9 WILD-TYPE    4   87
                        clus
vv                       MED9 MUTATED MED9 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(21) Variable = BHLHB9 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  BHLHB9 MUTATED    8  4
  BHLHB9 WILD-TYPE 55 58
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
              12              113 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
               4               58 
$`BHLHB9 MUTATED`
TCGA-3A-A9IJ TCGA-F2-A44G TCGA-2J-AAB1 TCGA-2J-AABE TCGA-2J-AABP TCGA-3A-A9IO 
       60.95         7.66         2.17        22.22        15.22        63.85 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-HV-A7OP TCGA-HV-AA8X TCGA-RB-AA9M TCGA-XN-A8T3 
       15.06        36.26        32.15        17.49         9.40        31.27 

$`BHLHB9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        58.98        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        19.96        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       42.31        15.91        14.47         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
       22.49         3.39        12.95         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS 
       20.84         7.36        24.26        33.57        50.70        32.81 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        22.06         8.28        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
            2.17             0.23 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
           63.85            90.12 
  BHLHB9 MUTATED BHLHB9 WILD-TYPE 
          19.855           15.120 
[1] "2.2 - 63.9 (19.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2"  
D21V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BHLHB9 MUTATED         0        0        3         1         7         0
  BHLHB9 WILD-TYPE       1        3        9        18        75         4
                  vv
clus               STAGE IV
  BHLHB9 MUTATED          0
  BHLHB9 WILD-TYPE        3
D21V3, multiclass
           clus
vv          BHLHB9 MUTATED BHLHB9 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               3                9
  STAGE IIA              1               18
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  BHLHB9 MUTATED    1  4     6
  BHLHB9 WILD-TYPE  4 13    96
D21V4, multiclass
       clus
vv      BHLHB9 MUTATED BHLHB9 WILD-TYPE
  T1                 1                4
  T2                 4               13
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                  cls
clus                0  1
  BHLHB9 MUTATED    4  7
  BHLHB9 WILD-TYPE 31 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      4    7
  BHLHB9 WILD-TYPE   31   82
   clus
vv  BHLHB9 MUTATED BHLHB9 WILD-TYPE
  0              4               31
  1              7               82
[1] 2 2
[1] FALSE
D21V6, binary
                  cls
clus                0  1
  BHLHB9 MUTATED    6  0
  BHLHB9 WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      6    0
  BHLHB9 WILD-TYPE   51    3
   clus
vv  BHLHB9 MUTATED BHLHB9 WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                0  1
  BHLHB9 MUTATED    4  8
  BHLHB9 WILD-TYPE 47 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      4    8
  BHLHB9 WILD-TYPE   47   67
        clus
vv       BHLHB9 MUTATED BHLHB9 WILD-TYPE
  FEMALE              4               47
  MALE                8               67
[1] 2 2
[1] FALSE
D21V8, binary
                  cls
clus                0  1
  BHLHB9 MUTATED    7  5
  BHLHB9 WILD-TYPE 81 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      7    5
  BHLHB9 WILD-TYPE   81   25
     clus
vv    BHLHB9 MUTATED BHLHB9 WILD-TYPE
  NO               7               81
  YES              5               25
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BHLHB9 MUTATED                                     6
  BHLHB9 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BHLHB9 MUTATED                                       5
  BHLHB9 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BHLHB9 MUTATED                                                  0
  BHLHB9 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  BHLHB9 MUTATED                                     1
  BHLHB9 WILD-TYPE                                   0
D21V9, multiclass
                                                  clus
vv                                                 BHLHB9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 BHLHB9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
                  vv
clus               R0 R1 R2 RX
  BHLHB9 MUTATED    9  2  1  0
  BHLHB9 WILD-TYPE 71 33  3  2
D21V12, multiclass
    clus
vv   BHLHB9 MUTATED BHLHB9 WILD-TYPE
  R0              9               71
  R1              2               33
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BHLHB9 MUTATED       2                         0    10
  BHLHB9 WILD-TYPE     4                         5   104
D21V14, multiclass
                           clus
vv                          BHLHB9 MUTATED BHLHB9 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                  cls
clus                0  1
  BHLHB9 MUTATED    1  6
  BHLHB9 WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BHLHB9 MUTATED      1    6
  BHLHB9 WILD-TYPE    4   85
                        clus
vv                       BHLHB9 MUTATED BHLHB9 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(22) Variable = ZNF185 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2               0  1
  ZNF185 MUTATED    5  5
  ZNF185 WILD-TYPE 58 57
  ZNF185 MUTATED ZNF185 WILD-TYPE 
              10              115 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               5               57 
$`ZNF185 MUTATED`
TCGA-2J-AABR TCGA-2J-AAB9 TCGA-2L-AAQJ TCGA-3A-A9I9 TCGA-F2-A8YN TCGA-FB-AAQ3 
       14.40        20.61        12.95        20.84        17.00         1.02 
TCGA-HZ-A9TJ TCGA-IB-A6UG TCGA-IB-AAUU TCGA-US-A776 
       19.82         1.35         8.05        39.98 

$`ZNF185 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM 
       24.43        75.12        71.74        19.46         3.12        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         4.04         5.03        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF185 MUTATED ZNF185 WILD-TYPE 
            1.02             0.23 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           39.98            90.12 
  ZNF185 MUTATED ZNF185 WILD-TYPE 
           15.70            15.22 
[1] "1.0 - 40.0 (15.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D22V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF185 MUTATED         0        0        0         4         4         1
  ZNF185 WILD-TYPE       1        3       12        15        78         3
                  vv
clus               STAGE IV
  ZNF185 MUTATED          1
  ZNF185 WILD-TYPE        2
D22V3, multiclass
           clus
vv          ZNF185 MUTATED ZNF185 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              4               15
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF185 MUTATED    0  0    10
  ZNF185 WILD-TYPE  5 17    92
D22V4, multiclass
       clus
vv      ZNF185 MUTATED ZNF185 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4             10               92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                  cls
clus                0  1
  ZNF185 MUTATED    6  4
  ZNF185 WILD-TYPE 29 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      6    4
  ZNF185 WILD-TYPE   29   85
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              6               29
  1              4               85
[1] 2 2
[1] FALSE
D22V6, binary
                  cls
clus                0  1
  ZNF185 MUTATED    5  1
  ZNF185 WILD-TYPE 52  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      5    1
  ZNF185 WILD-TYPE   52    2
   clus
vv  ZNF185 MUTATED ZNF185 WILD-TYPE
  0              5               52
  1              1                2
[1] 2 2
[1] FALSE
D22V7, binary
                  cls
clus                0  1
  ZNF185 MUTATED    4  6
  ZNF185 WILD-TYPE 47 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      4    6
  ZNF185 WILD-TYPE   47   69
        clus
vv       ZNF185 MUTATED ZNF185 WILD-TYPE
  FEMALE              4               47
  MALE                6               69
[1] 2 2
[1] FALSE
D22V8, binary
                  cls
clus                0  1
  ZNF185 MUTATED    8  2
  ZNF185 WILD-TYPE 80 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      8    2
  ZNF185 WILD-TYPE   80   28
     clus
vv    ZNF185 MUTATED ZNF185 WILD-TYPE
  NO               8               80
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF185 MUTATED                                     8
  ZNF185 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF185 MUTATED                                       1
  ZNF185 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF185 MUTATED                                                  1
  ZNF185 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF185 MUTATED                                     0
  ZNF185 WILD-TYPE                                   1
D22V9, multiclass
                                                  clus
vv                                                 ZNF185 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF185 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
[1] "Remove cluster labels:" "ZNF185 MUTATED"        
clus
  ZNF185 MUTATED ZNF185 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A7M4 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" "ZNF185 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF185 MUTATED    7  3  0  0
  ZNF185 WILD-TYPE 73 32  4  2
D22V12, multiclass
    clus
vv   ZNF185 MUTATED ZNF185 WILD-TYPE
  R0              7               73
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF185 MUTATED       0                         0    10
  ZNF185 WILD-TYPE     6                         5   104
D22V14, multiclass
                           clus
vv                          ZNF185 MUTATED ZNF185 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                  cls
clus                0  1
  ZNF185 MUTATED    0  7
  ZNF185 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF185 MUTATED      0    7
  ZNF185 WILD-TYPE    5   84
                        clus
vv                       ZNF185 MUTATED ZNF185 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(23) Variable = IRX4 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  IRX4 MUTATED    3  7
  IRX4 WILD-TYPE 60 55
  IRX4 MUTATED IRX4 WILD-TYPE 
            10            115 
  IRX4 MUTATED IRX4 WILD-TYPE 
             7             55 
$`IRX4 MUTATED`
TCGA-F2-A44G TCGA-US-A77E TCGA-2J-AAB1 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-HV-A7OP 
        7.66        14.14         2.17        20.84        24.26        32.15 
TCGA-HZ-8637 TCGA-US-A776 TCGA-US-A77J TCGA-YB-A89D 
       17.00        39.98        18.67        11.51 

$`IRX4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       45.47        43.50         7.36        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        17.49        31.86        20.19        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
       15.32         9.40         0.30        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  IRX4 MUTATED IRX4 WILD-TYPE 
          2.17           0.23 
  IRX4 MUTATED IRX4 WILD-TYPE 
         39.98          90.12 
  IRX4 MUTATED IRX4 WILD-TYPE 
        17.835         15.190 
[1] "2.2 - 40.0 (17.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D23V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IRX4 MUTATED         0        0        0         2         8         0
  IRX4 WILD-TYPE       1        3       12        17        74         4
                vv
clus             STAGE IV
  IRX4 MUTATED          0
  IRX4 WILD-TYPE        3
D23V3, multiclass
           clus
vv          IRX4 MUTATED IRX4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  IRX4 MUTATED    0  0    10
  IRX4 WILD-TYPE  5 17    92
D23V4, multiclass
       clus
vv      IRX4 MUTATED IRX4 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4           10             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                cls
clus              0  1
  IRX4 MUTATED    2  8
  IRX4 WILD-TYPE 33 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      2    8
  IRX4 WILD-TYPE   33   81
   clus
vv  IRX4 MUTATED IRX4 WILD-TYPE
  0            2             33
  1            8             81
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus              0  1
  IRX4 MUTATED    3  0
  IRX4 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      3    0
  IRX4 WILD-TYPE   54    3
   clus
vv  IRX4 MUTATED IRX4 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus              0  1
  IRX4 MUTATED    4  6
  IRX4 WILD-TYPE 47 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      4    6
  IRX4 WILD-TYPE   47   69
        clus
vv       IRX4 MUTATED IRX4 WILD-TYPE
  FEMALE            4             47
  MALE              6             69
[1] 2 2
[1] FALSE
D23V8, binary
                cls
clus              0  1
  IRX4 MUTATED    3  6
  IRX4 WILD-TYPE 85 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      3    6
  IRX4 WILD-TYPE   85   24
     clus
vv    IRX4 MUTATED IRX4 WILD-TYPE
  NO             3             85
  YES            6             24
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRX4 MUTATED                                     6
  IRX4 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRX4 MUTATED                                       3
  IRX4 WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRX4 MUTATED                                                  1
  IRX4 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  IRX4 MUTATED                                     0
  IRX4 WILD-TYPE                                   1
D23V9, multiclass
                                                  clus
vv                                                 IRX4 MUTATED IRX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
[1] "Remove cluster labels:" "IRX4 MUTATED"          
clus
  IRX4 MUTATED IRX4 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABA     TCGA-2J-AABE 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-YY-A8LH 
"IRX4 WILD-TYPE" 
D23V11, continuous
[1] "Remove cluster labels:" "IRX4 MUTATED"          
clus
  IRX4 MUTATED IRX4 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" "IRX4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  IRX4 MUTATED    8  2  0  0
  IRX4 WILD-TYPE 72 33  4  2
D23V12, multiclass
    clus
vv   IRX4 MUTATED IRX4 WILD-TYPE
  R0            8             72
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRX4 MUTATED       1                         0     9
  IRX4 WILD-TYPE     5                         5   105
D23V14, multiclass
                           clus
vv                          IRX4 MUTATED IRX4 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                cls
clus              0  1
  IRX4 MUTATED    1  7
  IRX4 WILD-TYPE  4 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      1    7
  IRX4 WILD-TYPE    4   84
                        clus
vv                       IRX4 MUTATED IRX4 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            7             84
[1] 2 2
[1] FALSE

Clustering(24) Variable = ZMIZ1 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2              0  1
  ZMIZ1 MUTATED    7  6
  ZMIZ1 WILD-TYPE 56 56
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             13             112 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              6              56 
$`ZMIZ1 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABK TCGA-2J-AABU TCGA-F2-A8YN TCGA-FB-AAPP TCGA-HZ-7925 
       12.92        15.91         9.11        17.00        15.95        20.19 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-YH-A8SY 
       19.82        41.33        15.19        14.17         6.02        12.76 
TCGA-Z5-AAPL 
       15.35 

$`ZMIZ1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        12.33        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-A5SO 
        5.26        10.85         0.23        19.82        36.69        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         0.26         4.73         7.86        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       31.27        23.67        11.51        66.28 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           6.02            0.23 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
          41.33           90.12 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
          15.35           15.17 
[1] "6.0 - 41.3 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D24V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZMIZ1 MUTATED         0        0        0         2         9         2
  ZMIZ1 WILD-TYPE       1        3       12        17        73         2
                 vv
clus              STAGE IV
  ZMIZ1 MUTATED          0
  ZMIZ1 WILD-TYPE        3
D24V3, multiclass
           clus
vv          ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             9              73
  STAGE III             2               2
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZMIZ1 MUTATED    0  0    13
  ZMIZ1 WILD-TYPE  5 17    89
D24V4, multiclass
       clus
vv      ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4            13              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    2 11
  ZMIZ1 WILD-TYPE 33 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      2   11
  ZMIZ1 WILD-TYPE   33   78
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             2              33
  1            11              78
[1] 2 2
[1] FALSE
D24V6, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    9  0
  ZMIZ1 WILD-TYPE 48  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      9    0
  ZMIZ1 WILD-TYPE   48    3
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             9              48
  1             0               3
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    6  7
  ZMIZ1 WILD-TYPE 45 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      6    7
  ZMIZ1 WILD-TYPE   45   68
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  FEMALE             6              45
  MALE               7              68
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED   10  3
  ZMIZ1 WILD-TYPE 78 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED     10    3
  ZMIZ1 WILD-TYPE   78   27
     clus
vv    ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  NO             10              78
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMIZ1 MUTATED                                    12
  ZMIZ1 WILD-TYPE                                  93
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMIZ1 MUTATED                                       0
  ZMIZ1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMIZ1 MUTATED                                                  0
  ZMIZ1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZMIZ1 MUTATED                                     0
  ZMIZ1 WILD-TYPE                                   1
D24V9, multiclass
                                                  clus
vv                                                 ZMIZ1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZMIZ1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
                 vv
clus              R0 R1 R2 RX
  ZMIZ1 MUTATED    6  6  0  0
  ZMIZ1 WILD-TYPE 74 29  4  2
D24V12, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  R0             6              74
  R1             6              29
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ1 MUTATED       0                         1    12
  ZMIZ1 WILD-TYPE     6                         4   102
D24V14, multiclass
                           clus
vv                          ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                12             102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    0 11
  ZMIZ1 WILD-TYPE  5 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      0   11
  ZMIZ1 WILD-TYPE    5   80
                        clus
vv                       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            11              80
[1] 2 2
[1] FALSE

Clustering(25) Variable = EDC4 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2             0  1
  EDC4 MUTATED    8  7
  EDC4 WILD-TYPE 55 55
  EDC4 MUTATED EDC4 WILD-TYPE 
            15            110 
  EDC4 MUTATED EDC4 WILD-TYPE 
             7             55 
$`EDC4 MUTATED`
TCGA-US-A77E TCGA-2J-AAB8 TCGA-2J-AABH TCGA-2L-AAQI TCGA-3A-A9IX TCGA-FZ-5920 
       14.14         2.63        42.31         3.39        34.09         2.01 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-AAUP 
        8.28        30.25        19.82        20.88         1.35        14.17 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Z5-AAPL 
       10.29         8.78        15.35 

$`EDC4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.22        22.72        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        36.26        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 
       15.55         4.04         5.03         1.02        24.36         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8X 
       36.20        20.35        17.79        22.06        32.15        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85         7.20        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       13.28         7.56        12.46        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

  EDC4 MUTATED EDC4 WILD-TYPE 
          1.35           0.23 
  EDC4 MUTATED EDC4 WILD-TYPE 
         42.31          90.12 
  EDC4 MUTATED EDC4 WILD-TYPE 
        14.140         15.435 
[1] "1.4 - 42.3 (14.1)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.1"
D25V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EDC4 MUTATED         0        1        0         4        11         0
  EDC4 WILD-TYPE       1        2       12        15        71         4
                vv
clus             STAGE IV
  EDC4 MUTATED          0
  EDC4 WILD-TYPE        3
D25V3, multiclass
           clus
vv          EDC4 MUTATED EDC4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            4             15
  STAGE IIB           11             71
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  EDC4 MUTATED    1  0    15
  EDC4 WILD-TYPE  4 17    87
D25V4, multiclass
       clus
vv      EDC4 MUTATED EDC4 WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4           15             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                cls
clus              0  1
  EDC4 MUTATED    5 11
  EDC4 WILD-TYPE 30 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      5   11
  EDC4 WILD-TYPE   30   78
   clus
vv  EDC4 MUTATED EDC4 WILD-TYPE
  0            5             30
  1           11             78
[1] 2 2
[1] FALSE
D25V6, binary
                cls
clus              0  1
  EDC4 MUTATED    9  0
  EDC4 WILD-TYPE 48  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      9    0
  EDC4 WILD-TYPE   48    3
   clus
vv  EDC4 MUTATED EDC4 WILD-TYPE
  0            9             48
  1            0              3
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus              0  1
  EDC4 MUTATED    4 12
  EDC4 WILD-TYPE 47 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      4   12
  EDC4 WILD-TYPE   47   63
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  FEMALE            4             47
  MALE             12             63
[1] 2 2
[1] FALSE
D25V8, binary
                cls
clus              0  1
  EDC4 MUTATED   11  3
  EDC4 WILD-TYPE 77 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED     11    3
  EDC4 WILD-TYPE   77   27
     clus
vv    EDC4 MUTATED EDC4 WILD-TYPE
  NO            11             77
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EDC4 MUTATED                                    14
  EDC4 WILD-TYPE                                  91
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EDC4 MUTATED                                       2
  EDC4 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EDC4 MUTATED                                                  0
  EDC4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EDC4 MUTATED                                     0
  EDC4 WILD-TYPE                                   1
D25V9, multiclass
                                                  clus
vv                                                 EDC4 MUTATED EDC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        14             91
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
                vv
clus             R0 R1 R2 RX
  EDC4 MUTATED    9  5  2  0
  EDC4 WILD-TYPE 71 30  2  2
D25V12, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  R0            9             71
  R1            5             30
  R2            2              2
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDC4 MUTATED       2                         1    13
  EDC4 WILD-TYPE     4                         4   101
D25V14, multiclass
                           clus
vv                          EDC4 MUTATED EDC4 WILD-TYPE
  ASIAN                                2              4
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               13            101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                cls
clus              0  1
  EDC4 MUTATED    0 11
  EDC4 WILD-TYPE  5 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      0   11
  EDC4 WILD-TYPE    5   80
                        clus
vv                       EDC4 MUTATED EDC4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           11             80
[1] 2 2
[1] FALSE

Clustering(26) Variable = CCDC135 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  CCDC135 MUTATED    8  5
  CCDC135 WILD-TYPE 55 57
  CCDC135 MUTATED CCDC135 WILD-TYPE 
               13               112 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                5                57 
$`CCDC135 MUTATED`
TCGA-2J-AABO TCGA-2J-AABU TCGA-2L-AAQI TCGA-3A-A9I9 TCGA-FB-AAQ0 TCGA-HV-A7OP 
       14.47         9.11         3.39        20.84        15.55        32.15 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-AAUM TCGA-RL-AAAS TCGA-US-A776 
       10.85        19.82        19.82         0.26         0.30        39.98 
TCGA-YB-A89D 
       11.51 

$`CCDC135 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
       15.22        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        5.26         0.23        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A779 
        8.78        13.68         3.12        15.32         9.40        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  CCDC135 MUTATED CCDC135 WILD-TYPE 
             0.26              0.23 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
            39.98             90.12 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
            14.47             15.27 
[1] "0.3 - 40.0 (14.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D26V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC135 MUTATED         0        0        1         3         8         0
  CCDC135 WILD-TYPE       1        3       11        16        74         4
                   vv
clus                STAGE IV
  CCDC135 MUTATED          1
  CCDC135 WILD-TYPE        2
D26V3, multiclass
           clus
vv          CCDC135 MUTATED CCDC135 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               3                16
  STAGE IIB               8                74
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC135 MUTATED    0  2    11
  CCDC135 WILD-TYPE  5 15    91
D26V4, multiclass
       clus
vv      CCDC135 MUTATED CCDC135 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4              11                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    5  8
  CCDC135 WILD-TYPE 30 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      5    8
  CCDC135 WILD-TYPE   30   81
   clus
vv  CCDC135 MUTATED CCDC135 WILD-TYPE
  0               5                30
  1               8                81
[1] 2 2
[1] FALSE
D26V6, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    6  1
  CCDC135 WILD-TYPE 51  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      6    1
  CCDC135 WILD-TYPE   51    2
   clus
vv  CCDC135 MUTATED CCDC135 WILD-TYPE
  0               6                51
  1               1                 2
[1] 2 2
[1] FALSE
D26V7, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    2 11
  CCDC135 WILD-TYPE 49 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      2   11
  CCDC135 WILD-TYPE   49   64
        clus
vv       CCDC135 MUTATED CCDC135 WILD-TYPE
  FEMALE               2                49
  MALE                11                64
[1] 2 2
[1] FALSE
D26V8, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    9  4
  CCDC135 WILD-TYPE 79 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      9    4
  CCDC135 WILD-TYPE   79   26
     clus
vv    CCDC135 MUTATED CCDC135 WILD-TYPE
  NO                9                79
  YES               4                26
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC135 MUTATED                                     9
  CCDC135 WILD-TYPE                                  96
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC135 MUTATED                                       3
  CCDC135 WILD-TYPE                                    15
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC135 MUTATED                                                  1
  CCDC135 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC135 MUTATED                                     0
  CCDC135 WILD-TYPE                                   1
D26V9, multiclass
                                                  clus
vv                                                 CCDC135 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC135 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
[1] "Remove cluster labels:" "CCDC135 MUTATED"       
clus
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC135 MUTATED   12  1  0  0
  CCDC135 WILD-TYPE 68 34  4  2
D26V12, multiclass
    clus
vv   CCDC135 MUTATED CCDC135 WILD-TYPE
  R0              12                68
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC135 MUTATED       1                         0    12
  CCDC135 WILD-TYPE     5                         5   102
D26V14, multiclass
                           clus
vv                          CCDC135 MUTATED CCDC135 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  12               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    0  9
  CCDC135 WILD-TYPE  5 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      0    9
  CCDC135 WILD-TYPE    5   82
                        clus
vv                       CCDC135 MUTATED CCDC135 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               9                82
[1] 2 2
[1] FALSE

Clustering(27) Variable = APP MUTATION ANALYSIS
D27V1, survival
               sevent
clus2            0  1
  APP MUTATED    5  7
  APP WILD-TYPE 58 55
  APP MUTATED APP WILD-TYPE 
           12           113 
  APP MUTATED APP WILD-TYPE 
            7            55 
$`APP MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQA TCGA-3A-A9IH TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FZ-5922 
       12.92         4.70        33.57         7.50        23.54        36.20 
TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-7885 TCGA-Q3-A5QY 
       17.49        20.19        17.00        19.82        41.33        13.68 

$`APP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
        5.10        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       30.25        31.86        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  APP MUTATED APP WILD-TYPE 
         4.70          0.23 
  APP MUTATED APP WILD-TYPE 
        41.33         90.12 
  APP MUTATED APP WILD-TYPE 
       18.655        15.120 
[1] "4.7 - 41.3 (18.7)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D27V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  APP MUTATED         0        1        0         1        10         0
  APP WILD-TYPE       1        2       12        18        72         4
               vv
clus            STAGE IV
  APP MUTATED          0
  APP WILD-TYPE        3
D27V3, multiclass
           clus
vv          APP MUTATED APP WILD-TYPE
  STAGE I             0             1
  STAGE IA            1             2
  STAGE IB            0            12
  STAGE IIA           1            18
  STAGE IIB          10            72
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  APP MUTATED    1  3     8
  APP WILD-TYPE  4 14    94
D27V4, multiclass
       clus
vv      APP MUTATED APP WILD-TYPE
  T1              1             4
  T2              3            14
  T3+T4           8            94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
               cls
clus             0  1
  APP MUTATED    2 10
  APP WILD-TYPE 33 79
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      2   10
  APP WILD-TYPE   33   79
   clus
vv  APP MUTATED APP WILD-TYPE
  0           2            33
  1          10            79
[1] 2 2
[1] FALSE
D27V6, binary
               cls
clus             0  1
  APP MUTATED    3  0
  APP WILD-TYPE 54  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      3    0
  APP WILD-TYPE   54    3
   clus
vv  APP MUTATED APP WILD-TYPE
  0           3            54
  1           0             3
[1] 2 2
[1] FALSE
D27V7, binary
               cls
clus             0  1
  APP MUTATED    7  5
  APP WILD-TYPE 44 70
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      7    5
  APP WILD-TYPE   44   70
        clus
vv       APP MUTATED APP WILD-TYPE
  FEMALE           7            44
  MALE             5            70
[1] 2 2
[1] FALSE
D27V8, binary
               cls
clus             0  1
  APP MUTATED   10  2
  APP WILD-TYPE 78 28
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED     10    2
  APP WILD-TYPE   78   28
     clus
vv    APP MUTATED APP WILD-TYPE
  NO           10            78
  YES           2            28
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  APP MUTATED                                    12
  APP WILD-TYPE                                  93
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  APP MUTATED                                       0
  APP WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  APP MUTATED                                                  0
  APP WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  APP MUTATED                                     0
  APP WILD-TYPE                                   1
D27V9, multiclass
                                                  clus
vv                                                 APP MUTATED APP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       12            93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
               vv
clus            R0 R1 R2 RX
  APP MUTATED    9  2  1  0
  APP WILD-TYPE 71 33  3  2
D27V12, multiclass
    clus
vv   APP MUTATED APP WILD-TYPE
  R0           9            71
  R1           2            33
  R2           1             3
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APP MUTATED       1                         1    10
  APP WILD-TYPE     5                         4   104
D27V14, multiclass
                           clus
vv                          APP MUTATED APP WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                              10           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
               cls
clus             0  1
  APP MUTATED    1  9
  APP WILD-TYPE  4 82
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      1    9
  APP WILD-TYPE    4   82
                        clus
vv                       APP MUTATED APP WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO           9            82
[1] 2 2
[1] FALSE

Clustering(28) Variable = TMC4 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2             0  1
  TMC4 MUTATED   11  9
  TMC4 WILD-TYPE 52 53
  TMC4 MUTATED TMC4 WILD-TYPE 
            20            105 
  TMC4 MUTATED TMC4 WILD-TYPE 
             9             53 
$`TMC4 MUTATED`
TCGA-FZ-5924 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO 
       15.78         9.63        20.61        22.72        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQE TCGA-3A-A9I7 TCGA-3A-A9IH TCGA-FB-AAPZ 
       15.22        21.44        22.49        43.50        33.57        23.54 
TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-8126 
        8.28        17.49        20.19        19.82        19.82        15.19 
TCGA-IB-A7M4 TCGA-RL-AAAS 
       15.88         0.30 

$`TMC4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
       16.37         2.17        23.97         2.63        19.96        22.22 
TCGA-2J-AABH TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       42.31         9.11         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR 
       45.47        20.84         7.36        24.26        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 
       12.33        15.95        37.15         7.50        12.53        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        17.00        10.13         5.26        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TMC4 MUTATED TMC4 WILD-TYPE 
          0.30           0.23 
  TMC4 MUTATED TMC4 WILD-TYPE 
         43.50          90.12 
  TMC4 MUTATED TMC4 WILD-TYPE 
        18.655         14.140 
[1] "0.3 - 43.5 (18.7)" "0.2 - 90.1 (14.1)"
[1] "hr=" "1.3"
D28V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMC4 MUTATED         0        1        1         3        13         1
  TMC4 WILD-TYPE       1        2       11        16        69         3
                vv
clus             STAGE IV
  TMC4 MUTATED          1
  TMC4 WILD-TYPE        2
D28V3, multiclass
           clus
vv          TMC4 MUTATED TMC4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             1             11
  STAGE IIA            3             16
  STAGE IIB           13             69
  STAGE III            1              3
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TMC4 MUTATED    1  3    16
  TMC4 WILD-TYPE  4 14    86
D28V4, multiclass
       clus
vv      TMC4 MUTATED TMC4 WILD-TYPE
  T1               1              4
  T2               3             14
  T3+T4           16             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                cls
clus              0  1
  TMC4 MUTATED    5 15
  TMC4 WILD-TYPE 30 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      5   15
  TMC4 WILD-TYPE   30   74
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0            5             30
  1           15             74
[1] 2 2
[1] FALSE
D28V6, binary
                cls
clus              0  1
  TMC4 MUTATED   12  1
  TMC4 WILD-TYPE 45  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     12    1
  TMC4 WILD-TYPE   45    2
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0           12             45
  1            1              2
[1] 2 2
[1] FALSE
D28V7, binary
                cls
clus              0  1
  TMC4 MUTATED    7 13
  TMC4 WILD-TYPE 44 62
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      7   13
  TMC4 WILD-TYPE   44   62
        clus
vv       TMC4 MUTATED TMC4 WILD-TYPE
  FEMALE            7             44
  MALE             13             62
[1] 2 2
[1] FALSE
D28V8, binary
                cls
clus              0  1
  TMC4 MUTATED   15  5
  TMC4 WILD-TYPE 73 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED     15    5
  TMC4 WILD-TYPE   73   25
     clus
vv    TMC4 MUTATED TMC4 WILD-TYPE
  NO            15             73
  YES            5             25
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMC4 MUTATED                                    18
  TMC4 WILD-TYPE                                  87
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMC4 MUTATED                                       1
  TMC4 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMC4 MUTATED                                                  0
  TMC4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMC4 MUTATED                                     1
  TMC4 WILD-TYPE                                   0
D28V9, multiclass
                                                  clus
vv                                                 TMC4 MUTATED TMC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        18             87
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         1              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
                vv
clus             R0 R1 R2 RX
  TMC4 MUTATED   14  4  2  0
  TMC4 WILD-TYPE 66 31  2  2
D28V12, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  R0           14             66
  R1            4             31
  R2            2              2
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMC4 MUTATED       2                         1    17
  TMC4 WILD-TYPE     4                         4    97
D28V14, multiclass
                           clus
vv                          TMC4 MUTATED TMC4 WILD-TYPE
  ASIAN                                2              4
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               17             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                cls
clus              0  1
  TMC4 MUTATED    0 10
  TMC4 WILD-TYPE  5 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      0   10
  TMC4 WILD-TYPE    5   81
                        clus
vv                       TMC4 MUTATED TMC4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           10             81
[1] 2 2
[1] FALSE

Clustering(29) Variable = PHF13 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  PHF13 MUTATED    4  4
  PHF13 WILD-TYPE 59 58
  PHF13 MUTATED PHF13 WILD-TYPE 
              8             117 
  PHF13 MUTATED PHF13 WILD-TYPE 
              4              58 
$`PHF13 MUTATED`
TCGA-3A-A9IJ TCGA-LB-A7SX TCGA-US-A77E TCGA-2J-AABK TCGA-2L-AAQE TCGA-3A-A9IR 
       60.95        12.92        14.14        15.91        22.49        50.70 
TCGA-3A-A9IZ TCGA-RB-AA9M 
       10.13         9.40 

$`PHF13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        15.12        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS 
       20.84         7.36        24.26        33.57        63.85        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PHF13 MUTATED PHF13 WILD-TYPE 
           9.40            0.23 
  PHF13 MUTATED PHF13 WILD-TYPE 
          60.95           90.12 
  PHF13 MUTATED PHF13 WILD-TYPE 
         15.025          15.220 
[1] "9.4 - 61.0 (15.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D29V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHF13 MUTATED         0        0        2         0         7         0
  PHF13 WILD-TYPE       1        3       10        19        75         4
                 vv
clus              STAGE IV
  PHF13 MUTATED          0
  PHF13 WILD-TYPE        3
D29V3, multiclass
           clus
vv          PHF13 MUTATED PHF13 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PHF13 MUTATED    1  2     6
  PHF13 WILD-TYPE  4 15    96
D29V4, multiclass
       clus
vv      PHF13 MUTATED PHF13 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                 cls
clus               0  1
  PHF13 MUTATED    2  7
  PHF13 WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      2    7
  PHF13 WILD-TYPE   33   82
   clus
vv  PHF13 MUTATED PHF13 WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D29V6, binary
                 cls
clus               0  1
  PHF13 MUTATED    2  0
  PHF13 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      2    0
  PHF13 WILD-TYPE   55    3
   clus
vv  PHF13 MUTATED PHF13 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus               0  1
  PHF13 MUTATED    2  7
  PHF13 WILD-TYPE 49 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      2    7
  PHF13 WILD-TYPE   49   68
        clus
vv       PHF13 MUTATED PHF13 WILD-TYPE
  FEMALE             2              49
  MALE               7              68
[1] 2 2
[1] FALSE
D29V8, binary
                 cls
clus               0  1
  PHF13 MUTATED    6  2
  PHF13 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      6    2
  PHF13 WILD-TYPE   82   28
     clus
vv    PHF13 MUTATED PHF13 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF13 MUTATED                                     6
  PHF13 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF13 MUTATED                                       3
  PHF13 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF13 MUTATED                                                  0
  PHF13 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHF13 MUTATED                                     0
  PHF13 WILD-TYPE                                   1
D29V9, multiclass
                                                  clus
vv                                                 PHF13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PHF13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
                 vv
clus              R0 R1 R2 RX
  PHF13 MUTATED    5  4  0  0
  PHF13 WILD-TYPE 75 31  4  2
D29V12, multiclass
    clus
vv   PHF13 MUTATED PHF13 WILD-TYPE
  R0             5              75
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF13 MUTATED       0                         1     8
  PHF13 WILD-TYPE     6                         4   106
D29V14, multiclass
                           clus
vv                          PHF13 MUTATED PHF13 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                 cls
clus               0  1
  PHF13 MUTATED    1  6
  PHF13 WILD-TYPE  4 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF13 MUTATED      1    6
  PHF13 WILD-TYPE    4   85
                        clus
vv                       PHF13 MUTATED PHF13 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(30) Variable = B4GALT2 MUTATION ANALYSIS
D30V1, survival
                   sevent
clus2                0  1
  B4GALT2 MUTATED    6  4
  B4GALT2 WILD-TYPE 57 58
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
               10               115 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                4                58 
$`B4GALT2 MUTATED`
TCGA-F2-A44G TCGA-HZ-A77Q TCGA-2J-AAB6 TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-HV-A7OP 
        7.66         1.08         9.63        34.09        10.13        32.15 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-US-A779 
       10.85        19.82        36.69        16.80 

$`B4GALT2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9J0 
       63.85        50.70        32.81        15.06        36.26        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        5.26         0.23        19.82        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
             1.08              0.23 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
            36.69             90.12 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
           13.825            15.220 
[1] "1.1 - 36.7 (13.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D30V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  B4GALT2 MUTATED         0        1        0         1         7         0
  B4GALT2 WILD-TYPE       1        2       12        18        75         4
                   vv
clus                STAGE IV
  B4GALT2 MUTATED          1
  B4GALT2 WILD-TYPE        2
D30V3, multiclass
           clus
vv          B4GALT2 MUTATED B4GALT2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               7                75
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  B4GALT2 MUTATED    1  0     9
  B4GALT2 WILD-TYPE  4 17    93
D30V4, multiclass
       clus
vv      B4GALT2 MUTATED B4GALT2 WILD-TYPE
  T1                  1                 4
  T2                  0                17
  T3+T4               9                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    3  7
  B4GALT2 WILD-TYPE 32 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      3    7
  B4GALT2 WILD-TYPE   32   82
   clus
vv  B4GALT2 MUTATED B4GALT2 WILD-TYPE
  0               3                32
  1               7                82
[1] 2 2
[1] FALSE
D30V6, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    4  1
  B4GALT2 WILD-TYPE 53  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      4    1
  B4GALT2 WILD-TYPE   53    2
   clus
vv  B4GALT2 MUTATED B4GALT2 WILD-TYPE
  0               4                53
  1               1                 2
[1] 2 2
[1] FALSE
D30V7, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    4  6
  B4GALT2 WILD-TYPE 47 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      4    6
  B4GALT2 WILD-TYPE   47   69
        clus
vv       B4GALT2 MUTATED B4GALT2 WILD-TYPE
  FEMALE               4                47
  MALE                 6                69
[1] 2 2
[1] FALSE
D30V8, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    5  3
  B4GALT2 WILD-TYPE 83 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      5    3
  B4GALT2 WILD-TYPE   83   27
     clus
vv    B4GALT2 MUTATED B4GALT2 WILD-TYPE
  NO                5                83
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  B4GALT2 MUTATED                                     6
  B4GALT2 WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  B4GALT2 MUTATED                                       4
  B4GALT2 WILD-TYPE                                    14
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  B4GALT2 MUTATED                                                  0
  B4GALT2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  B4GALT2 MUTATED                                     0
  B4GALT2 WILD-TYPE                                   1
D30V9, multiclass
                                                  clus
vv                                                 B4GALT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 B4GALT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
[1] "Remove cluster labels:" "B4GALT2 MUTATED"       
clus
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-F2-A8YN 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1        TCGA-IB-7651 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-YY-A8LH 
"B4GALT2 WILD-TYPE" 
D30V11, continuous
[1] "Remove cluster labels:" "B4GALT2 MUTATED"       
clus
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-FB-A5VM 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" "B4GALT2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  B4GALT2 MUTATED    7  3  0  0
  B4GALT2 WILD-TYPE 73 32  4  2
D30V12, multiclass
    clus
vv   B4GALT2 MUTATED B4GALT2 WILD-TYPE
  R0               7                73
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  B4GALT2 MUTATED       2                         0     8
  B4GALT2 WILD-TYPE     4                         5   106
D30V14, multiclass
                           clus
vv                          B4GALT2 MUTATED B4GALT2 WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   8               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    1  7
  B4GALT2 WILD-TYPE  4 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      1    7
  B4GALT2 WILD-TYPE    4   84
                        clus
vv                       B4GALT2 MUTATED B4GALT2 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               7                84
[1] 2 2
[1] FALSE

Clustering(31) Variable = GAGE2A MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2               0  1
  GAGE2A MUTATED    4  2
  GAGE2A WILD-TYPE 59 60
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               6              119 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2               60 
$`GAGE2A MUTATED`
TCGA-2J-AABH TCGA-3A-A9J0 TCGA-HZ-8637 TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-US-A776 
       42.31        24.43        17.00         7.20        20.88        39.98 

$`GAGE2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
       13.68         3.12        15.32         9.40         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
            7.20             0.23 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           42.31            90.12 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
          22.655           15.120 
[1] "7.2 - 42.3 (22.7)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2.3"
D31V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GAGE2A MUTATED         0        0        1         2         3         0
  GAGE2A WILD-TYPE       1        3       11        17        79         4
                  vv
clus               STAGE IV
  GAGE2A MUTATED          0
  GAGE2A WILD-TYPE        3
D31V3, multiclass
           clus
vv          GAGE2A MUTATED GAGE2A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              2               17
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GAGE2A MUTATED    0  1     5
  GAGE2A WILD-TYPE  5 16    97
D31V4, multiclass
       clus
vv      GAGE2A MUTATED GAGE2A WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                  cls
clus                0  1
  GAGE2A MUTATED    3  3
  GAGE2A WILD-TYPE 32 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      3    3
  GAGE2A WILD-TYPE   32   86
   clus
vv  GAGE2A MUTATED GAGE2A WILD-TYPE
  0              3               32
  1              3               86
[1] 2 2
[1] FALSE
D31V6, binary
                  cls
clus                0  1
  GAGE2A MUTATED    3  0
  GAGE2A WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      3    0
  GAGE2A WILD-TYPE   54    3
   clus
vv  GAGE2A MUTATED GAGE2A WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                0  1
  GAGE2A MUTATED    3  3
  GAGE2A WILD-TYPE 48 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      3    3
  GAGE2A WILD-TYPE   48   72
        clus
vv       GAGE2A MUTATED GAGE2A WILD-TYPE
  FEMALE              3               48
  MALE                3               72
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                0  1
  GAGE2A MUTATED    5  1
  GAGE2A WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      5    1
  GAGE2A WILD-TYPE   83   29
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GAGE2A MUTATED                                     4
  GAGE2A WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GAGE2A MUTATED                                       1
  GAGE2A WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GAGE2A MUTATED                                                  1
  GAGE2A WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GAGE2A MUTATED                                     0
  GAGE2A WILD-TYPE                                   1
D31V9, multiclass
                                                  clus
vv                                                 GAGE2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GAGE2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
                  vv
clus               R0 R1 R2 RX
  GAGE2A MUTATED    6  0  0  0
  GAGE2A WILD-TYPE 74 35  4  2
D31V12, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  R0              6               74
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAGE2A MUTATED       0                         0     6
  GAGE2A WILD-TYPE     6                         5   108
D31V14, multiclass
                           clus
vv                          GAGE2A MUTATED GAGE2A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                  cls
clus                0  1
  GAGE2A MUTATED    1  4
  GAGE2A WILD-TYPE  4 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      1    4
  GAGE2A WILD-TYPE    4   87
                        clus
vv                       GAGE2A MUTATED GAGE2A WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(32) Variable = YIPF2 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  YIPF2 MUTATED    5  6
  YIPF2 WILD-TYPE 58 56
  YIPF2 MUTATED YIPF2 WILD-TYPE 
             11             114 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              6              56 
$`YIPF2 MUTATED`
TCGA-2J-AABR TCGA-2J-AAB6 TCGA-2J-AABP TCGA-2L-AAQI TCGA-3A-A9IB TCGA-3A-A9IH 
       14.40         9.63        15.22         3.39         7.36        33.57 
TCGA-FB-A78T TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A7M4 TCGA-US-A779 
       12.33        10.85        19.82        15.88        16.80 

$`YIPF2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       43.50        20.84        24.26        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  YIPF2 MUTATED YIPF2 WILD-TYPE 
           3.39            0.23 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
          33.57           90.12 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
         14.400          15.335 
[1] "3.4 - 33.6 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D32V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  YIPF2 MUTATED         0        1        0         2         8         0
  YIPF2 WILD-TYPE       1        2       12        17        74         4
                 vv
clus              STAGE IV
  YIPF2 MUTATED          0
  YIPF2 WILD-TYPE        3
D32V3, multiclass
           clus
vv          YIPF2 MUTATED YIPF2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  YIPF2 MUTATED    1  0    10
  YIPF2 WILD-TYPE  4 17    92
D32V4, multiclass
       clus
vv      YIPF2 MUTATED YIPF2 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                 cls
clus               0  1
  YIPF2 MUTATED    3  8
  YIPF2 WILD-TYPE 32 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      3    8
  YIPF2 WILD-TYPE   32   81
   clus
vv  YIPF2 MUTATED YIPF2 WILD-TYPE
  0             3              32
  1             8              81
[1] 2 2
[1] FALSE
D32V6, binary
                 cls
clus               0  1
  YIPF2 MUTATED    5  0
  YIPF2 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      5    0
  YIPF2 WILD-TYPE   52    3
   clus
vv  YIPF2 MUTATED YIPF2 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus               0  1
  YIPF2 MUTATED    7  4
  YIPF2 WILD-TYPE 44 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      7    4
  YIPF2 WILD-TYPE   44   71
        clus
vv       YIPF2 MUTATED YIPF2 WILD-TYPE
  FEMALE             7              44
  MALE               4              71
[1] 2 2
[1] FALSE
D32V8, binary
                 cls
clus               0  1
  YIPF2 MUTATED   10  0
  YIPF2 WILD-TYPE 78 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED     10    0
  YIPF2 WILD-TYPE   78   30
     clus
vv    YIPF2 MUTATED YIPF2 WILD-TYPE
  NO             10              78
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  YIPF2 MUTATED                                     9
  YIPF2 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  YIPF2 MUTATED                                       1
  YIPF2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  YIPF2 MUTATED                                                  0
  YIPF2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  YIPF2 MUTATED                                     1
  YIPF2 WILD-TYPE                                   0
D32V9, multiclass
                                                  clus
vv                                                 YIPF2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 YIPF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
                 vv
clus              R0 R1 R2 RX
  YIPF2 MUTATED   10  1  0  0
  YIPF2 WILD-TYPE 70 34  4  2
D32V12, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  R0            10              70
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YIPF2 MUTATED       0                         0    11
  YIPF2 WILD-TYPE     6                         5   103
D32V14, multiclass
                           clus
vv                          YIPF2 MUTATED YIPF2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                 cls
clus               0  1
  YIPF2 MUTATED    0  7
  YIPF2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      0    7
  YIPF2 WILD-TYPE    5   84
                        clus
vv                       YIPF2 MUTATED YIPF2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(33) Variable = MED15 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  MED15 MUTATED    7  5
  MED15 WILD-TYPE 56 57
  MED15 MUTATED MED15 WILD-TYPE 
             12             113 
  MED15 MUTATED MED15 WILD-TYPE 
              5              57 
$`MED15 MUTATED`
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-2J-AABP TCGA-2L-AAQL TCGA-FB-A78T TCGA-HV-AA8V 
        1.08        15.12        15.22         9.60        12.33        30.25 
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-AAUR TCGA-IB-AAUU TCGA-RB-AA9M TCGA-YB-A89D 
        5.26        19.82        11.11         8.05         9.40        11.51 

$`MED15 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM 
       21.44         4.70        22.49         3.39        12.95        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        6.02         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  MED15 MUTATED MED15 WILD-TYPE 
           1.08            0.23 
  MED15 MUTATED MED15 WILD-TYPE 
          30.25           90.12 
  MED15 MUTATED MED15 WILD-TYPE 
          11.31           15.78 
[1] "1.1 - 30.2 (11.3)" "0.2 - 90.1 (15.8)"
[1] "hr=" "1.3"
D33V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MED15 MUTATED         0        0        0         0        12         0
  MED15 WILD-TYPE       1        3       12        19        70         4
                 vv
clus              STAGE IV
  MED15 MUTATED          0
  MED15 WILD-TYPE        3
D33V3, multiclass
           clus
vv          MED15 MUTATED MED15 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB            12              70
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MED15 MUTATED    1  1    10
  MED15 WILD-TYPE  4 16    92
D33V4, multiclass
       clus
vv      MED15 MUTATED MED15 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                 cls
clus               0  1
  MED15 MUTATED    0 12
  MED15 WILD-TYPE 35 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      0   12
  MED15 WILD-TYPE   35   77
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0             0              35
  1            12              77
[1] 2 2
[1] FALSE
D33V6, binary
                 cls
clus               0  1
  MED15 MUTATED    6  0
  MED15 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      6    0
  MED15 WILD-TYPE   51    3
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus               0  1
  MED15 MUTATED    6  6
  MED15 WILD-TYPE 45 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      6    6
  MED15 WILD-TYPE   45   69
        clus
vv       MED15 MUTATED MED15 WILD-TYPE
  FEMALE             6              45
  MALE               6              69
[1] 2 2
[1] FALSE
D33V8, binary
                 cls
clus               0  1
  MED15 MUTATED    9  2
  MED15 WILD-TYPE 79 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      9    2
  MED15 WILD-TYPE   79   28
     clus
vv    MED15 MUTATED MED15 WILD-TYPE
  NO              9              79
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED15 MUTATED                                    10
  MED15 WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED15 MUTATED                                       1
  MED15 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED15 MUTATED                                                  0
  MED15 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MED15 MUTATED                                     1
  MED15 WILD-TYPE                                   0
D33V9, multiclass
                                                  clus
vv                                                 MED15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 MED15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
                 vv
clus              R0 R1 R2 RX
  MED15 MUTATED    9  1  1  1
  MED15 WILD-TYPE 71 34  3  1
D33V12, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  R0             9              71
  R1             1              34
  R2             1               3
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED15 MUTATED       1                         0    11
  MED15 WILD-TYPE     5                         5   103
D33V14, multiclass
                           clus
vv                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                 cls
clus               0  1
  MED15 MUTATED    0  9
  MED15 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      0    9
  MED15 WILD-TYPE    5   82
                        clus
vv                       MED15 MUTATED MED15 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(34) Variable = MBD3 MUTATION ANALYSIS
D34V1, survival
                sevent
clus2             0  1
  MBD3 MUTATED    4  5
  MBD3 WILD-TYPE 59 57
  MBD3 MUTATED MBD3 WILD-TYPE 
             9            116 
  MBD3 MUTATED MBD3 WILD-TYPE 
             5             57 
$`MBD3 MUTATED`
TCGA-S4-A8RO TCGA-2J-AABK TCGA-F2-7273 TCGA-FB-AAQ0 TCGA-HV-A7OL TCGA-IB-7651 
       17.26        15.91        19.46        15.55         8.28        19.82 
TCGA-IB-A5SO TCGA-IB-A7LX TCGA-XD-AAUG 
       12.00         8.22        13.81 

$`MBD3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MBD3 MUTATED MBD3 WILD-TYPE 
          8.22           0.23 
  MBD3 MUTATED MBD3 WILD-TYPE 
         19.82          90.12 
  MBD3 MUTATED MBD3 WILD-TYPE 
        15.550         15.205 
[1] "8.2 - 19.8 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D34V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MBD3 MUTATED         0        0        0         2         6         0
  MBD3 WILD-TYPE       1        3       12        17        76         4
                vv
clus             STAGE IV
  MBD3 MUTATED          1
  MBD3 WILD-TYPE        2
D34V3, multiclass
           clus
vv          MBD3 MUTATED MBD3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  MBD3 MUTATED    0  0     9
  MBD3 WILD-TYPE  5 17    93
D34V4, multiclass
       clus
vv      MBD3 MUTATED MBD3 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            9             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                cls
clus              0  1
  MBD3 MUTATED    2  7
  MBD3 WILD-TYPE 33 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      2    7
  MBD3 WILD-TYPE   33   82
   clus
vv  MBD3 MUTATED MBD3 WILD-TYPE
  0            2             33
  1            7             82
[1] 2 2
[1] FALSE
D34V6, binary
                cls
clus              0  1
  MBD3 MUTATED    4  1
  MBD3 WILD-TYPE 53  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      4    1
  MBD3 WILD-TYPE   53    2
   clus
vv  MBD3 MUTATED MBD3 WILD-TYPE
  0            4             53
  1            1              2
[1] 2 2
[1] FALSE
D34V7, binary
                cls
clus              0  1
  MBD3 MUTATED    3  6
  MBD3 WILD-TYPE 48 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      3    6
  MBD3 WILD-TYPE   48   69
        clus
vv       MBD3 MUTATED MBD3 WILD-TYPE
  FEMALE            3             48
  MALE              6             69
[1] 2 2
[1] FALSE
D34V8, binary
                cls
clus              0  1
  MBD3 MUTATED    6  3
  MBD3 WILD-TYPE 82 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      6    3
  MBD3 WILD-TYPE   82   27
     clus
vv    MBD3 MUTATED MBD3 WILD-TYPE
  NO             6             82
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MBD3 MUTATED                                     9
  MBD3 WILD-TYPE                                  96
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MBD3 MUTATED                                       0
  MBD3 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MBD3 MUTATED                                                  0
  MBD3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MBD3 MUTATED                                     0
  MBD3 WILD-TYPE                                   1
D34V9, multiclass
                                                  clus
vv                                                 MBD3 MUTATED MBD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         9             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
[1] "Remove cluster labels:" "MBD3 MUTATED"          
clus
  MBD3 MUTATED MBD3 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
D34V11, continuous
[1] "Remove cluster labels:" "MBD3 MUTATED"          
clus
  MBD3 MUTATED MBD3 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MBD3 MUTATED    5  3  1  0
  MBD3 WILD-TYPE 75 32  3  2
D34V12, multiclass
    clus
vv   MBD3 MUTATED MBD3 WILD-TYPE
  R0            5             75
  R1            3             32
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MBD3 MUTATED       1                         1     7
  MBD3 WILD-TYPE     5                         4   107
D34V14, multiclass
                           clus
vv                          MBD3 MUTATED MBD3 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                cls
clus              0  1
  MBD3 MUTATED    0  6
  MBD3 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      0    6
  MBD3 WILD-TYPE    5   85
                        clus
vv                       MBD3 MUTATED MBD3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(35) Variable = WWTR1 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  WWTR1 MUTATED    4  8
  WWTR1 WILD-TYPE 59 54
  WWTR1 MUTATED WWTR1 WILD-TYPE 
             12             113 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              8              54 
$`WWTR1 MUTATED`
TCGA-3A-A9IB TCGA-3A-A9IZ TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-HV-A7OP TCGA-IB-7651 
        7.36        10.13        23.54         4.04        32.15        19.82 
TCGA-IB-A5SO TCGA-IB-AAUO TCGA-IB-AAUP TCGA-Q3-A5QY TCGA-US-A77G TCGA-XD-AAUI 
       12.00         7.86        14.17        13.68         0.39        12.03 

$`WWTR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
        7.50        12.53        15.55         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUQ 
        1.35         8.22        15.88         0.26         4.73         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 
       39.98        16.80        18.67        13.81        12.99        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  WWTR1 MUTATED WWTR1 WILD-TYPE 
           0.39            0.23 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          32.15           90.12 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
         12.015          15.550 
[1] "0.4 - 32.1 (12.0)" "0.2 - 90.1 (15.6)"
[1] "hr=" "2"  
D35V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WWTR1 MUTATED         0        0        0         0        12         0
  WWTR1 WILD-TYPE       1        3       12        19        70         4
                 vv
clus              STAGE IV
  WWTR1 MUTATED          0
  WWTR1 WILD-TYPE        3
D35V3, multiclass
           clus
vv          WWTR1 MUTATED WWTR1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB            12              70
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  WWTR1 MUTATED    0  1    11
  WWTR1 WILD-TYPE  5 16    91
D35V4, multiclass
       clus
vv      WWTR1 MUTATED WWTR1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                 cls
clus               0  1
  WWTR1 MUTATED    0 12
  WWTR1 WILD-TYPE 35 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      0   12
  WWTR1 WILD-TYPE   35   77
   clus
vv  WWTR1 MUTATED WWTR1 WILD-TYPE
  0             0              35
  1            12              77
[1] 2 2
[1] FALSE
D35V6, binary
                 cls
clus               0  1
  WWTR1 MUTATED    5  0
  WWTR1 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      5    0
  WWTR1 WILD-TYPE   52    3
   clus
vv  WWTR1 MUTATED WWTR1 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus               0  1
  WWTR1 MUTATED    4  8
  WWTR1 WILD-TYPE 47 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      4    8
  WWTR1 WILD-TYPE   47   67
        clus
vv       WWTR1 MUTATED WWTR1 WILD-TYPE
  FEMALE             4              47
  MALE               8              67
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus               0  1
  WWTR1 MUTATED   11  1
  WWTR1 WILD-TYPE 77 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED     11    1
  WWTR1 WILD-TYPE   77   29
     clus
vv    WWTR1 MUTATED WWTR1 WILD-TYPE
  NO             11              77
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WWTR1 MUTATED                                    11
  WWTR1 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WWTR1 MUTATED                                       1
  WWTR1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WWTR1 MUTATED                                                  0
  WWTR1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  WWTR1 MUTATED                                     0
  WWTR1 WILD-TYPE                                   1
D35V9, multiclass
                                                  clus
vv                                                 WWTR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 WWTR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
[1] "Remove cluster labels:" "WWTR1 MUTATED"         
clus
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IX 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" "WWTR1 WILD-TYPE" 
     TCGA-YY-A8LH 
"WWTR1 WILD-TYPE" 
D35V11, continuous
                 vv
clus              R0 R1 R2 RX
  WWTR1 MUTATED    7  5  0  0
  WWTR1 WILD-TYPE 73 30  4  2
D35V12, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  R0             7              73
  R1             5              30
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WWTR1 MUTATED       1                         0    11
  WWTR1 WILD-TYPE     5                         5   103
D35V14, multiclass
                           clus
vv                          WWTR1 MUTATED WWTR1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                 cls
clus               0  1
  WWTR1 MUTATED    1  9
  WWTR1 WILD-TYPE  4 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      1    9
  WWTR1 WILD-TYPE    4   82
                        clus
vv                       WWTR1 MUTATED WWTR1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(36) Variable = FAM63B MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  FAM63B MUTATED    5  6
  FAM63B WILD-TYPE 58 56
  FAM63B MUTATED FAM63B WILD-TYPE 
              11              114 
  FAM63B MUTATED FAM63B WILD-TYPE 
               6               56 
$`FAM63B MUTATED`
TCGA-3A-A9IJ TCGA-2L-AAQA TCGA-2L-AAQI TCGA-FB-AAPS TCGA-HZ-8637 TCGA-IB-7651 
       60.95         4.70         3.39         7.50        17.00        19.82 
TCGA-IB-A6UG TCGA-IB-AAUP TCGA-LB-A9Q5 TCGA-XN-A8T3 TCGA-YB-A89D 
        1.35        14.17        10.29        31.27        11.51 

$`FAM63B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
       15.22         9.11        21.44        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        23.67        12.76        66.28        15.35 

  FAM63B MUTATED FAM63B WILD-TYPE 
            1.35             0.23 
  FAM63B MUTATED FAM63B WILD-TYPE 
           60.95            90.12 
  FAM63B MUTATED FAM63B WILD-TYPE 
          11.510           15.335 
[1] "1.4 - 61.0 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D36V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM63B MUTATED         0        0        2         0         9         0
  FAM63B WILD-TYPE       1        3       10        19        73         4
                  vv
clus               STAGE IV
  FAM63B MUTATED          0
  FAM63B WILD-TYPE        3
D36V3, multiclass
           clus
vv          FAM63B MUTATED FAM63B WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              9               73
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  FAM63B MUTATED    0  3     8
  FAM63B WILD-TYPE  5 14    94
D36V4, multiclass
       clus
vv      FAM63B MUTATED FAM63B WILD-TYPE
  T1                 0                5
  T2                 3               14
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                  cls
clus                0  1
  FAM63B MUTATED    2  9
  FAM63B WILD-TYPE 33 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      2    9
  FAM63B WILD-TYPE   33   80
   clus
vv  FAM63B MUTATED FAM63B WILD-TYPE
  0              2               33
  1              9               80
[1] 2 2
[1] FALSE
D36V6, binary
                  cls
clus                0  1
  FAM63B MUTATED    4  0
  FAM63B WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      4    0
  FAM63B WILD-TYPE   53    3
   clus
vv  FAM63B MUTATED FAM63B WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                0  1
  FAM63B MUTATED    4  7
  FAM63B WILD-TYPE 47 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      4    7
  FAM63B WILD-TYPE   47   68
        clus
vv       FAM63B MUTATED FAM63B WILD-TYPE
  FEMALE              4               47
  MALE                7               68
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                0  1
  FAM63B MUTATED    6  5
  FAM63B WILD-TYPE 82 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      6    5
  FAM63B WILD-TYPE   82   25
     clus
vv    FAM63B MUTATED FAM63B WILD-TYPE
  NO               6               82
  YES              5               25
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM63B MUTATED                                    10
  FAM63B WILD-TYPE                                  95
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM63B MUTATED                                       1
  FAM63B WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM63B MUTATED                                                  0
  FAM63B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM63B MUTATED                                     0
  FAM63B WILD-TYPE                                   1
D36V9, multiclass
                                                  clus
vv                                                 FAM63B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 FAM63B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
                  vv
clus               R0 R1 R2 RX
  FAM63B MUTATED    6  5  0  0
  FAM63B WILD-TYPE 74 30  4  2
D36V12, multiclass
    clus
vv   FAM63B MUTATED FAM63B WILD-TYPE
  R0              6               74
  R1              5               30
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM63B MUTATED       0                         0    11
  FAM63B WILD-TYPE     6                         5   103
D36V14, multiclass
                           clus
vv                          FAM63B MUTATED FAM63B WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 11              103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                  cls
clus                0  1
  FAM63B MUTATED    2  7
  FAM63B WILD-TYPE  3 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      2    7
  FAM63B WILD-TYPE    3   84
                        clus
vv                       FAM63B MUTATED FAM63B WILD-TYPE
  HISPANIC OR LATINO                  2                3
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(37) Variable = C14ORF43 MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  C14ORF43 MUTATED    6  7
  C14ORF43 WILD-TYPE 57 55
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                13                112 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 7                 55 
$`C14ORF43 MUTATED`
TCGA-F2-A44G TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
        7.66         2.17        23.97        21.44         4.70         3.39 
TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-A6UG TCGA-Q3-A5QY TCGA-US-A776 TCGA-YB-A89D 
       17.00        19.82         1.35        13.68        39.98        11.51 
TCGA-Z5-AAPL 
       15.35 

$`C14ORF43 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       16.37         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78         3.12        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        12.76        66.28 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              1.35               0.23 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             39.98              90.12 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             13.68              15.27 
[1] "1.4 - 40.0 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C14ORF43 MUTATED         0        0        0         3        10         0
  C14ORF43 WILD-TYPE       1        3       12        16        72         4
                    vv
clus                 STAGE IV
  C14ORF43 MUTATED          0
  C14ORF43 WILD-TYPE        3
D37V3, multiclass
           clus
vv          C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                3                 16
  STAGE IIB               10                 72
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C14ORF43 MUTATED    0  1    12
  C14ORF43 WILD-TYPE  5 16    90
D37V4, multiclass
       clus
vv      C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4               12                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                    cls
clus                  0  1
  C14ORF43 MUTATED    3 10
  C14ORF43 WILD-TYPE 32 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      3   10
  C14ORF43 WILD-TYPE   32   79
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0                3                 32
  1               10                 79
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  C14ORF43 MUTATED    8  0
  C14ORF43 WILD-TYPE 49  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      8    0
  C14ORF43 WILD-TYPE   49    3
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0                8                 49
  1                0                  3
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                  0  1
  C14ORF43 MUTATED    3 10
  C14ORF43 WILD-TYPE 48 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      3   10
  C14ORF43 WILD-TYPE   48   65
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE                3                 48
  MALE                 10                 65
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                  0  1
  C14ORF43 MUTATED   11  2
  C14ORF43 WILD-TYPE 77 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     11    2
  C14ORF43 WILD-TYPE   77   28
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                11                 77
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C14ORF43 MUTATED                                    10
  C14ORF43 WILD-TYPE                                  95
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C14ORF43 MUTATED                                       2
  C14ORF43 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C14ORF43 MUTATED                                                  1
  C14ORF43 WILD-TYPE                                                0
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C14ORF43 MUTATED                                     0
  C14ORF43 WILD-TYPE                                   1
D37V9, multiclass
                                                  clus
vv                                                 C14ORF43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C14ORF43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
                    vv
clus                 R0 R1 R2 RX
  C14ORF43 MUTATED    7  6  0  0
  C14ORF43 WILD-TYPE 73 29  4  2
D37V12, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0                7                 73
  R1                6                 29
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF43 MUTATED       0                         0    13
  C14ORF43 WILD-TYPE     6                         5   101
D37V14, multiclass
                           clus
vv                          C14ORF43 MUTATED C14ORF43 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   13                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                    cls
clus                  0  1
  C14ORF43 MUTATED    0  8
  C14ORF43 WILD-TYPE  5 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED      0    8
  C14ORF43 WILD-TYPE    5   83
                        clus
vv                       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                8                 83
[1] 2 2
[1] FALSE

Clustering(38) Variable = ERCC3 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2              0  1
  ERCC3 MUTATED    5  4
  ERCC3 WILD-TYPE 58 58
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              9             116 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              4              58 
$`ERCC3 MUTATED`
TCGA-2J-AABR TCGA-F2-7273 TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5SO 
       14.40        19.46        30.25        19.82        15.19        12.00 
TCGA-IB-A6UG TCGA-IB-AAUS TCGA-YB-A89D 
        1.35         7.40        11.51 

$`ERCC3 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        32.15        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       19.82        36.69        41.33        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ERCC3 MUTATED ERCC3 WILD-TYPE 
           1.35            0.23 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
          30.25           90.12 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
         14.400          15.335 
[1] "1.4 - 30.2 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D38V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ERCC3 MUTATED         0        0        0         1         7         1
  ERCC3 WILD-TYPE       1        3       12        18        75         3
                 vv
clus              STAGE IV
  ERCC3 MUTATED          0
  ERCC3 WILD-TYPE        3
D38V3, multiclass
           clus
vv          ERCC3 MUTATED ERCC3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ERCC3 MUTATED    0  0     9
  ERCC3 WILD-TYPE  5 17    93
D38V4, multiclass
       clus
vv      ERCC3 MUTATED ERCC3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                 cls
clus               0  1
  ERCC3 MUTATED    1  8
  ERCC3 WILD-TYPE 34 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      1    8
  ERCC3 WILD-TYPE   34   81
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0             1              34
  1             8              81
[1] 2 2
[1] FALSE
D38V6, binary
                 cls
clus               0  1
  ERCC3 MUTATED    7  0
  ERCC3 WILD-TYPE 50  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      7    0
  ERCC3 WILD-TYPE   50    3
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0             7              50
  1             0               3
[1] 2 2
[1] FALSE
D38V7, binary
                 cls
clus               0  1
  ERCC3 MUTATED    4  5
  ERCC3 WILD-TYPE 47 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      4    5
  ERCC3 WILD-TYPE   47   70
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  FEMALE             4              47
  MALE               5              70
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus               0  1
  ERCC3 MUTATED    7  2
  ERCC3 WILD-TYPE 81 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      7    2
  ERCC3 WILD-TYPE   81   28
     clus
vv    ERCC3 MUTATED ERCC3 WILD-TYPE
  NO              7              81
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ERCC3 MUTATED                                     9
  ERCC3 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ERCC3 MUTATED                                       0
  ERCC3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ERCC3 MUTATED                                                  0
  ERCC3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ERCC3 MUTATED                                     0
  ERCC3 WILD-TYPE                                   1
D38V9, multiclass
                                                  clus
vv                                                 ERCC3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ERCC3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
                 vv
clus              R0 R1 R2 RX
  ERCC3 MUTATED    4  4  1  0
  ERCC3 WILD-TYPE 76 31  3  2
D38V12, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  R0             4              76
  R1             4              31
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERCC3 MUTATED       1                         1     7
  ERCC3 WILD-TYPE     5                         4   107
D38V14, multiclass
                           clus
vv                          ERCC3 MUTATED ERCC3 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                 cls
clus               0  1
  ERCC3 MUTATED    0  6
  ERCC3 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      0    6
  ERCC3 WILD-TYPE    5   85
                        clus
vv                       ERCC3 MUTATED ERCC3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(39) Variable = MYH10 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2              0  1
  MYH10 MUTATED    4  9
  MYH10 WILD-TYPE 59 53
  MYH10 MUTATED MYH10 WILD-TYPE 
             13             112 
  MYH10 MUTATED MYH10 WILD-TYPE 
              9              53 
$`MYH10 MUTATED`
TCGA-F2-A44G TCGA-2J-AAB4 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IV TCGA-3A-A9IZ 
        7.66        23.97        20.84         7.36        36.26        10.13 
TCGA-F2-7273 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-US-A77G 
       19.46        10.85        19.82         6.02        11.11         0.39 
TCGA-US-A77J 
       18.67 

$`MYH10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
        9.60        45.47        43.50        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        32.81        15.06        34.09        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUS 
       15.88         0.26         4.73         7.86        14.17         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       16.80        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MYH10 MUTATED MYH10 WILD-TYPE 
           0.39            0.23 
  MYH10 MUTATED MYH10 WILD-TYPE 
          36.26           90.12 
  MYH10 MUTATED MYH10 WILD-TYPE 
          11.11           15.27 
[1] "0.4 - 36.3 (11.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.7"
D39V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MYH10 MUTATED         0        0        1         1        12         0
  MYH10 WILD-TYPE       1        3       11        18        70         4
                 vv
clus              STAGE IV
  MYH10 MUTATED          0
  MYH10 WILD-TYPE        3
D39V3, multiclass
           clus
vv          MYH10 MUTATED MYH10 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB            12              70
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MYH10 MUTATED    0  2    12
  MYH10 WILD-TYPE  5 15    90
D39V4, multiclass
       clus
vv      MYH10 MUTATED MYH10 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4            12              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                 cls
clus               0  1
  MYH10 MUTATED    2 12
  MYH10 WILD-TYPE 33 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      2   12
  MYH10 WILD-TYPE   33   77
   clus
vv  MYH10 MUTATED MYH10 WILD-TYPE
  0             2              33
  1            12              77
[1] 2 2
[1] FALSE
D39V6, binary
                 cls
clus               0  1
  MYH10 MUTATED    6  0
  MYH10 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      6    0
  MYH10 WILD-TYPE   51    3
   clus
vv  MYH10 MUTATED MYH10 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus               0  1
  MYH10 MUTATED    5  9
  MYH10 WILD-TYPE 46 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      5    9
  MYH10 WILD-TYPE   46   66
        clus
vv       MYH10 MUTATED MYH10 WILD-TYPE
  FEMALE             5              46
  MALE               9              66
[1] 2 2
[1] FALSE
D39V8, binary
                 cls
clus               0  1
  MYH10 MUTATED    9  3
  MYH10 WILD-TYPE 79 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      9    3
  MYH10 WILD-TYPE   79   27
     clus
vv    MYH10 MUTATED MYH10 WILD-TYPE
  NO              9              79
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MYH10 MUTATED                                    11
  MYH10 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MYH10 MUTATED                                       3
  MYH10 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MYH10 MUTATED                                                  0
  MYH10 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MYH10 MUTATED                                     0
  MYH10 WILD-TYPE                                   1
D39V9, multiclass
                                                  clus
vv                                                 MYH10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MYH10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
                 vv
clus              R0 R1 R2 RX
  MYH10 MUTATED    9  5  0  0
  MYH10 WILD-TYPE 71 30  4  2
D39V12, multiclass
    clus
vv   MYH10 MUTATED MYH10 WILD-TYPE
  R0             9              71
  R1             5              30
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYH10 MUTATED       0                         1    13
  MYH10 WILD-TYPE     6                         4   101
D39V14, multiclass
                           clus
vv                          MYH10 MUTATED MYH10 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                13             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                 cls
clus               0  1
  MYH10 MUTATED    1 12
  MYH10 WILD-TYPE  4 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      1   12
  MYH10 WILD-TYPE    4   79
                        clus
vv                       MYH10 MUTATED MYH10 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            12              79
[1] 2 2
[1] FALSE

Clustering(40) Variable = ZMYM5 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2              0  1
  ZMYM5 MUTATED    8  5
  ZMYM5 WILD-TYPE 55 57
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
             13             112 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              5              57 
$`ZMYM5 MUTATED`
TCGA-XD-AAUL TCGA-2J-AAB6 TCGA-2J-AABH TCGA-2L-AAQM TCGA-3A-A9J0 TCGA-FB-AAPZ 
       16.37         9.63        42.31        45.47        24.43        23.54 
TCGA-H8-A6C1 TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A49I TCGA-IB-7651 TCGA-US-A776 
       22.06        17.49        20.19        10.13        19.82        39.98 
TCGA-YB-A89D 
       11.51 

$`ZMYM5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14         2.17        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.22        22.72        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 
       12.33        15.95        37.15         7.50        12.53        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
       13.68         3.12        15.32         9.40         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
           9.63            0.23 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
          45.47           90.12 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
         20.190          14.765 
[1] "9.6 - 45.5 (20.2)" "0.2 - 90.1 (14.8)"
[1] "hr=" "1.9"
D40V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZMYM5 MUTATED         0        0        0         5         8         0
  ZMYM5 WILD-TYPE       1        3       12        14        74         4
                 vv
clus              STAGE IV
  ZMYM5 MUTATED          0
  ZMYM5 WILD-TYPE        3
D40V3, multiclass
           clus
vv          ZMYM5 MUTATED ZMYM5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             5              14
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZMYM5 MUTATED    0  2    11
  ZMYM5 WILD-TYPE  5 15    91
D40V4, multiclass
       clus
vv      ZMYM5 MUTATED ZMYM5 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    5  8
  ZMYM5 WILD-TYPE 30 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      5    8
  ZMYM5 WILD-TYPE   30   81
   clus
vv  ZMYM5 MUTATED ZMYM5 WILD-TYPE
  0             5              30
  1             8              81
[1] 2 2
[1] FALSE
D40V6, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    3  0
  ZMYM5 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      3    0
  ZMYM5 WILD-TYPE   54    3
   clus
vv  ZMYM5 MUTATED ZMYM5 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D40V7, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    2 11
  ZMYM5 WILD-TYPE 49 64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      2   11
  ZMYM5 WILD-TYPE   49   64
        clus
vv       ZMYM5 MUTATED ZMYM5 WILD-TYPE
  FEMALE             2              49
  MALE              11              64
[1] 2 2
[1] FALSE
D40V8, binary
                 cls
clus               0  1
  ZMYM5 MUTATED   11  2
  ZMYM5 WILD-TYPE 77 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED     11    2
  ZMYM5 WILD-TYPE   77   28
     clus
vv    ZMYM5 MUTATED ZMYM5 WILD-TYPE
  NO             11              77
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYM5 MUTATED                                     9
  ZMYM5 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYM5 MUTATED                                       3
  ZMYM5 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYM5 MUTATED                                                  1
  ZMYM5 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZMYM5 MUTATED                                     0
  ZMYM5 WILD-TYPE                                   1
D40V9, multiclass
                                                  clus
vv                                                 ZMYM5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZMYM5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
                 vv
clus              R0 R1 R2 RX
  ZMYM5 MUTATED   10  2  1  0
  ZMYM5 WILD-TYPE 70 33  3  2
D40V12, multiclass
    clus
vv   ZMYM5 MUTATED ZMYM5 WILD-TYPE
  R0            10              70
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM5 MUTATED       1                         0    12
  ZMYM5 WILD-TYPE     5                         5   102
D40V14, multiclass
                           clus
vv                          ZMYM5 MUTATED ZMYM5 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                12             102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    0  9
  ZMYM5 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      0    9
  ZMYM5 WILD-TYPE    5   82
                        clus
vv                       ZMYM5 MUTATED ZMYM5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(41) Variable = CDCA8 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  CDCA8 MUTATED    8  1
  CDCA8 WILD-TYPE 55 61
  CDCA8 MUTATED CDCA8 WILD-TYPE 
              9             116 
  CDCA8 MUTATED CDCA8 WILD-TYPE 
              1              61 
$`CDCA8 MUTATED`
TCGA-HZ-A77Q TCGA-XD-AAUL TCGA-2J-AABE TCGA-3E-AAAY TCGA-IB-7651 TCGA-IB-A6UF 
        1.08        16.37        22.22        75.12        19.82        21.90 
TCGA-IB-A7M4 TCGA-US-A776 TCGA-YB-A89D 
       15.88        39.98        11.51 

$`CDCA8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88         1.35         8.22         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CDCA8 MUTATED CDCA8 WILD-TYPE 
           1.08            0.23 
  CDCA8 MUTATED CDCA8 WILD-TYPE 
          75.12           90.12 
  CDCA8 MUTATED CDCA8 WILD-TYPE 
          19.82           15.09 
[1] "1.1 - 75.1 (19.8)" "0.2 - 90.1 (15.1)"
[1] "hr=" "6.4"
D41V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDCA8 MUTATED         0        0        0         3         6         0
  CDCA8 WILD-TYPE       1        3       12        16        76         4
                 vv
clus              STAGE IV
  CDCA8 MUTATED          0
  CDCA8 WILD-TYPE        3
D41V3, multiclass
           clus
vv          CDCA8 MUTATED CDCA8 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CDCA8 MUTATED    0  0     9
  CDCA8 WILD-TYPE  5 17    93
D41V4, multiclass
       clus
vv      CDCA8 MUTATED CDCA8 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                 cls
clus               0  1
  CDCA8 MUTATED    3  6
  CDCA8 WILD-TYPE 32 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDCA8 MUTATED      3    6
  CDCA8 WILD-TYPE   32   83
   clus
vv  CDCA8 MUTATED CDCA8 WILD-TYPE
  0             3              32
  1             6              83
[1] 2 2
[1] FALSE
D41V6, binary
                 cls
clus               0  1
  CDCA8 MUTATED    3  0
  CDCA8 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDCA8 MUTATED      3    0
  CDCA8 WILD-TYPE   54    3
   clus
vv  CDCA8 MUTATED CDCA8 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus               0  1
  CDCA8 MUTATED    2  7
  CDCA8 WILD-TYPE 49 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDCA8 MUTATED      2    7
  CDCA8 WILD-TYPE   49   68
        clus
vv       CDCA8 MUTATED CDCA8 WILD-TYPE
  FEMALE             2              49
  MALE               7              68
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus               0  1
  CDCA8 MUTATED    6  2
  CDCA8 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDCA8 MUTATED      6    2
  CDCA8 WILD-TYPE   82   28
     clus
vv    CDCA8 MUTATED CDCA8 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDCA8 MUTATED                                     7
  CDCA8 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDCA8 MUTATED                                       1
  CDCA8 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDCA8 MUTATED                                                  1
  CDCA8 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDCA8 MUTATED                                     0
  CDCA8 WILD-TYPE                                   1
D41V9, multiclass
                                                  clus
vv                                                 CDCA8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CDCA8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
                 vv
clus              R0 R1 R2 RX
  CDCA8 MUTATED    7  1  0  0
  CDCA8 WILD-TYPE 73 34  4  2
D41V12, multiclass
    clus
vv   CDCA8 MUTATED CDCA8 WILD-TYPE
  R0             7              73
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDCA8 MUTATED       0                         0     9
  CDCA8 WILD-TYPE     6                         5   105
D41V14, multiclass
                           clus
vv                          CDCA8 MUTATED CDCA8 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                 cls
clus               0  1
  CDCA8 MUTATED    0  8
  CDCA8 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDCA8 MUTATED      0    8
  CDCA8 WILD-TYPE    5   83
                        clus
vv                       CDCA8 MUTATED CDCA8 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(42) Variable = PAK1 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2             0  1
  PAK1 MUTATED    4  7
  PAK1 WILD-TYPE 59 55
  PAK1 MUTATED PAK1 WILD-TYPE 
            11            114 
  PAK1 MUTATED PAK1 WILD-TYPE 
             7             55 
$`PAK1 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABU TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       20.61        19.96         9.11        22.49         3.39        12.95 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-FB-AAQ0 TCGA-HZ-A9TJ 
       50.70        32.81        24.43        15.55        19.82 

$`PAK1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
       21.44         4.70         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IU TCGA-3A-A9IV 
        7.36        24.26        33.57        63.85        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  PAK1 MUTATED PAK1 WILD-TYPE 
          3.39           0.23 
  PAK1 MUTATED PAK1 WILD-TYPE 
         50.70          90.12 
  PAK1 MUTATED PAK1 WILD-TYPE 
         19.96          15.09 
[1] "3.4 - 50.7 (20.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D42V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PAK1 MUTATED         0        0        2         1         6         1
  PAK1 WILD-TYPE       1        3       10        18        76         3
                vv
clus             STAGE IV
  PAK1 MUTATED          1
  PAK1 WILD-TYPE        2
D42V3, multiclass
           clus
vv          PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            1             18
  STAGE IIB            6             76
  STAGE III            1              3
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PAK1 MUTATED    0  2     9
  PAK1 WILD-TYPE  5 15    93
D42V4, multiclass
       clus
vv      PAK1 MUTATED PAK1 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            9             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                cls
clus              0  1
  PAK1 MUTATED    5  6
  PAK1 WILD-TYPE 30 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      5    6
  PAK1 WILD-TYPE   30   83
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0            5             30
  1            6             83
[1] 2 2
[1] FALSE
D42V6, binary
                cls
clus              0  1
  PAK1 MUTATED    4  1
  PAK1 WILD-TYPE 53  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      4    1
  PAK1 WILD-TYPE   53    2
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0            4             53
  1            1              2
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus              0  1
  PAK1 MUTATED    3  8
  PAK1 WILD-TYPE 48 67
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      3    8
  PAK1 WILD-TYPE   48   67
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            3             48
  MALE              8             67
[1] 2 2
[1] FALSE
D42V8, binary
                cls
clus              0  1
  PAK1 MUTATED   10  1
  PAK1 WILD-TYPE 78 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED     10    1
  PAK1 WILD-TYPE   78   29
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO            10             78
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PAK1 MUTATED                                     8
  PAK1 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PAK1 MUTATED                                       3
  PAK1 WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PAK1 MUTATED                                                  0
  PAK1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PAK1 MUTATED                                     0
  PAK1 WILD-TYPE                                   1
D42V9, multiclass
                                                  clus
vv                                                 PAK1 MUTATED PAK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
[1] "Remove cluster labels:" "PAK1 MUTATED"          
clus
  PAK1 MUTATED PAK1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-YY-A8LH 
"PAK1 WILD-TYPE" 
D42V11, continuous
[1] "Remove cluster labels:" "PAK1 MUTATED"          
clus
  PAK1 MUTATED PAK1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IX 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" "PAK1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PAK1 MUTATED    8  3  0  0
  PAK1 WILD-TYPE 72 32  4  2
D42V12, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            8             72
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAK1 MUTATED       0                         0    11
  PAK1 WILD-TYPE     6                         5   103
D42V14, multiclass
                           clus
vv                          PAK1 MUTATED PAK1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               11            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                cls
clus              0  1
  PAK1 MUTATED    0  5
  PAK1 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      0    5
  PAK1 WILD-TYPE    5   86
                        clus
vv                       PAK1 MUTATED PAK1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(43) Variable = WRN MUTATION ANALYSIS
D43V1, survival
               sevent
clus2            0  1
  WRN MUTATED    8  7
  WRN WILD-TYPE 55 55
  WRN MUTATED WRN WILD-TYPE 
           15           110 
  WRN MUTATED WRN WILD-TYPE 
            7            55 
$`WRN MUTATED`
TCGA-3A-A9IJ TCGA-LB-A7SX TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       60.95        12.92         2.17         2.63        20.61        19.96 
TCGA-3A-A9IB TCGA-3A-A9IS TCGA-FB-AAQ1 TCGA-HV-A7OL TCGA-IB-AAUR TCGA-US-A77G 
        7.36        32.81         4.04         8.28        11.11         0.39 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

$`WRN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       23.97         9.63        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17         6.02         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-Z5-AAPL 
       23.67        15.35 

  WRN MUTATED WRN WILD-TYPE 
         0.39          0.23 
  WRN MUTATED WRN WILD-TYPE 
        66.28         90.12 
  WRN MUTATED WRN WILD-TYPE 
        11.51         15.45 
[1] "0.4 - 66.3 (11.5)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.2"
D43V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WRN MUTATED         0        0        2         1        11         1
  WRN WILD-TYPE       1        3       10        18        71         3
               vv
clus            STAGE IV
  WRN MUTATED          0
  WRN WILD-TYPE        3
D43V3, multiclass
           clus
vv          WRN MUTATED WRN WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            2            10
  STAGE IIA           1            18
  STAGE IIB          11            71
  STAGE III           1             3
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  WRN MUTATED    0  2    13
  WRN WILD-TYPE  5 15    89
D43V4, multiclass
       clus
vv      WRN MUTATED WRN WILD-TYPE
  T1              0             5
  T2              2            15
  T3+T4          13            89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
               cls
clus             0  1
  WRN MUTATED    3 12
  WRN WILD-TYPE 32 77
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      3   12
  WRN WILD-TYPE   32   77
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           3            32
  1          12            77
[1] 2 2
[1] FALSE
D43V6, binary
               cls
clus             0  1
  WRN MUTATED    5  0
  WRN WILD-TYPE 52  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      5    0
  WRN WILD-TYPE   52    3
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           5            52
  1           0             3
[1] 2 2
[1] FALSE
D43V7, binary
               cls
clus             0  1
  WRN MUTATED    5 10
  WRN WILD-TYPE 46 65
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      5   10
  WRN WILD-TYPE   46   65
        clus
vv       WRN MUTATED WRN WILD-TYPE
  FEMALE           5            46
  MALE            10            65
[1] 2 2
[1] FALSE
D43V8, binary
               cls
clus             0  1
  WRN MUTATED   10  4
  WRN WILD-TYPE 78 26
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED     10    4
  WRN WILD-TYPE   78   26
     clus
vv    WRN MUTATED WRN WILD-TYPE
  NO           10            78
  YES           4            26
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WRN MUTATED                                    11
  WRN WILD-TYPE                                  94
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WRN MUTATED                                       3
  WRN WILD-TYPE                                    15
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WRN MUTATED                                                  0
  WRN WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  WRN MUTATED                                     0
  WRN WILD-TYPE                                   1
D43V9, multiclass
                                                  clus
vv                                                 WRN MUTATED WRN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       11            94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      3            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
               vv
clus            R0 R1 R2 RX
  WRN MUTATED    8  5  1  0
  WRN WILD-TYPE 72 30  3  2
D43V12, multiclass
    clus
vv   WRN MUTATED WRN WILD-TYPE
  R0           8            72
  R1           5            30
  R2           1             3
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WRN MUTATED       1                         1    13
  WRN WILD-TYPE     5                         4   101
D43V14, multiclass
                           clus
vv                          WRN MUTATED WRN WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                              13           101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
               cls
clus             0  1
  WRN MUTATED    0 10
  WRN WILD-TYPE  5 81
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0   10
  WRN WILD-TYPE    5   81
                        clus
vv                       WRN MUTATED WRN WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          10            81
[1] 2 2
[1] FALSE

Clustering(44) Variable = CLOCK MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  CLOCK MUTATED    9  3
  CLOCK WILD-TYPE 54 59
  CLOCK MUTATED CLOCK WILD-TYPE 
             12             113 
  CLOCK MUTATED CLOCK WILD-TYPE 
              3              59 
$`CLOCK MUTATED`
TCGA-3A-A9IO TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-AAPS TCGA-FZ-5920 TCGA-H8-A6C1 
       63.85        36.26         3.12         7.50         2.01        22.06 
TCGA-HV-A7OP TCGA-IB-7651 TCGA-RL-AAAS TCGA-US-A776 TCGA-YH-A8SY TCGA-YY-A8LH 
       32.15        19.82         0.30        39.98        12.76        66.28 

$`CLOCK WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-AA8V 
        5.10        36.20        20.35        17.79         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        9.40        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        15.35 

  CLOCK MUTATED CLOCK WILD-TYPE 
           0.30            0.23 
  CLOCK MUTATED CLOCK WILD-TYPE 
          66.28           90.12 
  CLOCK MUTATED CLOCK WILD-TYPE 
          20.94           15.19 
[1] "0.3 - 66.3 (20.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.5"
D44V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CLOCK MUTATED         0        0        2         2         6         1
  CLOCK WILD-TYPE       1        3       10        17        76         3
                 vv
clus              STAGE IV
  CLOCK MUTATED          0
  CLOCK WILD-TYPE        3
D44V3, multiclass
           clus
vv          CLOCK MUTATED CLOCK WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             2              17
  STAGE IIB             6              76
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CLOCK MUTATED    0  3     8
  CLOCK WILD-TYPE  5 14    94
D44V4, multiclass
       clus
vv      CLOCK MUTATED CLOCK WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                 cls
clus               0  1
  CLOCK MUTATED    4  7
  CLOCK WILD-TYPE 31 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLOCK MUTATED      4    7
  CLOCK WILD-TYPE   31   82
   clus
vv  CLOCK MUTATED CLOCK WILD-TYPE
  0             4              31
  1             7              82
[1] 2 2
[1] FALSE
D44V6, binary
                 cls
clus               0  1
  CLOCK MUTATED    5  0
  CLOCK WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLOCK MUTATED      5    0
  CLOCK WILD-TYPE   52    3
   clus
vv  CLOCK MUTATED CLOCK WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus               0  1
  CLOCK MUTATED    6  6
  CLOCK WILD-TYPE 45 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLOCK MUTATED      6    6
  CLOCK WILD-TYPE   45   69
        clus
vv       CLOCK MUTATED CLOCK WILD-TYPE
  FEMALE             6              45
  MALE               6              69
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus               0  1
  CLOCK MUTATED    8  4
  CLOCK WILD-TYPE 80 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLOCK MUTATED      8    4
  CLOCK WILD-TYPE   80   26
     clus
vv    CLOCK MUTATED CLOCK WILD-TYPE
  NO              8              80
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CLOCK MUTATED                                     6
  CLOCK WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CLOCK MUTATED                                       4
  CLOCK WILD-TYPE                                    14
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CLOCK MUTATED                                                  1
  CLOCK WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CLOCK MUTATED                                     0
  CLOCK WILD-TYPE                                   1
D44V9, multiclass
                                                  clus
vv                                                 CLOCK MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CLOCK WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
D44V11, continuous
                 vv
clus              R0 R1 R2 RX
  CLOCK MUTATED   10  1  0  0
  CLOCK WILD-TYPE 70 34  4  2
D44V12, multiclass
    clus
vv   CLOCK MUTATED CLOCK WILD-TYPE
  R0            10              70
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLOCK MUTATED       1                         1    10
  CLOCK WILD-TYPE     5                         4   104
D44V14, multiclass
                           clus
vv                          CLOCK MUTATED CLOCK WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                 cls
clus               0  1
  CLOCK MUTATED    0 10
  CLOCK WILD-TYPE  5 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLOCK MUTATED      0   10
  CLOCK WILD-TYPE    5   81
                        clus
vv                       CLOCK MUTATED CLOCK WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            10              81
[1] 2 2
[1] FALSE

Clustering(45) Variable = TMEM175 MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  TMEM175 MUTATED    8  5
  TMEM175 WILD-TYPE 55 57
  TMEM175 MUTATED TMEM175 WILD-TYPE 
               13               112 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                5                57 
$`TMEM175 MUTATED`
TCGA-HZ-A77Q TCGA-XD-AAUL TCGA-2J-AABE TCGA-2J-AABV TCGA-2L-AAQE TCGA-3E-AAAZ 
        1.08        16.37        22.22        21.44        22.49        71.74 
TCGA-FB-AAQ1 TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A6UF TCGA-RB-AA9M 
        4.04        30.25        19.82        41.33        21.90         9.40 
TCGA-US-A776 
       39.98 

$`TMEM175 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       75.12        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        32.15        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G 
       13.68         3.12        15.32         0.30        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  TMEM175 MUTATED TMEM175 WILD-TYPE 
             1.08              0.23 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
            71.74             90.12 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
           21.900            14.765 
[1] "1.1 - 71.7 (21.9)" "0.2 - 90.1 (14.8)"
[1] "hr=" "1.9"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM175 MUTATED         0        0        0         4         9         0
  TMEM175 WILD-TYPE       1        3       12        15        73         4
                   vv
clus                STAGE IV
  TMEM175 MUTATED          0
  TMEM175 WILD-TYPE        3
D45V3, multiclass
           clus
vv          TMEM175 MUTATED TMEM175 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               4                15
  STAGE IIB               9                73
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TMEM175 MUTATED    1  0    12
  TMEM175 WILD-TYPE  4 17    90
D45V4, multiclass
       clus
vv      TMEM175 MUTATED TMEM175 WILD-TYPE
  T1                  1                 4
  T2                  0                17
  T3+T4              12                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    4  9
  TMEM175 WILD-TYPE 31 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      4    9
  TMEM175 WILD-TYPE   31   80
   clus
vv  TMEM175 MUTATED TMEM175 WILD-TYPE
  0               4                31
  1               9                80
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    6  0
  TMEM175 WILD-TYPE 51  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      6    0
  TMEM175 WILD-TYPE   51    3
   clus
vv  TMEM175 MUTATED TMEM175 WILD-TYPE
  0               6                51
  1               0                 3
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    3 10
  TMEM175 WILD-TYPE 48 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      3   10
  TMEM175 WILD-TYPE   48   65
        clus
vv       TMEM175 MUTATED TMEM175 WILD-TYPE
  FEMALE               3                48
  MALE                10                65
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    9  2
  TMEM175 WILD-TYPE 79 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      9    2
  TMEM175 WILD-TYPE   79   28
     clus
vv    TMEM175 MUTATED TMEM175 WILD-TYPE
  NO                9                79
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM175 MUTATED                                    11
  TMEM175 WILD-TYPE                                  94
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM175 MUTATED                                       1
  TMEM175 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM175 MUTATED                                                  1
  TMEM175 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM175 MUTATED                                     0
  TMEM175 WILD-TYPE                                   1
D45V9, multiclass
                                                  clus
vv                                                 TMEM175 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TMEM175 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
D45V11, continuous
                   vv
clus                R0 R1 R2 RX
  TMEM175 MUTATED    8  3  1  0
  TMEM175 WILD-TYPE 72 32  3  2
D45V12, multiclass
    clus
vv   TMEM175 MUTATED TMEM175 WILD-TYPE
  R0               8                72
  R1               3                32
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM175 MUTATED       1                         0    12
  TMEM175 WILD-TYPE     5                         5   102
D45V14, multiclass
                           clus
vv                          TMEM175 MUTATED TMEM175 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  12               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    1  8
  TMEM175 WILD-TYPE  4 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      1    8
  TMEM175 WILD-TYPE    4   83
                        clus
vv                       TMEM175 MUTATED TMEM175 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               8                83
[1] 2 2
[1] FALSE

Clustering(46) Variable = THBS4 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2              0  1
  THBS4 MUTATED    9  7
  THBS4 WILD-TYPE 54 55
  THBS4 MUTATED THBS4 WILD-TYPE 
             16             109 
  THBS4 MUTATED THBS4 WILD-TYPE 
              7              55 
$`THBS4 MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB8 TCGA-2J-AABF TCGA-2J-AABP TCGA-3A-A9I7 TCGA-FB-AAQ1 
       17.26         2.63        22.72        15.22        43.50         4.04 
TCGA-FB-AAQ3 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ 
        1.02        19.82        41.33        15.19        15.85         7.20 
TCGA-IB-AAUM TCGA-OE-A75W TCGA-US-A776 TCGA-XD-AAUI 
        0.26         8.78        39.98        12.03 

$`THBS4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.22        42.31        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
       15.55         5.03        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-A5SO TCGA-IB-A5ST 
       10.85         0.23        19.82        36.69        12.00        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22        15.88         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  THBS4 MUTATED THBS4 WILD-TYPE 
           0.26            0.23 
  THBS4 MUTATED THBS4 WILD-TYPE 
          43.50           90.12 
  THBS4 MUTATED THBS4 WILD-TYPE 
         15.205          15.320 
[1] "0.3 - 43.5 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D46V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  THBS4 MUTATED         0        0        1         3        11         1
  THBS4 WILD-TYPE       1        3       11        16        71         3
                 vv
clus              STAGE IV
  THBS4 MUTATED          0
  THBS4 WILD-TYPE        3
D46V3, multiclass
           clus
vv          THBS4 MUTATED THBS4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             3              16
  STAGE IIB            11              71
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  THBS4 MUTATED    0  2    14
  THBS4 WILD-TYPE  5 15    88
D46V4, multiclass
       clus
vv      THBS4 MUTATED THBS4 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4            14              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                 cls
clus               0  1
  THBS4 MUTATED    4 12
  THBS4 WILD-TYPE 31 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      4   12
  THBS4 WILD-TYPE   31   77
   clus
vv  THBS4 MUTATED THBS4 WILD-TYPE
  0             4              31
  1            12              77
[1] 2 2
[1] FALSE
D46V6, binary
                 cls
clus               0  1
  THBS4 MUTATED   10  0
  THBS4 WILD-TYPE 47  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED     10    0
  THBS4 WILD-TYPE   47    3
   clus
vv  THBS4 MUTATED THBS4 WILD-TYPE
  0            10              47
  1             0               3
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus               0  1
  THBS4 MUTATED    8  8
  THBS4 WILD-TYPE 43 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      8    8
  THBS4 WILD-TYPE   43   67
        clus
vv       THBS4 MUTATED THBS4 WILD-TYPE
  FEMALE             8              43
  MALE               8              67
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus               0  1
  THBS4 MUTATED   11  4
  THBS4 WILD-TYPE 77 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED     11    4
  THBS4 WILD-TYPE   77   26
     clus
vv    THBS4 MUTATED THBS4 WILD-TYPE
  NO             11              77
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  THBS4 MUTATED                                    14
  THBS4 WILD-TYPE                                  91
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  THBS4 MUTATED                                       0
  THBS4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  THBS4 MUTATED                                                  1
  THBS4 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  THBS4 MUTATED                                     1
  THBS4 WILD-TYPE                                   0
D46V9, multiclass
                                                  clus
vv                                                 THBS4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 THBS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           91
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
D46V11, continuous
                 vv
clus              R0 R1 R2 RX
  THBS4 MUTATED    9  7  0  0
  THBS4 WILD-TYPE 71 28  4  2
D46V12, multiclass
    clus
vv   THBS4 MUTATED THBS4 WILD-TYPE
  R0             9              71
  R1             7              28
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THBS4 MUTATED       0                         1    15
  THBS4 WILD-TYPE     6                         4    99
D46V14, multiclass
                           clus
vv                          THBS4 MUTATED THBS4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                15              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                 cls
clus               0  1
  THBS4 MUTATED    0 12
  THBS4 WILD-TYPE  5 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      0   12
  THBS4 WILD-TYPE    5   79
                        clus
vv                       THBS4 MUTATED THBS4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            12              79
[1] 2 2
[1] FALSE

Clustering(47) Variable = TMED10 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2               0  1
  TMED10 MUTATED    3  5
  TMED10 WILD-TYPE 60 57
  TMED10 MUTATED TMED10 WILD-TYPE 
               8              117 
  TMED10 MUTATED TMED10 WILD-TYPE 
               5               57 
$`TMED10 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IC TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3E-AAAY TCGA-HZ-A77O 
       22.49        24.26        15.06        34.09        75.12         5.26 
TCGA-IB-7651 TCGA-RB-AA9M 
       19.82         9.40 

$`TMED10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IZ 
       33.57        63.85        50.70        32.81        36.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       24.43        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TMED10 MUTATED TMED10 WILD-TYPE 
            5.26             0.23 
  TMED10 MUTATED TMED10 WILD-TYPE 
           75.12            90.12 
  TMED10 MUTATED TMED10 WILD-TYPE 
          21.155           15.190 
[1] "5.3 - 75.1 (21.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D47V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMED10 MUTATED         0        1        0         0         7         0
  TMED10 WILD-TYPE       1        2       12        19        75         4
                  vv
clus               STAGE IV
  TMED10 MUTATED          0
  TMED10 WILD-TYPE        3
D47V3, multiclass
           clus
vv          TMED10 MUTATED TMED10 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TMED10 MUTATED    2  1     5
  TMED10 WILD-TYPE  3 16    97
D47V4, multiclass
       clus
vv      TMED10 MUTATED TMED10 WILD-TYPE
  T1                 2                3
  T2                 1               16
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                  cls
clus                0  1
  TMED10 MUTATED    1  7
  TMED10 WILD-TYPE 34 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMED10 MUTATED      1    7
  TMED10 WILD-TYPE   34   82
   clus
vv  TMED10 MUTATED TMED10 WILD-TYPE
  0              1               34
  1              7               82
[1] 2 2
[1] FALSE
D47V6, binary
                  cls
clus                0  1
  TMED10 MUTATED    2  0
  TMED10 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMED10 MUTATED      2    0
  TMED10 WILD-TYPE   55    3
   clus
vv  TMED10 MUTATED TMED10 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D47V7, binary
                  cls
clus                0  1
  TMED10 MUTATED    3  5
  TMED10 WILD-TYPE 48 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMED10 MUTATED      3    5
  TMED10 WILD-TYPE   48   70
        clus
vv       TMED10 MUTATED TMED10 WILD-TYPE
  FEMALE              3               48
  MALE                5               70
[1] 2 2
[1] FALSE
D47V8, binary
                  cls
clus                0  1
  TMED10 MUTATED    5  3
  TMED10 WILD-TYPE 83 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMED10 MUTATED      5    3
  TMED10 WILD-TYPE   83   27
     clus
vv    TMED10 MUTATED TMED10 WILD-TYPE
  NO               5               83
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMED10 MUTATED                                     8
  TMED10 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMED10 MUTATED                                       0
  TMED10 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMED10 MUTATED                                                  0
  TMED10 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMED10 MUTATED                                     0
  TMED10 WILD-TYPE                                   1
D47V9, multiclass
                                                  clus
vv                                                 TMED10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TMED10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
D47V11, continuous
[1] "Remove cluster labels:" "TMED10 MUTATED"        
clus
  TMED10 MUTATED TMED10 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TMED10 WILD-TYPE" "TMED10 WILD-TYPE" "TMED10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TMED10 MUTATED    7  0  0  0
  TMED10 WILD-TYPE 73 35  4  2
D47V12, multiclass
    clus
vv   TMED10 MUTATED TMED10 WILD-TYPE
  R0              7               73
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMED10 MUTATED       0                         0     8
  TMED10 WILD-TYPE     6                         5   106
D47V14, multiclass
                           clus
vv                          TMED10 MUTATED TMED10 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                  cls
clus                0  1
  TMED10 MUTATED    0  7
  TMED10 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMED10 MUTATED      0    7
  TMED10 WILD-TYPE    5   84
                        clus
vv                       TMED10 MUTATED TMED10 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(48) Variable = NFIL3 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2              0  1
  NFIL3 MUTATED    5  5
  NFIL3 WILD-TYPE 58 57
  NFIL3 MUTATED NFIL3 WILD-TYPE 
             10             115 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              5              57 
$`NFIL3 MUTATED`
TCGA-2J-AAB4 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-A7M4 
       23.97        10.13        10.85        19.82        12.00        15.88 
TCGA-OE-A75W TCGA-US-A77J TCGA-XN-A8T5 TCGA-YB-A89D 
        8.78        18.67        23.67        11.51 

$`NFIL3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A8P1 
       17.49        31.86        20.19        17.00         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        15.19        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        31.27        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  NFIL3 MUTATED NFIL3 WILD-TYPE 
           8.78            0.23 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
          23.97           90.12 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
          13.94           15.22 
[1] "8.8 - 24.0 (13.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D48V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NFIL3 MUTATED         0        0        1         1         8         0
  NFIL3 WILD-TYPE       1        3       11        18        74         4
                 vv
clus              STAGE IV
  NFIL3 MUTATED          0
  NFIL3 WILD-TYPE        3
D48V3, multiclass
           clus
vv          NFIL3 MUTATED NFIL3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NFIL3 MUTATED    0  2     8
  NFIL3 WILD-TYPE  5 15    94
D48V4, multiclass
       clus
vv      NFIL3 MUTATED NFIL3 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                 cls
clus               0  1
  NFIL3 MUTATED    2  8
  NFIL3 WILD-TYPE 33 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      2    8
  NFIL3 WILD-TYPE   33   81
   clus
vv  NFIL3 MUTATED NFIL3 WILD-TYPE
  0             2              33
  1             8              81
[1] 2 2
[1] FALSE
D48V6, binary
                 cls
clus               0  1
  NFIL3 MUTATED    5  0
  NFIL3 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      5    0
  NFIL3 WILD-TYPE   52    3
   clus
vv  NFIL3 MUTATED NFIL3 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus               0  1
  NFIL3 MUTATED    3  7
  NFIL3 WILD-TYPE 48 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      3    7
  NFIL3 WILD-TYPE   48   68
        clus
vv       NFIL3 MUTATED NFIL3 WILD-TYPE
  FEMALE             3              48
  MALE               7              68
[1] 2 2
[1] FALSE
D48V8, binary
                 cls
clus               0  1
  NFIL3 MUTATED    5  4
  NFIL3 WILD-TYPE 83 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      5    4
  NFIL3 WILD-TYPE   83   26
     clus
vv    NFIL3 MUTATED NFIL3 WILD-TYPE
  NO              5              83
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFIL3 MUTATED                                     7
  NFIL3 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFIL3 MUTATED                                       3
  NFIL3 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFIL3 MUTATED                                                  0
  NFIL3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NFIL3 MUTATED                                     0
  NFIL3 WILD-TYPE                                   1
D48V9, multiclass
                                                  clus
vv                                                 NFIL3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NFIL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
D48V11, continuous
                 vv
clus              R0 R1 R2 RX
  NFIL3 MUTATED    8  2  0  0
  NFIL3 WILD-TYPE 72 33  4  2
D48V12, multiclass
    clus
vv   NFIL3 MUTATED NFIL3 WILD-TYPE
  R0             8              72
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFIL3 MUTATED       0                         0    10
  NFIL3 WILD-TYPE     6                         5   104
D48V14, multiclass
                           clus
vv                          NFIL3 MUTATED NFIL3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                 cls
clus               0  1
  NFIL3 MUTATED    1  7
  NFIL3 WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      1    7
  NFIL3 WILD-TYPE    4   84
                        clus
vv                       NFIL3 MUTATED NFIL3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(49) Variable = RGPD5 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  RGPD5 MUTATED    1  4
  RGPD5 WILD-TYPE 62 58
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5             120 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              4              58 
$`RGPD5 MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IU TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-XD-AAUI 
       20.84        15.06         3.12        15.32        12.03 

$`RGPD5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        32.81        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-RL-AAAS 
       12.46        10.29         8.78        13.68         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RGPD5 MUTATED RGPD5 WILD-TYPE 
           3.12            0.23 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
          20.84           90.12 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
         15.060          15.285 
[1] "3.1 - 20.8 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.2"
D49V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RGPD5 MUTATED         0        0        1         1         4         0
  RGPD5 WILD-TYPE       1        3       11        18        78         4
                 vv
clus              STAGE IV
  RGPD5 MUTATED          0
  RGPD5 WILD-TYPE        3
D49V3, multiclass
           clus
vv          RGPD5 MUTATED RGPD5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RGPD5 MUTATED    0  0     6
  RGPD5 WILD-TYPE  5 17    96
D49V4, multiclass
       clus
vv      RGPD5 MUTATED RGPD5 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                 cls
clus               0  1
  RGPD5 MUTATED    1  5
  RGPD5 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      1    5
  RGPD5 WILD-TYPE   34   84
   clus
vv  RGPD5 MUTATED RGPD5 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D49V6, binary
                 cls
clus               0  1
  RGPD5 MUTATED    0  0
  RGPD5 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      0    0
  RGPD5 WILD-TYPE   57    3
D49V7, binary
                 cls
clus               0  1
  RGPD5 MUTATED    3  3
  RGPD5 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      3    3
  RGPD5 WILD-TYPE   48   72
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus               0  1
  RGPD5 MUTATED    4  1
  RGPD5 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      4    1
  RGPD5 WILD-TYPE   84   29
     clus
vv    RGPD5 MUTATED RGPD5 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RGPD5 MUTATED                                     5
  RGPD5 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RGPD5 MUTATED                                       1
  RGPD5 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RGPD5 MUTATED                                                  0
  RGPD5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RGPD5 MUTATED                                     0
  RGPD5 WILD-TYPE                                   1
D49V9, multiclass
                                                  clus
vv                                                 RGPD5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RGPD5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
[1] "Remove cluster labels:" "RGPD5 MUTATED"         
clus
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-YY-A8LH 
"RGPD5 WILD-TYPE" 
D49V11, continuous
[1] "Remove cluster labels:" "RGPD5 MUTATED"         
clus
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" "RGPD5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RGPD5 MUTATED    4  1  0  1
  RGPD5 WILD-TYPE 76 34  4  1
D49V12, multiclass
    clus
vv   RGPD5 MUTATED RGPD5 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGPD5 MUTATED       0                         0     6
  RGPD5 WILD-TYPE     6                         5   108
D49V14, multiclass
                           clus
vv                          RGPD5 MUTATED RGPD5 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                 cls
clus               0  1
  RGPD5 MUTATED    0  6
  RGPD5 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      0    6
  RGPD5 WILD-TYPE    5   85
                        clus
vv                       RGPD5 MUTATED RGPD5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(50) Variable = EMG1 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2             0  1
  EMG1 MUTATED    2  6
  EMG1 WILD-TYPE 61 56
  EMG1 MUTATED EMG1 WILD-TYPE 
             8            117 
  EMG1 MUTATED EMG1 WILD-TYPE 
             6             56 
$`EMG1 MUTATED`
TCGA-US-A77E TCGA-FB-A78T TCGA-FZ-5922 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-OE-A75W 
       14.14        12.33        36.20        12.00        20.88         8.78 
TCGA-Q3-A5QY TCGA-US-A77G 
       13.68         0.39 

$`EMG1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
       19.82        19.82        36.69        41.33        15.19        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-AA2A 
        8.05        13.28         7.56        12.46        10.29         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J 
       15.32         9.40         0.30        39.98        16.80        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  EMG1 MUTATED EMG1 WILD-TYPE 
          0.39           0.23 
  EMG1 MUTATED EMG1 WILD-TYPE 
         36.20          90.12 
  EMG1 MUTATED EMG1 WILD-TYPE 
        13.005         15.350 
[1] "0.4 - 36.2 (13.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D50V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EMG1 MUTATED         0        0        0         2         6         0
  EMG1 WILD-TYPE       1        3       12        17        76         4
                vv
clus             STAGE IV
  EMG1 MUTATED          0
  EMG1 WILD-TYPE        3
D50V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  EMG1 MUTATED    0  0     8
  EMG1 WILD-TYPE  5 17    94
D50V4, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                cls
clus              0  1
  EMG1 MUTATED    2  6
  EMG1 WILD-TYPE 33 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    6
  EMG1 WILD-TYPE   33   83
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            2             33
  1            6             83
[1] 2 2
[1] FALSE
D50V6, binary
                cls
clus              0  1
  EMG1 MUTATED    5  0
  EMG1 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      5    0
  EMG1 WILD-TYPE   52    3
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D50V7, binary
                cls
clus              0  1
  EMG1 MUTATED    2  6
  EMG1 WILD-TYPE 49 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    6
  EMG1 WILD-TYPE   49   69
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            2             49
  MALE              6             69
[1] 2 2
[1] FALSE
D50V8, binary
                cls
clus              0  1
  EMG1 MUTATED    7  1
  EMG1 WILD-TYPE 81 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      7    1
  EMG1 WILD-TYPE   81   29
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             7             81
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EMG1 MUTATED                                     7
  EMG1 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EMG1 MUTATED                                       1
  EMG1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EMG1 MUTATED                                                  0
  EMG1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EMG1 MUTATED                                     0
  EMG1 WILD-TYPE                                   1
D50V9, multiclass
                                                  clus
vv                                                 EMG1 MUTATED EMG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-AAPQ 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-XN-A8T5 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-YY-A8LH 
"EMG1 WILD-TYPE" 
D50V11, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  EMG1 MUTATED    7  1  0  0
  EMG1 WILD-TYPE 73 34  4  2
D50V12, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  R0            7             73
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     8
  EMG1 WILD-TYPE     6                         5   106
D50V14, multiclass
                           clus
vv                          EMG1 MUTATED EMG1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                cls
clus              0  1
  EMG1 MUTATED    0  7
  EMG1 WILD-TYPE  5 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    7
  EMG1 WILD-TYPE    5   84
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7             84
[1] 2 2
[1] FALSE

Clustering(51) Variable = MED12 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2              0  1
  MED12 MUTATED    6  7
  MED12 WILD-TYPE 57 55
  MED12 MUTATED MED12 WILD-TYPE 
             13             112 
  MED12 MUTATED MED12 WILD-TYPE 
              7              55 
$`MED12 MUTATED`
TCGA-2J-AABR TCGA-F2-A44G TCGA-US-A77E TCGA-FB-AAPS TCGA-HV-AA8X TCGA-HZ-8637 
       14.40         7.66        14.14         7.50        17.49        17.00 
TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-LB-A8F3 TCGA-Q3-AA2A TCGA-RB-A7B8 
       19.82        12.00        15.85        12.46         3.12        15.32 
TCGA-RL-AAAS 
        0.30 

$`MED12 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       10.49        58.98        60.95        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
        1.08        15.12        12.92        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
        8.28        32.15        30.25        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.19         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        8.78        13.68         9.40        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MED12 MUTATED MED12 WILD-TYPE 
           0.30            0.23 
  MED12 MUTATED MED12 WILD-TYPE 
          19.82           90.12 
  MED12 MUTATED MED12 WILD-TYPE 
          14.14           15.45 
[1] "0.3 - 19.8 (14.1)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.8"
D51V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MED12 MUTATED         0        0        2         3         8         0
  MED12 WILD-TYPE       1        3       10        16        74         4
                 vv
clus              STAGE IV
  MED12 MUTATED          0
  MED12 WILD-TYPE        3
D51V3, multiclass
           clus
vv          MED12 MUTATED MED12 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             3              16
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MED12 MUTATED    0  3    10
  MED12 WILD-TYPE  5 14    92
D51V4, multiclass
       clus
vv      MED12 MUTATED MED12 WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                 cls
clus               0  1
  MED12 MUTATED    4  9
  MED12 WILD-TYPE 31 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      4    9
  MED12 WILD-TYPE   31   80
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             4              31
  1             9              80
[1] 2 2
[1] FALSE
D51V6, binary
                 cls
clus               0  1
  MED12 MUTATED    6  0
  MED12 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      6    0
  MED12 WILD-TYPE   51    3
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus               0  1
  MED12 MUTATED   10  3
  MED12 WILD-TYPE 41 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED     10    3
  MED12 WILD-TYPE   41   72
        clus
vv       MED12 MUTATED MED12 WILD-TYPE
  FEMALE            10              41
  MALE               3              72
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus               0  1
  MED12 MUTATED    9  4
  MED12 WILD-TYPE 79 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      9    4
  MED12 WILD-TYPE   79   26
     clus
vv    MED12 MUTATED MED12 WILD-TYPE
  NO              9              79
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED12 MUTATED                                    11
  MED12 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED12 MUTATED                                       2
  MED12 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED12 MUTATED                                                  0
  MED12 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MED12 MUTATED                                     0
  MED12 WILD-TYPE                                   1
D51V9, multiclass
                                                  clus
vv                                                 MED12 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MED12 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
[1] "Remove cluster labels:" "MED12 MUTATED"         
clus
  MED12 MUTATED MED12 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-YY-A8LH 
"MED12 WILD-TYPE" 
D51V11, continuous
[1] "Remove cluster labels:" "MED12 MUTATED"         
clus
  MED12 MUTATED MED12 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MED12 MUTATED    8  3  1  1
  MED12 WILD-TYPE 72 32  3  1
D51V12, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0             8              72
  R1             3              32
  R2             1               3
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED       1                         1    11
  MED12 WILD-TYPE     5                         4   103
D51V14, multiclass
                           clus
vv                          MED12 MUTATED MED12 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                 cls
clus               0  1
  MED12 MUTATED    1  8
  MED12 WILD-TYPE  4 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      1    8
  MED12 WILD-TYPE    4   83
                        clus
vv                       MED12 MUTATED MED12 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(52) Variable = SYT15 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  SYT15 MUTATED    4  6
  SYT15 WILD-TYPE 59 56
  SYT15 MUTATED SYT15 WILD-TYPE 
             10             115 
  SYT15 MUTATED SYT15 WILD-TYPE 
              6              56 
$`SYT15 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABH TCGA-3A-A9IU TCGA-3E-AAAZ TCGA-F2-7273 TCGA-HV-A7OP 
        1.08        42.31        15.06        71.74        19.46        32.15 
TCGA-IB-7651 TCGA-IB-AAUW TCGA-RB-A7B8 TCGA-US-A776 
       19.82         7.56        15.32        39.98 

$`SYT15 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       10.13        24.43        75.12         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SYT15 MUTATED SYT15 WILD-TYPE 
           1.08            0.23 
  SYT15 MUTATED SYT15 WILD-TYPE 
          71.74           90.12 
  SYT15 MUTATED SYT15 WILD-TYPE 
          19.64           15.12 
[1] "1.1 - 71.7 (19.6)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.1"
D52V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYT15 MUTATED         0        0        0         3         8         0
  SYT15 WILD-TYPE       1        3       12        16        74         4
                 vv
clus              STAGE IV
  SYT15 MUTATED          0
  SYT15 WILD-TYPE        3
D52V3, multiclass
           clus
vv          SYT15 MUTATED SYT15 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SYT15 MUTATED    0  0    11
  SYT15 WILD-TYPE  5 17    91
D52V4, multiclass
       clus
vv      SYT15 MUTATED SYT15 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                 cls
clus               0  1
  SYT15 MUTATED    3  8
  SYT15 WILD-TYPE 32 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      3    8
  SYT15 WILD-TYPE   32   81
   clus
vv  SYT15 MUTATED SYT15 WILD-TYPE
  0             3              32
  1             8              81
[1] 2 2
[1] FALSE
D52V6, binary
                 cls
clus               0  1
  SYT15 MUTATED    5  0
  SYT15 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      5    0
  SYT15 WILD-TYPE   52    3
   clus
vv  SYT15 MUTATED SYT15 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D52V7, binary
                 cls
clus               0  1
  SYT15 MUTATED    4  7
  SYT15 WILD-TYPE 47 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      4    7
  SYT15 WILD-TYPE   47   68
        clus
vv       SYT15 MUTATED SYT15 WILD-TYPE
  FEMALE             4              47
  MALE               7              68
[1] 2 2
[1] FALSE
D52V8, binary
                 cls
clus               0  1
  SYT15 MUTATED    6  2
  SYT15 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      6    2
  SYT15 WILD-TYPE   82   28
     clus
vv    SYT15 MUTATED SYT15 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYT15 MUTATED                                     6
  SYT15 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYT15 MUTATED                                       4
  SYT15 WILD-TYPE                                    14
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYT15 MUTATED                                                  1
  SYT15 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYT15 MUTATED                                     0
  SYT15 WILD-TYPE                                   1
D52V9, multiclass
                                                  clus
vv                                                 SYT15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SYT15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
                 vv
clus              R0 R1 R2 RX
  SYT15 MUTATED    9  1  0  0
  SYT15 WILD-TYPE 71 34  4  2
D52V12, multiclass
    clus
vv   SYT15 MUTATED SYT15 WILD-TYPE
  R0             9              71
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYT15 MUTATED       1                         1     9
  SYT15 WILD-TYPE     5                         4   105
D52V14, multiclass
                           clus
vv                          SYT15 MUTATED SYT15 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                 cls
clus               0  1
  SYT15 MUTATED    1  8
  SYT15 WILD-TYPE  4 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      1    8
  SYT15 WILD-TYPE    4   83
                        clus
vv                       SYT15 MUTATED SYT15 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(53) Variable = OTUD4 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2              0  1
  OTUD4 MUTATED   11  7
  OTUD4 WILD-TYPE 52 55
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             18             107 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              7              55 
$`OTUD4 MUTATED`
TCGA-XD-AAUL TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9J0 
       16.37         7.36        33.57        15.06        36.26        24.43 
TCGA-FB-A5VM TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A7M4 
       16.37        20.19        19.82        15.85         7.20        15.88 
TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-US-A776 TCGA-XD-AAUH 
       12.46        13.68         3.12        15.32        39.98        12.99 

$`OTUD4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       63.85        50.70        32.81        34.09        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-RB-AA9M TCGA-RL-AAAS 
       13.28         7.56        10.29         8.78         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  OTUD4 MUTATED OTUD4 WILD-TYPE 
           3.12            0.23 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
          39.98           90.12 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
         15.865          15.120 
[1] "3.1 - 40.0 (15.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.4"
D53V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OTUD4 MUTATED         0        1        4         4         9         0
  OTUD4 WILD-TYPE       1        2        8        15        73         4
                 vv
clus              STAGE IV
  OTUD4 MUTATED          0
  OTUD4 WILD-TYPE        3
D53V3, multiclass
           clus
vv          OTUD4 MUTATED OTUD4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              4               8
  STAGE IIA             4              15
  STAGE IIB             9              73
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OTUD4 MUTATED    1  3    14
  OTUD4 WILD-TYPE  4 14    88
D53V4, multiclass
       clus
vv      OTUD4 MUTATED OTUD4 WILD-TYPE
  T1                1               4
  T2                3              14
  T3+T4            14              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                 cls
clus               0  1
  OTUD4 MUTATED    8 10
  OTUD4 WILD-TYPE 27 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      8   10
  OTUD4 WILD-TYPE   27   79
   clus
vv  OTUD4 MUTATED OTUD4 WILD-TYPE
  0             8              27
  1            10              79
[1] 2 2
[1] FALSE
D53V6, binary
                 cls
clus               0  1
  OTUD4 MUTATED    5  0
  OTUD4 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      5    0
  OTUD4 WILD-TYPE   52    3
   clus
vv  OTUD4 MUTATED OTUD4 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D53V7, binary
                 cls
clus               0  1
  OTUD4 MUTATED    9  9
  OTUD4 WILD-TYPE 42 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      9    9
  OTUD4 WILD-TYPE   42   66
        clus
vv       OTUD4 MUTATED OTUD4 WILD-TYPE
  FEMALE             9              42
  MALE               9              66
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus               0  1
  OTUD4 MUTATED   16  2
  OTUD4 WILD-TYPE 72 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     16    2
  OTUD4 WILD-TYPE   72   28
     clus
vv    OTUD4 MUTATED OTUD4 WILD-TYPE
  NO             16              72
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTUD4 MUTATED                                    15
  OTUD4 WILD-TYPE                                  90
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTUD4 MUTATED                                       2
  OTUD4 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTUD4 MUTATED                                                  1
  OTUD4 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OTUD4 MUTATED                                     0
  OTUD4 WILD-TYPE                                   1
D53V9, multiclass
                                                  clus
vv                                                 OTUD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 OTUD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           90
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
                 vv
clus              R0 R1 R2 RX
  OTUD4 MUTATED   15  1  1  1
  OTUD4 WILD-TYPE 65 34  3  1
D53V12, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  R0            15              65
  R1             1              34
  R2             1               3
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTUD4 MUTATED       0                         1    17
  OTUD4 WILD-TYPE     6                         4    97
D53V14, multiclass
                           clus
vv                          OTUD4 MUTATED OTUD4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                17              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                 cls
clus               0  1
  OTUD4 MUTATED    0 17
  OTUD4 WILD-TYPE  5 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      0   17
  OTUD4 WILD-TYPE    5   74
                        clus
vv                       OTUD4 MUTATED OTUD4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            17              74
[1] 2 2
[1] FALSE

Clustering(54) Variable = KIAA1949 MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  KIAA1949 MUTATED    7  3
  KIAA1949 WILD-TYPE 56 59
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                10                115 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
                 3                 59 
$`KIAA1949 MUTATED`
TCGA-2J-AABP TCGA-3A-A9IB TCGA-F2-A8YN TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7885 
       15.22         7.36        17.00         0.23        19.82        41.33 
TCGA-IB-AAUM TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-YH-A8SY 
        0.26         8.05        10.29        12.76 

$`KIAA1949 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26        10.85        19.82 
TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22        15.88         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
              0.23               0.30 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
             41.33              90.12 
  KIAA1949 MUTATED KIAA1949 WILD-TYPE 
            11.525             15.350 
[1] "0.2 - 41.3 (11.5)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.2"
D54V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA1949 MUTATED         0        0        1         1         7         1
  KIAA1949 WILD-TYPE       1        3       11        18        75         3
                    vv
clus                 STAGE IV
  KIAA1949 MUTATED          0
  KIAA1949 WILD-TYPE        3
D54V3, multiclass
           clus
vv          KIAA1949 MUTATED KIAA1949 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                7                 75
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA1949 MUTATED    0  2     8
  KIAA1949 WILD-TYPE  5 15    94
D54V4, multiclass
       clus
vv      KIAA1949 MUTATED KIAA1949 WILD-TYPE
  T1                   0                  5
  T2                   2                 15
  T3+T4                8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                    cls
clus                  0  1
  KIAA1949 MUTATED    2  8
  KIAA1949 WILD-TYPE 33 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      2    8
  KIAA1949 WILD-TYPE   33   81
   clus
vv  KIAA1949 MUTATED KIAA1949 WILD-TYPE
  0                2                 33
  1                8                 81
[1] 2 2
[1] FALSE
D54V6, binary
                    cls
clus                  0  1
  KIAA1949 MUTATED    6  0
  KIAA1949 WILD-TYPE 51  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      6    0
  KIAA1949 WILD-TYPE   51    3
   clus
vv  KIAA1949 MUTATED KIAA1949 WILD-TYPE
  0                6                 51
  1                0                  3
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                  0  1
  KIAA1949 MUTATED    6  4
  KIAA1949 WILD-TYPE 45 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      6    4
  KIAA1949 WILD-TYPE   45   71
        clus
vv       KIAA1949 MUTATED KIAA1949 WILD-TYPE
  FEMALE                6                 45
  MALE                  4                 71
[1] 2 2
[1] FALSE
D54V8, binary
                    cls
clus                  0  1
  KIAA1949 MUTATED    7  2
  KIAA1949 WILD-TYPE 81 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      7    2
  KIAA1949 WILD-TYPE   81   28
     clus
vv    KIAA1949 MUTATED KIAA1949 WILD-TYPE
  NO                 7                 81
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA1949 MUTATED                                     8
  KIAA1949 WILD-TYPE                                  97
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA1949 MUTATED                                       0
  KIAA1949 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA1949 MUTATED                                                  0
  KIAA1949 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA1949 MUTATED                                     1
  KIAA1949 WILD-TYPE                                   0
D54V9, multiclass
                                                  clus
vv                                                 KIAA1949 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 KIAA1949 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
D54V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA1949 MUTATED    8  1  0  0
  KIAA1949 WILD-TYPE 72 34  4  2
D54V12, multiclass
    clus
vv   KIAA1949 MUTATED KIAA1949 WILD-TYPE
  R0                8                 72
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1949 MUTATED       0                         0    10
  KIAA1949 WILD-TYPE     6                         5   104
D54V14, multiclass
                           clus
vv                          KIAA1949 MUTATED KIAA1949 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                   10                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                    cls
clus                  0  1
  KIAA1949 MUTATED    0  9
  KIAA1949 WILD-TYPE  5 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1949 MUTATED      0    9
  KIAA1949 WILD-TYPE    5   82
                        clus
vv                       KIAA1949 MUTATED KIAA1949 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                9                 82
[1] 2 2
[1] FALSE

Clustering(55) Variable = OR10A7 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2               0  1
  OR10A7 MUTATED    5  7
  OR10A7 WILD-TYPE 58 55
  OR10A7 MUTATED OR10A7 WILD-TYPE 
              12              113 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               7               55 
$`OR10A7 MUTATED`
TCGA-3A-A9IJ TCGA-F2-A44G TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABK TCGA-2J-AABP 
       60.95         7.66         9.63        20.61        15.91        15.22 
TCGA-2L-AAQJ TCGA-3A-A9I9 TCGA-FB-A78T TCGA-FB-AAPZ TCGA-FZ-5922 TCGA-HZ-A8P1 
       12.95        20.84        12.33        23.54        36.20         0.23 

$`OR10A7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        58.98        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
        2.17        23.97         2.63        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       42.31        14.47         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        2.01         5.10        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
       10.13         5.26        10.85        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  OR10A7 MUTATED OR10A7 WILD-TYPE 
            0.23             0.26 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
           60.95            90.12 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
          15.565           15.190 
[1] "0.2 - 61.0 (15.6)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.1"
D55V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR10A7 MUTATED         0        0        2         3         6         1
  OR10A7 WILD-TYPE       1        3       10        16        76         3
                  vv
clus               STAGE IV
  OR10A7 MUTATED          0
  OR10A7 WILD-TYPE        3
D55V3, multiclass
           clus
vv          OR10A7 MUTATED OR10A7 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              3               16
  STAGE IIB              6               76
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  OR10A7 MUTATED    0  3     9
  OR10A7 WILD-TYPE  5 14    93
D55V4, multiclass
       clus
vv      OR10A7 MUTATED OR10A7 WILD-TYPE
  T1                 0                5
  T2                 3               14
  T3+T4              9               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                  cls
clus                0  1
  OR10A7 MUTATED    6  6
  OR10A7 WILD-TYPE 29 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      6    6
  OR10A7 WILD-TYPE   29   83
   clus
vv  OR10A7 MUTATED OR10A7 WILD-TYPE
  0              6               29
  1              6               83
[1] 2 2
[1] FALSE
D55V6, binary
                  cls
clus                0  1
  OR10A7 MUTATED    7  0
  OR10A7 WILD-TYPE 50  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      7    0
  OR10A7 WILD-TYPE   50    3
   clus
vv  OR10A7 MUTATED OR10A7 WILD-TYPE
  0              7               50
  1              0                3
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                0  1
  OR10A7 MUTATED    5  7
  OR10A7 WILD-TYPE 46 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      5    7
  OR10A7 WILD-TYPE   46   68
        clus
vv       OR10A7 MUTATED OR10A7 WILD-TYPE
  FEMALE              5               46
  MALE                7               68
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                0  1
  OR10A7 MUTATED    7  4
  OR10A7 WILD-TYPE 81 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      7    4
  OR10A7 WILD-TYPE   81   26
     clus
vv    OR10A7 MUTATED OR10A7 WILD-TYPE
  NO               7               81
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR10A7 MUTATED                                    10
  OR10A7 WILD-TYPE                                  95
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR10A7 MUTATED                                       1
  OR10A7 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR10A7 MUTATED                                                  0
  OR10A7 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR10A7 MUTATED                                     1
  OR10A7 WILD-TYPE                                   0
D55V9, multiclass
                                                  clus
vv                                                 OR10A7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 OR10A7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
D55V11, continuous
                  vv
clus               R0 R1 R2 RX
  OR10A7 MUTATED    9  3  0  0
  OR10A7 WILD-TYPE 71 32  4  2
D55V12, multiclass
    clus
vv   OR10A7 MUTATED OR10A7 WILD-TYPE
  R0              9               71
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR10A7 MUTATED       0                         0    12
  OR10A7 WILD-TYPE     6                         5   102
D55V14, multiclass
                           clus
vv                          OR10A7 MUTATED OR10A7 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 12              102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                  cls
clus                0  1
  OR10A7 MUTATED    0  7
  OR10A7 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      0    7
  OR10A7 WILD-TYPE    5   84
                        clus
vv                       OR10A7 MUTATED OR10A7 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(56) Variable = SYNGAP1 MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  SYNGAP1 MUTATED    8  7
  SYNGAP1 WILD-TYPE 55 55
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
               15               110 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                7                55 
$`SYNGAP1 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-F2-7273 TCGA-FB-AAPS 
       23.97        20.61        15.06        24.43        19.46         7.50 
TCGA-FB-AAPZ TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-AAUP TCGA-RB-A7B8 
       23.54        17.49        19.82        41.33        14.17        15.32 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YH-A8SY 
       12.99        12.03        12.76 

$`SYNGAP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       14.14        16.37         2.17         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       10.13        75.12        71.74         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       12.33        15.95        37.15        12.53        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
        0.39        18.67        13.81        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
             7.50              0.23 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
            41.33             90.12 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
           17.490            15.155 
[1] "7.5 - 41.3 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYNGAP1 MUTATED         0        0        0         0        14         1
  SYNGAP1 WILD-TYPE       1        3       12        19        68         3
                   vv
clus                STAGE IV
  SYNGAP1 MUTATED          0
  SYNGAP1 WILD-TYPE        3
D56V3, multiclass
           clus
vv          SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB              14                68
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SYNGAP1 MUTATED    0  4    11
  SYNGAP1 WILD-TYPE  5 13    91
D56V4, multiclass
       clus
vv      SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  T1                  0                 5
  T2                  4                13
  T3+T4              11                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    0 15
  SYNGAP1 WILD-TYPE 35 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      0   15
  SYNGAP1 WILD-TYPE   35   74
   clus
vv  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  0               0                35
  1              15                74
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    7  0
  SYNGAP1 WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      7    0
  SYNGAP1 WILD-TYPE   50    3
   clus
vv  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  0               7                50
  1               0                 3
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    9  6
  SYNGAP1 WILD-TYPE 42 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      9    6
  SYNGAP1 WILD-TYPE   42   69
        clus
vv       SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  FEMALE               9                42
  MALE                 6                69
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED   10  5
  SYNGAP1 WILD-TYPE 78 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED     10    5
  SYNGAP1 WILD-TYPE   78   25
     clus
vv    SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  NO               10                78
  YES               5                25
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYNGAP1 MUTATED                                    12
  SYNGAP1 WILD-TYPE                                  93
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYNGAP1 MUTATED                                       2
  SYNGAP1 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYNGAP1 MUTATED                                                  0
  SYNGAP1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYNGAP1 MUTATED                                     0
  SYNGAP1 WILD-TYPE                                   1
D56V9, multiclass
                                                  clus
vv                                                 SYNGAP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SYNGAP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
D56V11, continuous
                   vv
clus                R0 R1 R2 RX
  SYNGAP1 MUTATED    9  3  2  0
  SYNGAP1 WILD-TYPE 71 32  2  2
D56V12, multiclass
    clus
vv   SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  R0               9                71
  R1               3                32
  R2               2                 2
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNGAP1 MUTATED       1                         1    13
  SYNGAP1 WILD-TYPE     5                         4   101
D56V14, multiclass
                           clus
vv                          SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  13               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    0 12
  SYNGAP1 WILD-TYPE  5 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      0   12
  SYNGAP1 WILD-TYPE    5   79
                        clus
vv                       SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              12                79
[1] 2 2
[1] FALSE

Clustering(57) Variable = TOX4 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2             0  1
  TOX4 MUTATED    6  3
  TOX4 WILD-TYPE 57 59
  TOX4 MUTATED TOX4 WILD-TYPE 
             9            116 
  TOX4 MUTATED TOX4 WILD-TYPE 
             3             59 
$`TOX4 MUTATED`
TCGA-IB-A5SS TCGA-S4-A8RO TCGA-2J-AAB4 TCGA-2J-AABO TCGA-FB-AAPS TCGA-HV-AA8V 
       15.12        17.26        23.97        14.47         7.50        30.25 
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A6UG 
       10.85        19.82         1.35 

$`TOX4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        15.91        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        12.33        15.95        37.15        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TOX4 MUTATED TOX4 WILD-TYPE 
          1.35           0.23 
  TOX4 MUTATED TOX4 WILD-TYPE 
         30.25          90.12 
  TOX4 MUTATED TOX4 WILD-TYPE 
         15.12          15.27 
[1] "1.4 - 30.2 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D57V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TOX4 MUTATED         0        0        0         0         9         0
  TOX4 WILD-TYPE       1        3       12        19        73         4
                vv
clus             STAGE IV
  TOX4 MUTATED          0
  TOX4 WILD-TYPE        3
D57V3, multiclass
           clus
vv          TOX4 MUTATED TOX4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            9             73
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TOX4 MUTATED    0  2     7
  TOX4 WILD-TYPE  5 15    95
D57V4, multiclass
       clus
vv      TOX4 MUTATED TOX4 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                cls
clus              0  1
  TOX4 MUTATED    0  9
  TOX4 WILD-TYPE 35 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      0    9
  TOX4 WILD-TYPE   35   80
   clus
vv  TOX4 MUTATED TOX4 WILD-TYPE
  0            0             35
  1            9             80
[1] 2 2
[1] FALSE
D57V6, binary
                cls
clus              0  1
  TOX4 MUTATED    5  0
  TOX4 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      5    0
  TOX4 WILD-TYPE   52    3
   clus
vv  TOX4 MUTATED TOX4 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus              0  1
  TOX4 MUTATED    4  5
  TOX4 WILD-TYPE 47 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      4    5
  TOX4 WILD-TYPE   47   70
        clus
vv       TOX4 MUTATED TOX4 WILD-TYPE
  FEMALE            4             47
  MALE              5             70
[1] 2 2
[1] FALSE
D57V8, binary
                cls
clus              0  1
  TOX4 MUTATED    6  3
  TOX4 WILD-TYPE 82 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      6    3
  TOX4 WILD-TYPE   82   27
     clus
vv    TOX4 MUTATED TOX4 WILD-TYPE
  NO             6             82
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TOX4 MUTATED                                     7
  TOX4 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TOX4 MUTATED                                       2
  TOX4 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TOX4 MUTATED                                                  0
  TOX4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TOX4 MUTATED                                     0
  TOX4 WILD-TYPE                                   1
D57V9, multiclass
                                                  clus
vv                                                 TOX4 MUTATED TOX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
                vv
clus             R0 R1 R2 RX
  TOX4 MUTATED    6  2  1  0
  TOX4 WILD-TYPE 74 33  3  2
D57V12, multiclass
    clus
vv   TOX4 MUTATED TOX4 WILD-TYPE
  R0            6             74
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TOX4 MUTATED       1                         0     8
  TOX4 WILD-TYPE     5                         5   106
D57V14, multiclass
                           clus
vv                          TOX4 MUTATED TOX4 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                cls
clus              0  1
  TOX4 MUTATED    0  6
  TOX4 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      0    6
  TOX4 WILD-TYPE    5   85
                        clus
vv                       TOX4 MUTATED TOX4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(58) Variable = CUL4B MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2              0  1
  CUL4B MUTATED    9  4
  CUL4B WILD-TYPE 54 58
  CUL4B MUTATED CUL4B WILD-TYPE 
             13             112 
  CUL4B MUTATED CUL4B WILD-TYPE 
              4              58 
$`CUL4B MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABO TCGA-2L-AAQM TCGA-3A-A9IU TCGA-FB-AAPZ TCGA-HZ-8637 
        2.17        14.47        45.47        15.06        23.54        17.00 
TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A6UF TCGA-RL-AAAS TCGA-US-A776 TCGA-XD-AAUH 
       19.82        15.19        21.90         0.30        39.98        12.99 
TCGA-Z5-AAPL 
       15.35 

$`CUL4B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        32.81        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       23.67        11.51        12.76        66.28 

  CUL4B MUTATED CUL4B WILD-TYPE 
           0.30            0.23 
  CUL4B MUTATED CUL4B WILD-TYPE 
          45.47           90.12 
  CUL4B MUTATED CUL4B WILD-TYPE 
          15.35           15.17 
[1] "0.3 - 45.5 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CUL4B MUTATED         0        0        1         2         9         1
  CUL4B WILD-TYPE       1        3       11        17        73         3
                 vv
clus              STAGE IV
  CUL4B MUTATED          0
  CUL4B WILD-TYPE        3
D58V3, multiclass
           clus
vv          CUL4B MUTATED CUL4B WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             9              73
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CUL4B MUTATED    0  2    11
  CUL4B WILD-TYPE  5 15    91
D58V4, multiclass
       clus
vv      CUL4B MUTATED CUL4B WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                 cls
clus               0  1
  CUL4B MUTATED    3 10
  CUL4B WILD-TYPE 32 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      3   10
  CUL4B WILD-TYPE   32   79
   clus
vv  CUL4B MUTATED CUL4B WILD-TYPE
  0             3              32
  1            10              79
[1] 2 2
[1] FALSE
D58V6, binary
                 cls
clus               0  1
  CUL4B MUTATED    8  0
  CUL4B WILD-TYPE 49  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      8    0
  CUL4B WILD-TYPE   49    3
   clus
vv  CUL4B MUTATED CUL4B WILD-TYPE
  0             8              49
  1             0               3
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus               0  1
  CUL4B MUTATED    6  7
  CUL4B WILD-TYPE 45 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      6    7
  CUL4B WILD-TYPE   45   68
        clus
vv       CUL4B MUTATED CUL4B WILD-TYPE
  FEMALE             6              45
  MALE               7              68
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus               0  1
  CUL4B MUTATED   10  3
  CUL4B WILD-TYPE 78 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED     10    3
  CUL4B WILD-TYPE   78   27
     clus
vv    CUL4B MUTATED CUL4B WILD-TYPE
  NO             10              78
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CUL4B MUTATED                                    10
  CUL4B WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CUL4B MUTATED                                       2
  CUL4B WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CUL4B MUTATED                                                  1
  CUL4B WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CUL4B MUTATED                                     0
  CUL4B WILD-TYPE                                   1
D58V9, multiclass
                                                  clus
vv                                                 CUL4B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CUL4B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
                 vv
clus              R0 R1 R2 RX
  CUL4B MUTATED    9  3  1  0
  CUL4B WILD-TYPE 71 32  3  2
D58V12, multiclass
    clus
vv   CUL4B MUTATED CUL4B WILD-TYPE
  R0             9              71
  R1             3              32
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUL4B MUTATED       0                         0    13
  CUL4B WILD-TYPE     6                         5   101
D58V14, multiclass
                           clus
vv                          CUL4B MUTATED CUL4B WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                13             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                 cls
clus               0  1
  CUL4B MUTATED    1  9
  CUL4B WILD-TYPE  4 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      1    9
  CUL4B WILD-TYPE    4   82
                        clus
vv                       CUL4B MUTATED CUL4B WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(59) Variable = NFAT5 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  NFAT5 MUTATED    5  8
  NFAT5 WILD-TYPE 58 54
  NFAT5 MUTATED NFAT5 WILD-TYPE 
             13             112 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              8              54 
$`NFAT5 MUTATED`
TCGA-F2-A44G TCGA-IB-A5SS TCGA-LB-A7SX TCGA-2J-AABE TCGA-3A-A9I9 TCGA-FB-AAQ3 
        7.66        15.12        12.92        22.22        20.84         1.02 
TCGA-HV-AA8X TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7885 TCGA-RB-A7B8 TCGA-RB-AA9M 
       17.49        10.85        19.82        41.33        15.32         9.40 
TCGA-YB-A89D 
       11.51 

$`NFAT5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        19.96        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       42.31        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         4.04         5.03        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        8.78        13.68         3.12         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
           1.02            0.23 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
          41.33           90.12 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         15.120          15.285 
[1] "1.0 - 41.3 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D59V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NFAT5 MUTATED         0        0        0         2        11         0
  NFAT5 WILD-TYPE       1        3       12        17        71         4
                 vv
clus              STAGE IV
  NFAT5 MUTATED          0
  NFAT5 WILD-TYPE        3
D59V3, multiclass
           clus
vv          NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB            11              71
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NFAT5 MUTATED    1  1    11
  NFAT5 WILD-TYPE  4 16    91
D59V4, multiclass
       clus
vv      NFAT5 MUTATED NFAT5 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                 cls
clus               0  1
  NFAT5 MUTATED    2 11
  NFAT5 WILD-TYPE 33 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      2   11
  NFAT5 WILD-TYPE   33   78
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             2              33
  1            11              78
[1] 2 2
[1] FALSE
D59V6, binary
                 cls
clus               0  1
  NFAT5 MUTATED    5  0
  NFAT5 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      5    0
  NFAT5 WILD-TYPE   52    3
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus               0  1
  NFAT5 MUTATED    8  5
  NFAT5 WILD-TYPE 43 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      8    5
  NFAT5 WILD-TYPE   43   70
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             8              43
  MALE               5              70
[1] 2 2
[1] FALSE
D59V8, binary
                 cls
clus               0  1
  NFAT5 MUTATED    8  5
  NFAT5 WILD-TYPE 80 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      8    5
  NFAT5 WILD-TYPE   80   25
     clus
vv    NFAT5 MUTATED NFAT5 WILD-TYPE
  NO              8              80
  YES             5              25
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFAT5 MUTATED                                    11
  NFAT5 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFAT5 MUTATED                                       2
  NFAT5 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFAT5 MUTATED                                                  0
  NFAT5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NFAT5 MUTATED                                     0
  NFAT5 WILD-TYPE                                   1
D59V9, multiclass
                                                  clus
vv                                                 NFAT5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NFAT5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
                 vv
clus              R0 R1 R2 RX
  NFAT5 MUTATED   10  2  1  0
  NFAT5 WILD-TYPE 70 33  3  2
D59V12, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  R0            10              70
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFAT5 MUTATED       1                         1    11
  NFAT5 WILD-TYPE     5                         4   103
D59V14, multiclass
                           clus
vv                          NFAT5 MUTATED NFAT5 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                 cls
clus               0  1
  NFAT5 MUTATED    0 11
  NFAT5 WILD-TYPE  5 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0   11
  NFAT5 WILD-TYPE    5   80
                        clus
vv                       NFAT5 MUTATED NFAT5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            11              80
[1] 2 2
[1] FALSE

Clustering(60) Variable = OTOF MUTATION ANALYSIS
D60V1, survival
                sevent
clus2             0  1
  OTOF MUTATED    8 10
  OTOF WILD-TYPE 55 52
  OTOF MUTATED OTOF WILD-TYPE 
            18            107 
  OTOF MUTATED OTOF WILD-TYPE 
            10             52 
$`OTOF MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-FB-A5VM TCGA-FB-AAPU TCGA-FB-AAQ2 TCGA-FZ-5926 
        4.70        12.95        16.37        12.53         5.03        17.79 
TCGA-HV-A7OL TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-8126 
        8.28         5.26        10.85        19.82        19.82        15.19 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-AAUP TCGA-RB-A7B8 TCGA-US-A776 TCGA-XD-AAUH 
        7.20        20.88        14.17        15.32        39.98        12.99 

$`OTOF WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        12.33        15.95        37.15         7.50 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
        5.10        36.20        20.35        22.06        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A8P1 
       17.49        31.86        20.19        17.00        10.13         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UF TCGA-IB-A6UG 
       36.69        41.33        12.00        15.85        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73         7.86         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  OTOF MUTATED OTOF WILD-TYPE 
          4.70           0.23 
  OTOF MUTATED OTOF WILD-TYPE 
         39.98          90.12 
  OTOF MUTATED OTOF WILD-TYPE 
         13.58          15.55 
[1] "4.7 - 40.0 (13.6)" "0.2 - 90.1 (15.6)"
[1] "hr=" "1.5"
D60V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OTOF MUTATED         0        0        2         3         9         3
  OTOF WILD-TYPE       1        3       10        16        73         1
                vv
clus             STAGE IV
  OTOF MUTATED          1
  OTOF WILD-TYPE        2
D60V3, multiclass
           clus
vv          OTOF MUTATED OTOF WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            3             16
  STAGE IIB            9             73
  STAGE III            3              1
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  OTOF MUTATED    0  3    15
  OTOF WILD-TYPE  5 14    87
D60V4, multiclass
       clus
vv      OTOF MUTATED OTOF WILD-TYPE
  T1               0              5
  T2               3             14
  T3+T4           15             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                cls
clus              0  1
  OTOF MUTATED    7 11
  OTOF WILD-TYPE 28 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      7   11
  OTOF WILD-TYPE   28   78
   clus
vv  OTOF MUTATED OTOF WILD-TYPE
  0            7             28
  1           11             78
[1] 2 2
[1] FALSE
D60V6, binary
                cls
clus              0  1
  OTOF MUTATED    8  1
  OTOF WILD-TYPE 49  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      8    1
  OTOF WILD-TYPE   49    2
   clus
vv  OTOF MUTATED OTOF WILD-TYPE
  0            8             49
  1            1              2
[1] 2 2
[1] FALSE
D60V7, binary
                cls
clus              0  1
  OTOF MUTATED   11  7
  OTOF WILD-TYPE 40 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED     11    7
  OTOF WILD-TYPE   40   68
        clus
vv       OTOF MUTATED OTOF WILD-TYPE
  FEMALE           11             40
  MALE              7             68
[1] 2 2
[1] FALSE
D60V8, binary
                cls
clus              0  1
  OTOF MUTATED   17  1
  OTOF WILD-TYPE 71 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED     17    1
  OTOF WILD-TYPE   71   29
     clus
vv    OTOF MUTATED OTOF WILD-TYPE
  NO            17             71
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTOF MUTATED                                    14
  OTOF WILD-TYPE                                  91
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTOF MUTATED                                       3
  OTOF WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTOF MUTATED                                                  1
  OTOF WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  OTOF MUTATED                                     0
  OTOF WILD-TYPE                                   1
D60V9, multiclass
                                                  clus
vv                                                 OTOF MUTATED OTOF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        14             91
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
                vv
clus             R0 R1 R2 RX
  OTOF MUTATED   10  6  2  0
  OTOF WILD-TYPE 70 29  2  2
D60V12, multiclass
    clus
vv   OTOF MUTATED OTOF WILD-TYPE
  R0           10             70
  R1            6             29
  R2            2              2
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTOF MUTATED       2                         0    16
  OTOF WILD-TYPE     4                         5    98
D60V14, multiclass
                           clus
vv                          OTOF MUTATED OTOF WILD-TYPE
  ASIAN                                2              4
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               16             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                cls
clus              0  1
  OTOF MUTATED    0 15
  OTOF WILD-TYPE  5 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      0   15
  OTOF WILD-TYPE    5   76
                        clus
vv                       OTOF MUTATED OTOF WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           15             76
[1] 2 2
[1] FALSE

Clustering(61) Variable = SMG7 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2             0  1
  SMG7 MUTATED    5  5
  SMG7 WILD-TYPE 58 57
  SMG7 MUTATED SMG7 WILD-TYPE 
            10            115 
  SMG7 MUTATED SMG7 WILD-TYPE 
             5             57 
$`SMG7 MUTATED`
TCGA-S4-A8RO TCGA-2J-AABE TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-HV-AA8X TCGA-IB-7651 
       17.26        22.22        15.06        24.43        17.49        19.82 
TCGA-IB-A6UF TCGA-IB-AAUM TCGA-IB-AAUQ TCGA-RB-A7B8 
       21.90         0.26         6.02        15.32 

$`SMG7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22        15.88         4.73         7.86        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SMG7 MUTATED SMG7 WILD-TYPE 
          0.26           0.23 
  SMG7 MUTATED SMG7 WILD-TYPE 
         24.43          90.12 
  SMG7 MUTATED SMG7 WILD-TYPE 
        17.375         15.120 
[1] "0.3 - 24.4 (17.4)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D61V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMG7 MUTATED         0        0        0         1         9         0
  SMG7 WILD-TYPE       1        3       12        18        73         4
                vv
clus             STAGE IV
  SMG7 MUTATED          0
  SMG7 WILD-TYPE        3
D61V3, multiclass
           clus
vv          SMG7 MUTATED SMG7 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            9             73
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  SMG7 MUTATED    0  2     8
  SMG7 WILD-TYPE  5 15    94
D61V4, multiclass
       clus
vv      SMG7 MUTATED SMG7 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                cls
clus              0  1
  SMG7 MUTATED    1  9
  SMG7 WILD-TYPE 34 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      1    9
  SMG7 WILD-TYPE   34   80
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            1             34
  1            9             80
[1] 2 2
[1] FALSE
D61V6, binary
                cls
clus              0  1
  SMG7 MUTATED    5  0
  SMG7 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      5    0
  SMG7 WILD-TYPE   52    3
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus              0  1
  SMG7 MUTATED    4  6
  SMG7 WILD-TYPE 47 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      4    6
  SMG7 WILD-TYPE   47   69
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  FEMALE            4             47
  MALE              6             69
[1] 2 2
[1] FALSE
D61V8, binary
                cls
clus              0  1
  SMG7 MUTATED    8  2
  SMG7 WILD-TYPE 80 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      8    2
  SMG7 WILD-TYPE   80   28
     clus
vv    SMG7 MUTATED SMG7 WILD-TYPE
  NO             8             80
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMG7 MUTATED                                     9
  SMG7 WILD-TYPE                                  96
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMG7 MUTATED                                       1
  SMG7 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMG7 MUTATED                                                  0
  SMG7 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMG7 MUTATED                                     0
  SMG7 WILD-TYPE                                   1
D61V9, multiclass
                                                  clus
vv                                                 SMG7 MUTATED SMG7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         9             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
                vv
clus             R0 R1 R2 RX
  SMG7 MUTATED    6  3  1  0
  SMG7 WILD-TYPE 74 32  3  2
D61V12, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  R0            6             74
  R1            3             32
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMG7 MUTATED       1                         0     9
  SMG7 WILD-TYPE     5                         5   105
D61V14, multiclass
                           clus
vv                          SMG7 MUTATED SMG7 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                cls
clus              0  1
  SMG7 MUTATED    0  8
  SMG7 WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      0    8
  SMG7 WILD-TYPE    5   83
                        clus
vv                       SMG7 MUTATED SMG7 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(62) Variable = SLC6A9 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2               0  1
  SLC6A9 MUTATED    6  3
  SLC6A9 WILD-TYPE 57 59
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
               9              116 
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
               3               59 
$`SLC6A9 MUTATED`
TCGA-2J-AABA TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-FB-A5VM TCGA-FB-AAPZ TCGA-HZ-8637 
       19.96        36.26        24.43        16.37        23.54        17.00 
TCGA-IB-AAUP TCGA-IB-AAUS TCGA-XN-A8T3 
       14.17         7.40        31.27 

$`SLC6A9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        7.86         6.02        11.11         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
            7.40             0.23 
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
           36.26            90.12 
  SLC6A9 MUTATED SLC6A9 WILD-TYPE 
           19.96            15.09 
[1] "7.4 - 36.3 (20.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2"  
D62V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC6A9 MUTATED         0        0        3         0         7         0
  SLC6A9 WILD-TYPE       1        3        9        19        75         4
                  vv
clus               STAGE IV
  SLC6A9 MUTATED          0
  SLC6A9 WILD-TYPE        3
D62V3, multiclass
           clus
vv          SLC6A9 MUTATED SLC6A9 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               3                9
  STAGE IIA              0               19
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SLC6A9 MUTATED    0  4     6
  SLC6A9 WILD-TYPE  5 13    96
D62V4, multiclass
       clus
vv      SLC6A9 MUTATED SLC6A9 WILD-TYPE
  T1                 0                5
  T2                 4               13
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                  cls
clus                0  1
  SLC6A9 MUTATED    3  7
  SLC6A9 WILD-TYPE 32 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A9 MUTATED      3    7
  SLC6A9 WILD-TYPE   32   82
   clus
vv  SLC6A9 MUTATED SLC6A9 WILD-TYPE
  0              3               32
  1              7               82
[1] 2 2
[1] FALSE
D62V6, binary
                  cls
clus                0  1
  SLC6A9 MUTATED    5  0
  SLC6A9 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A9 MUTATED      5    0
  SLC6A9 WILD-TYPE   52    3
   clus
vv  SLC6A9 MUTATED SLC6A9 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D62V7, binary
                  cls
clus                0  1
  SLC6A9 MUTATED    3  7
  SLC6A9 WILD-TYPE 48 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A9 MUTATED      3    7
  SLC6A9 WILD-TYPE   48   68
        clus
vv       SLC6A9 MUTATED SLC6A9 WILD-TYPE
  FEMALE              3               48
  MALE                7               68
[1] 2 2
[1] FALSE
D62V8, binary
                  cls
clus                0  1
  SLC6A9 MUTATED    7  2
  SLC6A9 WILD-TYPE 81 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A9 MUTATED      7    2
  SLC6A9 WILD-TYPE   81   28
     clus
vv    SLC6A9 MUTATED SLC6A9 WILD-TYPE
  NO               7               81
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC6A9 MUTATED                                     9
  SLC6A9 WILD-TYPE                                  96
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC6A9 MUTATED                                       1
  SLC6A9 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC6A9 MUTATED                                                  0
  SLC6A9 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC6A9 MUTATED                                     0
  SLC6A9 WILD-TYPE                                   1
D62V9, multiclass
                                                  clus
vv                                                 SLC6A9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SLC6A9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
                  vv
clus               R0 R1 R2 RX
  SLC6A9 MUTATED    6  4  0  0
  SLC6A9 WILD-TYPE 74 31  4  2
D62V12, multiclass
    clus
vv   SLC6A9 MUTATED SLC6A9 WILD-TYPE
  R0              6               74
  R1              4               31
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC6A9 MUTATED       0                         0    10
  SLC6A9 WILD-TYPE     6                         5   104
D62V14, multiclass
                           clus
vv                          SLC6A9 MUTATED SLC6A9 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                  cls
clus                0  1
  SLC6A9 MUTATED    2  7
  SLC6A9 WILD-TYPE  3 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A9 MUTATED      2    7
  SLC6A9 WILD-TYPE    3   84
                        clus
vv                       SLC6A9 MUTATED SLC6A9 WILD-TYPE
  HISPANIC OR LATINO                  2                3
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(63) Variable = INTS7 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  INTS7 MUTATED    5  4
  INTS7 WILD-TYPE 58 58
  INTS7 MUTATED INTS7 WILD-TYPE 
              9             116 
  INTS7 MUTATED INTS7 WILD-TYPE 
              4              58 
$`INTS7 MUTATED`
TCGA-2J-AAB4 TCGA-2L-AAQI TCGA-F2-7273 TCGA-HV-A7OL TCGA-HZ-A9TJ TCGA-IB-7651 
       23.97         3.39        19.46         8.28        19.82        19.82 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-YY-A8LH 
        8.22        15.88        66.28 

$`INTS7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 
       17.00        10.13         5.26        10.85         0.23        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
       21.90         1.35         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  INTS7 MUTATED INTS7 WILD-TYPE 
           3.39            0.23 
  INTS7 MUTATED INTS7 WILD-TYPE 
          66.28           90.12 
  INTS7 MUTATED INTS7 WILD-TYPE 
         19.460          15.155 
[1] "3.4 - 66.3 (19.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D63V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  INTS7 MUTATED         0        0        0         1         7         0
  INTS7 WILD-TYPE       1        3       12        18        75         4
                 vv
clus              STAGE IV
  INTS7 MUTATED          1
  INTS7 WILD-TYPE        2
D63V3, multiclass
           clus
vv          INTS7 MUTATED INTS7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  INTS7 MUTATED    0  1     8
  INTS7 WILD-TYPE  5 16    94
D63V4, multiclass
       clus
vv      INTS7 MUTATED INTS7 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                 cls
clus               0  1
  INTS7 MUTATED    2  7
  INTS7 WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      2    7
  INTS7 WILD-TYPE   33   82
   clus
vv  INTS7 MUTATED INTS7 WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D63V6, binary
                 cls
clus               0  1
  INTS7 MUTATED    3  1
  INTS7 WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      3    1
  INTS7 WILD-TYPE   54    2
   clus
vv  INTS7 MUTATED INTS7 WILD-TYPE
  0             3              54
  1             1               2
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus               0  1
  INTS7 MUTATED    2  7
  INTS7 WILD-TYPE 49 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      2    7
  INTS7 WILD-TYPE   49   68
        clus
vv       INTS7 MUTATED INTS7 WILD-TYPE
  FEMALE             2              49
  MALE               7              68
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus               0  1
  INTS7 MUTATED    7  2
  INTS7 WILD-TYPE 81 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      7    2
  INTS7 WILD-TYPE   81   28
     clus
vv    INTS7 MUTATED INTS7 WILD-TYPE
  NO              7              81
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  INTS7 MUTATED                                     7
  INTS7 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  INTS7 MUTATED                                       2
  INTS7 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  INTS7 MUTATED                                                  0
  INTS7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  INTS7 MUTATED                                     0
  INTS7 WILD-TYPE                                   1
D63V9, multiclass
                                                  clus
vv                                                 INTS7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 INTS7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, continuous
                 vv
clus              R0 R1 R2 RX
  INTS7 MUTATED    6  2  1  0
  INTS7 WILD-TYPE 74 33  3  2
D63V12, multiclass
    clus
vv   INTS7 MUTATED INTS7 WILD-TYPE
  R0             6              74
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INTS7 MUTATED       1                         1     7
  INTS7 WILD-TYPE     5                         4   107
D63V14, multiclass
                           clus
vv                          INTS7 MUTATED INTS7 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                 cls
clus               0  1
  INTS7 MUTATED    0  6
  INTS7 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS7 MUTATED      0    6
  INTS7 WILD-TYPE    5   85
                        clus
vv                       INTS7 MUTATED INTS7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(64) Variable = PASD1 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  PASD1 MUTATED    7  5
  PASD1 WILD-TYPE 56 57
  PASD1 MUTATED PASD1 WILD-TYPE 
             12             113 
  PASD1 MUTATED PASD1 WILD-TYPE 
              5              57 
$`PASD1 MUTATED`
TCGA-2J-AABE TCGA-2J-AABH TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPS 
       22.22        42.31        19.46        16.37        15.95         7.50 
TCGA-FB-AAQ0 TCGA-HZ-7918 TCGA-IB-7651 TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-RL-AAAS 
       15.55        31.86        19.82        13.68         9.40         0.30 

$`PASD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       20.61        19.96        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 
       17.00        12.33        37.15        12.53        23.54         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-US-A776 TCGA-US-A779 
       10.29         8.78         3.12        15.32        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PASD1 MUTATED PASD1 WILD-TYPE 
           0.30            0.23 
  PASD1 MUTATED PASD1 WILD-TYPE 
          42.31           90.12 
  PASD1 MUTATED PASD1 WILD-TYPE 
          16.16           15.12 
[1] "0.3 - 42.3 (16.2)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.2"
D64V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PASD1 MUTATED         0        0        2         3         7         0
  PASD1 WILD-TYPE       1        3       10        16        75         4
                 vv
clus              STAGE IV
  PASD1 MUTATED          0
  PASD1 WILD-TYPE        3
D64V3, multiclass
           clus
vv          PASD1 MUTATED PASD1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             3              16
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PASD1 MUTATED    1  3     8
  PASD1 WILD-TYPE  4 14    94
D64V4, multiclass
       clus
vv      PASD1 MUTATED PASD1 WILD-TYPE
  T1                1               4
  T2                3              14
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                 cls
clus               0  1
  PASD1 MUTATED    5  7
  PASD1 WILD-TYPE 30 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      5    7
  PASD1 WILD-TYPE   30   82
   clus
vv  PASD1 MUTATED PASD1 WILD-TYPE
  0             5              30
  1             7              82
[1] 2 2
[1] FALSE
D64V6, binary
                 cls
clus               0  1
  PASD1 MUTATED    7  0
  PASD1 WILD-TYPE 50  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      7    0
  PASD1 WILD-TYPE   50    3
   clus
vv  PASD1 MUTATED PASD1 WILD-TYPE
  0             7              50
  1             0               3
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus               0  1
  PASD1 MUTATED    3  9
  PASD1 WILD-TYPE 48 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      3    9
  PASD1 WILD-TYPE   48   66
        clus
vv       PASD1 MUTATED PASD1 WILD-TYPE
  FEMALE             3              48
  MALE               9              66
[1] 2 2
[1] FALSE
D64V8, binary
                 cls
clus               0  1
  PASD1 MUTATED    6  6
  PASD1 WILD-TYPE 82 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      6    6
  PASD1 WILD-TYPE   82   24
     clus
vv    PASD1 MUTATED PASD1 WILD-TYPE
  NO              6              82
  YES             6              24
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PASD1 MUTATED                                    11
  PASD1 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PASD1 MUTATED                                       1
  PASD1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PASD1 MUTATED                                                  0
  PASD1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PASD1 MUTATED                                     0
  PASD1 WILD-TYPE                                   1
D64V9, multiclass
                                                  clus
vv                                                 PASD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PASD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
D64V11, continuous
                 vv
clus              R0 R1 R2 RX
  PASD1 MUTATED   11  1  0  0
  PASD1 WILD-TYPE 69 34  4  2
D64V12, multiclass
    clus
vv   PASD1 MUTATED PASD1 WILD-TYPE
  R0            11              69
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PASD1 MUTATED       0                         1    11
  PASD1 WILD-TYPE     6                         4   103
D64V14, multiclass
                           clus
vv                          PASD1 MUTATED PASD1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                 cls
clus               0  1
  PASD1 MUTATED    0 10
  PASD1 WILD-TYPE  5 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      0   10
  PASD1 WILD-TYPE    5   81
                        clus
vv                       PASD1 MUTATED PASD1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            10              81
[1] 2 2
[1] FALSE

Clustering(65) Variable = BRDT MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  BRDT MUTATED    3  8
  BRDT WILD-TYPE 60 54
  BRDT MUTATED BRDT WILD-TYPE 
            11            114 
  BRDT MUTATED BRDT WILD-TYPE 
             8             54 
$`BRDT MUTATED`
TCGA-US-A77E TCGA-F2-7273 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-HV-A7OP TCGA-HZ-8637 
       14.14        19.46         5.03         1.02        32.15        17.00 
TCGA-HZ-A77O TCGA-IB-7651 TCGA-OE-A75W TCGA-US-A776 TCGA-YB-A89D 
        5.26        19.82         8.78        39.98        11.51 

$`BRDT WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FZ-5919 
        7.50        12.53        23.54        15.55         4.04        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
        8.28        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  BRDT MUTATED BRDT WILD-TYPE 
          1.02           0.23 
  BRDT MUTATED BRDT WILD-TYPE 
         39.98          90.12 
  BRDT MUTATED BRDT WILD-TYPE 
         14.14          15.27 
[1] "1.0 - 40.0 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D65V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BRDT MUTATED         0        0        0         2         9         0
  BRDT WILD-TYPE       1        3       12        17        73         4
                vv
clus             STAGE IV
  BRDT MUTATED          0
  BRDT WILD-TYPE        3
D65V3, multiclass
           clus
vv          BRDT MUTATED BRDT WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            9             73
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  BRDT MUTATED    0  1    10
  BRDT WILD-TYPE  5 16    92
D65V4, multiclass
       clus
vv      BRDT MUTATED BRDT WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4           10             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V5, binary
                cls
clus              0  1
  BRDT MUTATED    2  9
  BRDT WILD-TYPE 33 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      2    9
  BRDT WILD-TYPE   33   80
   clus
vv  BRDT MUTATED BRDT WILD-TYPE
  0            2             33
  1            9             80
[1] 2 2
[1] FALSE
D65V6, binary
                cls
clus              0  1
  BRDT MUTATED    4  0
  BRDT WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      4    0
  BRDT WILD-TYPE   53    3
   clus
vv  BRDT MUTATED BRDT WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D65V7, binary
                cls
clus              0  1
  BRDT MUTATED    5  6
  BRDT WILD-TYPE 46 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      5    6
  BRDT WILD-TYPE   46   69
        clus
vv       BRDT MUTATED BRDT WILD-TYPE
  FEMALE            5             46
  MALE              6             69
[1] 2 2
[1] FALSE
D65V8, binary
                cls
clus              0  1
  BRDT MUTATED    6  5
  BRDT WILD-TYPE 82 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      6    5
  BRDT WILD-TYPE   82   25
     clus
vv    BRDT MUTATED BRDT WILD-TYPE
  NO             6             82
  YES            5             25
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRDT MUTATED                                     8
  BRDT WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRDT MUTATED                                       2
  BRDT WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRDT MUTATED                                                  1
  BRDT WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  BRDT MUTATED                                     0
  BRDT WILD-TYPE                                   1
D65V9, multiclass
                                                  clus
vv                                                 BRDT MUTATED BRDT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
[1] "Remove cluster labels:" "BRDT MUTATED"          
clus
  BRDT MUTATED BRDT WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-XN-A8T5 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-YY-A8LH 
"BRDT WILD-TYPE" 
D65V11, continuous
[1] "Remove cluster labels:" "BRDT MUTATED"          
clus
  BRDT MUTATED BRDT WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BRDT MUTATED    8  3  0  0
  BRDT WILD-TYPE 72 32  4  2
D65V12, multiclass
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  R0            8             72
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRDT MUTATED       1                         1     9
  BRDT WILD-TYPE     5                         4   105
D65V14, multiclass
                           clus
vv                          BRDT MUTATED BRDT WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                cls
clus              0  1
  BRDT MUTATED    1  9
  BRDT WILD-TYPE  4 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      1    9
  BRDT WILD-TYPE    4   82
                        clus
vv                       BRDT MUTATED BRDT WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            9             82
[1] 2 2
[1] FALSE

Clustering(66) Variable = CDH3 MUTATION ANALYSIS
D66V1, survival
                sevent
clus2             0  1
  CDH3 MUTATED    2  5
  CDH3 WILD-TYPE 61 57
  CDH3 MUTATED CDH3 WILD-TYPE 
             7            118 
  CDH3 MUTATED CDH3 WILD-TYPE 
             5             57 
$`CDH3 MUTATED`
TCGA-3A-A9IJ TCGA-FB-AAQ0 TCGA-FZ-5920 TCGA-HV-A7OP TCGA-HV-AA8X TCGA-IB-7651 
       60.95        15.55         2.01        32.15        17.49        19.82 
TCGA-IB-A5SQ 
        7.20 

$`CDH3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       22.06         8.28        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  CDH3 MUTATED CDH3 WILD-TYPE 
          2.01           0.23 
  CDH3 MUTATED CDH3 WILD-TYPE 
         60.95          90.12 
  CDH3 MUTATED CDH3 WILD-TYPE 
        17.490         15.155 
[1] "2.0 - 61.0 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D66V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDH3 MUTATED         0        0        2         1         4         0
  CDH3 WILD-TYPE       1        3       10        18        78         4
                vv
clus             STAGE IV
  CDH3 MUTATED          0
  CDH3 WILD-TYPE        3
D66V3, multiclass
           clus
vv          CDH3 MUTATED CDH3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            1             18
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CDH3 MUTATED    0  3     4
  CDH3 WILD-TYPE  5 14    98
D66V4, multiclass
       clus
vv      CDH3 MUTATED CDH3 WILD-TYPE
  T1               0              5
  T2               3             14
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                cls
clus              0  1
  CDH3 MUTATED    3  4
  CDH3 WILD-TYPE 32 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      3    4
  CDH3 WILD-TYPE   32   85
   clus
vv  CDH3 MUTATED CDH3 WILD-TYPE
  0            3             32
  1            4             85
[1] 2 2
[1] FALSE
D66V6, binary
                cls
clus              0  1
  CDH3 MUTATED    4  0
  CDH3 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      4    0
  CDH3 WILD-TYPE   53    3
   clus
vv  CDH3 MUTATED CDH3 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D66V7, binary
                cls
clus              0  1
  CDH3 MUTATED    3  4
  CDH3 WILD-TYPE 48 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      3    4
  CDH3 WILD-TYPE   48   71
        clus
vv       CDH3 MUTATED CDH3 WILD-TYPE
  FEMALE            3             48
  MALE              4             71
[1] 2 2
[1] FALSE
D66V8, binary
                cls
clus              0  1
  CDH3 MUTATED    6  1
  CDH3 WILD-TYPE 82 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      6    1
  CDH3 WILD-TYPE   82   29
     clus
vv    CDH3 MUTATED CDH3 WILD-TYPE
  NO             6             82
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDH3 MUTATED                                     5
  CDH3 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDH3 MUTATED                                       2
  CDH3 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDH3 MUTATED                                                  0
  CDH3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDH3 MUTATED                                     0
  CDH3 WILD-TYPE                                   1
D66V9, multiclass
                                                  clus
vv                                                 CDH3 MUTATED CDH3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
[1] "Remove cluster labels:" "CDH3 MUTATED"          
clus
  CDH3 MUTATED CDH3 WILD-TYPE 
             2             37 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-YY-A8LH 
"CDH3 WILD-TYPE" 
D66V11, continuous
[1] "Remove cluster labels:" "CDH3 MUTATED"          
clus
  CDH3 MUTATED CDH3 WILD-TYPE 
             2             31 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CDH3 WILD-TYPE" "CDH3 WILD-TYPE" "CDH3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CDH3 MUTATED    6  0  1  0
  CDH3 WILD-TYPE 74 35  3  2
D66V12, multiclass
    clus
vv   CDH3 MUTATED CDH3 WILD-TYPE
  R0            6             74
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH3 MUTATED       2                         1     4
  CDH3 WILD-TYPE     4                         4   110
D66V14, multiclass
                           clus
vv                          CDH3 MUTATED CDH3 WILD-TYPE
  ASIAN                                2              4
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                cls
clus              0  1
  CDH3 MUTATED    0  5
  CDH3 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH3 MUTATED      0    5
  CDH3 WILD-TYPE    5   86
                        clus
vv                       CDH3 MUTATED CDH3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(67) Variable = CTAGE5 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2               0  1
  CTAGE5 MUTATED    3  5
  CTAGE5 WILD-TYPE 60 57
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
               8              117 
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
               5               57 
$`CTAGE5 MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IO TCGA-FB-AAPQ TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-A5SP 
       20.84        63.85        37.15        10.13        19.82        15.85 
TCGA-IB-A5SQ TCGA-IB-A7M4 
        7.20        15.88 

$`CTAGE5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        15.95         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A6UF 
       36.69        41.33        15.19        12.00        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
            7.20             0.23 
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
           63.85            90.12 
  CTAGE5 MUTATED CTAGE5 WILD-TYPE 
           17.85            15.12 
[1] "7.2 - 63.9 (17.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.1"
D67V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CTAGE5 MUTATED         0        0        1         2         4         0
  CTAGE5 WILD-TYPE       1        3       11        17        78         4
                  vv
clus               STAGE IV
  CTAGE5 MUTATED          0
  CTAGE5 WILD-TYPE        3
D67V3, multiclass
           clus
vv          CTAGE5 MUTATED CTAGE5 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              2               17
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CTAGE5 MUTATED    0  1     6
  CTAGE5 WILD-TYPE  5 16    96
D67V4, multiclass
       clus
vv      CTAGE5 MUTATED CTAGE5 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                  cls
clus                0  1
  CTAGE5 MUTATED    3  4
  CTAGE5 WILD-TYPE 32 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTAGE5 MUTATED      3    4
  CTAGE5 WILD-TYPE   32   85
   clus
vv  CTAGE5 MUTATED CTAGE5 WILD-TYPE
  0              3               32
  1              4               85
[1] 2 2
[1] FALSE
D67V6, binary
                  cls
clus                0  1
  CTAGE5 MUTATED    3  0
  CTAGE5 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTAGE5 MUTATED      3    0
  CTAGE5 WILD-TYPE   54    3
   clus
vv  CTAGE5 MUTATED CTAGE5 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D67V7, binary
                  cls
clus                0  1
  CTAGE5 MUTATED    2  6
  CTAGE5 WILD-TYPE 49 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTAGE5 MUTATED      2    6
  CTAGE5 WILD-TYPE   49   69
        clus
vv       CTAGE5 MUTATED CTAGE5 WILD-TYPE
  FEMALE              2               49
  MALE                6               69
[1] 2 2
[1] FALSE
D67V8, binary
                  cls
clus                0  1
  CTAGE5 MUTATED    6  2
  CTAGE5 WILD-TYPE 82 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTAGE5 MUTATED      6    2
  CTAGE5 WILD-TYPE   82   28
     clus
vv    CTAGE5 MUTATED CTAGE5 WILD-TYPE
  NO               6               82
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CTAGE5 MUTATED                                     7
  CTAGE5 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CTAGE5 MUTATED                                       1
  CTAGE5 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CTAGE5 MUTATED                                                  0
  CTAGE5 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CTAGE5 MUTATED                                     0
  CTAGE5 WILD-TYPE                                   1
D67V9, multiclass
                                                  clus
vv                                                 CTAGE5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CTAGE5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
D67V11, continuous
                  vv
clus               R0 R1 R2 RX
  CTAGE5 MUTATED    6  2  0  0
  CTAGE5 WILD-TYPE 74 33  4  2
D67V12, multiclass
    clus
vv   CTAGE5 MUTATED CTAGE5 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTAGE5 MUTATED       0                         0     8
  CTAGE5 WILD-TYPE     6                         5   106
D67V14, multiclass
                           clus
vv                          CTAGE5 MUTATED CTAGE5 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                  cls
clus                0  1
  CTAGE5 MUTATED    0  7
  CTAGE5 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTAGE5 MUTATED      0    7
  CTAGE5 WILD-TYPE    5   84
                        clus
vv                       CTAGE5 MUTATED CTAGE5 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(68) Variable = C6ORF165 MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  C6ORF165 MUTATED    5  3
  C6ORF165 WILD-TYPE 58 59
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 8                117 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
                 3                 59 
$`C6ORF165 MUTATED`
TCGA-LB-A7SX TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AABP TCGA-3A-A9IR TCGA-HV-A7OP 
       12.92        16.37         2.17        15.22        50.70        32.15 
TCGA-IB-7651 TCGA-RB-AA9M 
       19.82         9.40 

$`C6ORF165 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
              2.17               0.23 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
             50.70              90.12 
  C6ORF165 MUTATED C6ORF165 WILD-TYPE 
            15.795             15.190 
[1] "2.2 - 50.7 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C6ORF165 MUTATED         0        0        1         1         7         0
  C6ORF165 WILD-TYPE       1        3       11        18        75         4
                    vv
clus                 STAGE IV
  C6ORF165 MUTATED          0
  C6ORF165 WILD-TYPE        3
D68V3, multiclass
           clus
vv          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                7                 75
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C6ORF165 MUTATED    1  1     7
  C6ORF165 WILD-TYPE  4 16    95
D68V4, multiclass
       clus
vv      C6ORF165 MUTATED C6ORF165 WILD-TYPE
  T1                   1                  4
  T2                   1                 16
  T3+T4                7                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    2  7
  C6ORF165 WILD-TYPE 33 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      2    7
  C6ORF165 WILD-TYPE   33   82
   clus
vv  C6ORF165 MUTATED C6ORF165 WILD-TYPE
  0                2                 33
  1                7                 82
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    4  0
  C6ORF165 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      4    0
  C6ORF165 WILD-TYPE   53    3
   clus
vv  C6ORF165 MUTATED C6ORF165 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    4  5
  C6ORF165 WILD-TYPE 47 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      4    5
  C6ORF165 WILD-TYPE   47   70
        clus
vv       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  FEMALE                4                 47
  MALE                  5                 70
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    6  2
  C6ORF165 WILD-TYPE 82 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      6    2
  C6ORF165 WILD-TYPE   82   28
     clus
vv    C6ORF165 MUTATED C6ORF165 WILD-TYPE
  NO                 6                 82
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C6ORF165 MUTATED                                     5
  C6ORF165 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C6ORF165 MUTATED                                       3
  C6ORF165 WILD-TYPE                                    15
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C6ORF165 MUTATED                                                  0
  C6ORF165 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C6ORF165 MUTATED                                     1
  C6ORF165 WILD-TYPE                                   0
D68V9, multiclass
                                                  clus
vv                                                 C6ORF165 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 C6ORF165 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
D68V11, continuous
                    vv
clus                 R0 R1 R2 RX
  C6ORF165 MUTATED    8  1  0  0
  C6ORF165 WILD-TYPE 72 34  4  2
D68V12, multiclass
    clus
vv   C6ORF165 MUTATED C6ORF165 WILD-TYPE
  R0                8                 72
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C6ORF165 MUTATED       1                         1     7
  C6ORF165 WILD-TYPE     5                         4   107
D68V14, multiclass
                           clus
vv                          C6ORF165 MUTATED C6ORF165 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                    cls
clus                  0  1
  C6ORF165 MUTATED    0  6
  C6ORF165 WILD-TYPE  5 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF165 MUTATED      0    6
  C6ORF165 WILD-TYPE    5   85
                        clus
vv                       C6ORF165 MUTATED C6ORF165 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                6                 85
[1] 2 2
[1] FALSE

Clustering(69) Variable = POP5 MUTATION ANALYSIS
D69V1, survival
                sevent
clus2             0  1
  POP5 MUTATED    5  1
  POP5 WILD-TYPE 58 61
  POP5 MUTATED POP5 WILD-TYPE 
             6            119 
  POP5 MUTATED POP5 WILD-TYPE 
             1             61 
$`POP5 MUTATED`
TCGA-FB-AAPZ TCGA-HZ-A9TJ TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-AAUQ TCGA-US-A776 
       23.54        19.82        15.19        15.85         6.02        39.98 

$`POP5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
       13.68         3.12        15.32         9.40         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  POP5 MUTATED POP5 WILD-TYPE 
          6.02           0.23 
  POP5 MUTATED POP5 WILD-TYPE 
         39.98          90.12 
  POP5 MUTATED POP5 WILD-TYPE 
        17.835         15.120 
[1] "6.0 - 40.0 (17.8)" "0.2 - 90.1 (15.1)"
[1] "hr=" "3.6"
D69V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  POP5 MUTATED         0        0        0         2         2         1
  POP5 WILD-TYPE       1        3       12        17        80         3
                vv
clus             STAGE IV
  POP5 MUTATED          1
  POP5 WILD-TYPE        2
D69V3, multiclass
           clus
vv          POP5 MUTATED POP5 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            2             80
  STAGE III            1              3
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  POP5 MUTATED    0  1     5
  POP5 WILD-TYPE  5 16    97
D69V4, multiclass
       clus
vv      POP5 MUTATED POP5 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V5, binary
                cls
clus              0  1
  POP5 MUTATED    3  3
  POP5 WILD-TYPE 32 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      3    3
  POP5 WILD-TYPE   32   86
   clus
vv  POP5 MUTATED POP5 WILD-TYPE
  0            3             32
  1            3             86
[1] 2 2
[1] FALSE
D69V6, binary
                cls
clus              0  1
  POP5 MUTATED    3  1
  POP5 WILD-TYPE 54  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      3    1
  POP5 WILD-TYPE   54    2
   clus
vv  POP5 MUTATED POP5 WILD-TYPE
  0            3             54
  1            1              2
[1] 2 2
[1] FALSE
D69V7, binary
                cls
clus              0  1
  POP5 MUTATED    1  5
  POP5 WILD-TYPE 50 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      1    5
  POP5 WILD-TYPE   50   70
        clus
vv       POP5 MUTATED POP5 WILD-TYPE
  FEMALE            1             50
  MALE              5             70
[1] 2 2
[1] FALSE
D69V8, binary
                cls
clus              0  1
  POP5 MUTATED    6  0
  POP5 WILD-TYPE 82 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      6    0
  POP5 WILD-TYPE   82   30
     clus
vv    POP5 MUTATED POP5 WILD-TYPE
  NO             6             82
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POP5 MUTATED                                     4
  POP5 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POP5 MUTATED                                       1
  POP5 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POP5 MUTATED                                                  1
  POP5 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  POP5 MUTATED                                     0
  POP5 WILD-TYPE                                   1
D69V9, multiclass
                                                  clus
vv                                                 POP5 MUTATED POP5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
[1] "Remove cluster labels:" "POP5 MUTATED"          
clus
  POP5 MUTATED POP5 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-A6UF 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUS     TCGA-IB-AAUU 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-YY-A8LH 
"POP5 WILD-TYPE" 
D69V11, continuous
[1] "Remove cluster labels:" "POP5 MUTATED"          
clus
  POP5 MUTATED POP5 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  POP5 MUTATED    3  3  0  0
  POP5 WILD-TYPE 77 32  4  2
D69V12, multiclass
    clus
vv   POP5 MUTATED POP5 WILD-TYPE
  R0            3             77
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POP5 MUTATED       0                         0     6
  POP5 WILD-TYPE     6                         5   108
D69V14, multiclass
                           clus
vv                          POP5 MUTATED POP5 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                cls
clus              0  1
  POP5 MUTATED    0  5
  POP5 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      0    5
  POP5 WILD-TYPE    5   86
                        clus
vv                       POP5 MUTATED POP5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(70) Variable = CEL MUTATION ANALYSIS
D70V1, survival
               sevent
clus2            0  1
  CEL MUTATED    5  2
  CEL WILD-TYPE 58 60
  CEL MUTATED CEL WILD-TYPE 
            7           118 
  CEL MUTATED CEL WILD-TYPE 
            2            60 
$`CEL MUTATED`
TCGA-HV-A7OL TCGA-HV-AA8X TCGA-IB-A5SQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-RB-AA9M 
        8.28        17.49         7.20        11.11         7.40         9.40 
TCGA-XD-AAUG 
       13.81 

$`CEL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  CEL MUTATED CEL WILD-TYPE 
         7.20          0.23 
  CEL MUTATED CEL WILD-TYPE 
        17.49         90.12 
  CEL MUTATED CEL WILD-TYPE 
         9.40         15.45 
[1] "7.2 - 17.5 (9.4)"  "0.2 - 90.1 (15.4)"
[1] "hr=" "1.1"
D70V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CEL MUTATED         0        0        1         1         4         0
  CEL WILD-TYPE       1        3       11        18        78         4
               vv
clus            STAGE IV
  CEL MUTATED          1
  CEL WILD-TYPE        2
D70V3, multiclass
           clus
vv          CEL MUTATED CEL WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            1            11
  STAGE IIA           1            18
  STAGE IIB           4            78
  STAGE III           0             4
  STAGE IV            1             2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  CEL MUTATED    1  2     4
  CEL WILD-TYPE  4 15    98
D70V4, multiclass
       clus
vv      CEL MUTATED CEL WILD-TYPE
  T1              1             4
  T2              2            15
  T3+T4           4            98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
               cls
clus             0  1
  CEL MUTATED    2  5
  CEL WILD-TYPE 33 84
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      2    5
  CEL WILD-TYPE   33   84
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0           2            33
  1           5            84
[1] 2 2
[1] FALSE
D70V6, binary
               cls
clus             0  1
  CEL MUTATED    3  1
  CEL WILD-TYPE 54  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      3    1
  CEL WILD-TYPE   54    2
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0           3            54
  1           1             2
[1] 2 2
[1] FALSE
D70V7, binary
               cls
clus             0  1
  CEL MUTATED    4  3
  CEL WILD-TYPE 47 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      4    3
  CEL WILD-TYPE   47   72
        clus
vv       CEL MUTATED CEL WILD-TYPE
  FEMALE           4            47
  MALE             3            72
[1] 2 2
[1] FALSE
D70V8, binary
               cls
clus             0  1
  CEL MUTATED    6  1
  CEL WILD-TYPE 82 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    1
  CEL WILD-TYPE   82   29
     clus
vv    CEL MUTATED CEL WILD-TYPE
  NO            6            82
  YES           1            29
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEL MUTATED                                     7
  CEL WILD-TYPE                                  98
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEL MUTATED                                       0
  CEL WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEL MUTATED                                                  0
  CEL WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  CEL MUTATED                                     0
  CEL WILD-TYPE                                   1
D70V9, multiclass
                                                  clus
vv                                                 CEL MUTATED CEL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        7            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
[1] "Remove cluster labels:" "CEL MUTATED"           
clus
  CEL MUTATED CEL WILD-TYPE 
            1            38 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-IB-7651    TCGA-IB-7885    TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-OE-A75W    TCGA-XN-A8T5    TCGA-YY-A8LH 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
D70V11, continuous
[1] "Remove cluster labels:" "CEL MUTATED"           
clus
  CEL MUTATED CEL WILD-TYPE 
            1            32 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7651 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-IB-AAUQ    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI 
"CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" "CEL WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"CEL WILD-TYPE" "CEL WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  CEL MUTATED    3  2  2  0
  CEL WILD-TYPE 77 33  2  2
D70V12, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  R0           3            77
  R1           2            33
  R2           2             2
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEL MUTATED       2                         0     5
  CEL WILD-TYPE     4                         5   109
D70V14, multiclass
                           clus
vv                          CEL MUTATED CEL WILD-TYPE
  ASIAN                               2             4
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               5           109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
               cls
clus             0  1
  CEL MUTATED    0  5
  CEL WILD-TYPE  5 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      0    5
  CEL WILD-TYPE    5   86
                        clus
vv                       CEL MUTATED CEL WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           5            86
[1] 2 2
[1] FALSE

Clustering(71) Variable = EIF3C MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2              0  1
  EIF3C MUTATED    5  4
  EIF3C WILD-TYPE 58 58
  EIF3C MUTATED EIF3C WILD-TYPE 
              9             116 
  EIF3C MUTATED EIF3C WILD-TYPE 
              4              58 
$`EIF3C MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB8 TCGA-2J-AABP TCGA-2L-AAQE TCGA-3A-A9IX TCGA-FB-AAQ0 
       17.26         2.63        15.22        22.49        34.09        15.55 
TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-IB-A6UF 
        5.03        19.82        21.90 

$`EIF3C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        36.26        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  EIF3C MUTATED EIF3C WILD-TYPE 
           2.63            0.23 
  EIF3C MUTATED EIF3C WILD-TYPE 
          34.09           90.12 
  EIF3C MUTATED EIF3C WILD-TYPE 
          17.26           15.09 
[1] "2.6 - 34.1 (17.3)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.2"
D71V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EIF3C MUTATED         0        1        0         1         7         0
  EIF3C WILD-TYPE       1        2       12        18        75         4
                 vv
clus              STAGE IV
  EIF3C MUTATED          0
  EIF3C WILD-TYPE        3
D71V3, multiclass
           clus
vv          EIF3C MUTATED EIF3C WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  EIF3C MUTATED    1  0     8
  EIF3C WILD-TYPE  4 17    94
D71V4, multiclass
       clus
vv      EIF3C MUTATED EIF3C WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                 cls
clus               0  1
  EIF3C MUTATED    2  7
  EIF3C WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      2    7
  EIF3C WILD-TYPE   33   82
   clus
vv  EIF3C MUTATED EIF3C WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D71V6, binary
                 cls
clus               0  1
  EIF3C MUTATED    5  0
  EIF3C WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      5    0
  EIF3C WILD-TYPE   52    3
   clus
vv  EIF3C MUTATED EIF3C WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D71V7, binary
                 cls
clus               0  1
  EIF3C MUTATED    4  5
  EIF3C WILD-TYPE 47 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      4    5
  EIF3C WILD-TYPE   47   70
        clus
vv       EIF3C MUTATED EIF3C WILD-TYPE
  FEMALE             4              47
  MALE               5              70
[1] 2 2
[1] FALSE
D71V8, binary
                 cls
clus               0  1
  EIF3C MUTATED    6  2
  EIF3C WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      6    2
  EIF3C WILD-TYPE   82   28
     clus
vv    EIF3C MUTATED EIF3C WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EIF3C MUTATED                                     8
  EIF3C WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EIF3C MUTATED                                       0
  EIF3C WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EIF3C MUTATED                                                  0
  EIF3C WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EIF3C MUTATED                                     1
  EIF3C WILD-TYPE                                   0
D71V9, multiclass
                                                  clus
vv                                                 EIF3C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 EIF3C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
D71V11, continuous
                 vv
clus              R0 R1 R2 RX
  EIF3C MUTATED    5  4  0  0
  EIF3C WILD-TYPE 75 31  4  2
D71V12, multiclass
    clus
vv   EIF3C MUTATED EIF3C WILD-TYPE
  R0             5              75
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF3C MUTATED       0                         0     9
  EIF3C WILD-TYPE     6                         5   105
D71V14, multiclass
                           clus
vv                          EIF3C MUTATED EIF3C WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                 cls
clus               0  1
  EIF3C MUTATED    0  6
  EIF3C WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      0    6
  EIF3C WILD-TYPE    5   85
                        clus
vv                       EIF3C MUTATED EIF3C WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(72) Variable = NR4A3 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2              0  1
  NR4A3 MUTATED    3  4
  NR4A3 WILD-TYPE 60 58
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              7             118 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              4              58 
$`NR4A3 MUTATED`
TCGA-2J-AABT TCGA-2L-AAQI TCGA-FB-AAPU TCGA-HV-A7OL TCGA-HZ-7925 TCGA-IB-7651 
       10.49         3.39        12.53         8.28        20.19        19.82 
TCGA-US-A776 
       39.98 

$`NR4A3 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 
       22.06        32.15        30.25        17.49        31.86        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         9.40         0.30        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  NR4A3 MUTATED NR4A3 WILD-TYPE 
           3.39            0.23 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
          39.98           90.12 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
          12.53           15.27 
[1] "3.4 - 40.0 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D72V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NR4A3 MUTATED         0        0        0         3         4         0
  NR4A3 WILD-TYPE       1        3       12        16        78         4
                 vv
clus              STAGE IV
  NR4A3 MUTATED          0
  NR4A3 WILD-TYPE        3
D72V3, multiclass
           clus
vv          NR4A3 MUTATED NR4A3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NR4A3 MUTATED    0  0     7
  NR4A3 WILD-TYPE  5 17    95
D72V4, multiclass
       clus
vv      NR4A3 MUTATED NR4A3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                 cls
clus               0  1
  NR4A3 MUTATED    3  4
  NR4A3 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      3    4
  NR4A3 WILD-TYPE   32   85
   clus
vv  NR4A3 MUTATED NR4A3 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D72V6, binary
                 cls
clus               0  1
  NR4A3 MUTATED    2  0
  NR4A3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      2    0
  NR4A3 WILD-TYPE   55    3
   clus
vv  NR4A3 MUTATED NR4A3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus               0  1
  NR4A3 MUTATED    3  4
  NR4A3 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      3    4
  NR4A3 WILD-TYPE   48   71
        clus
vv       NR4A3 MUTATED NR4A3 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus               0  1
  NR4A3 MUTATED    6  0
  NR4A3 WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      6    0
  NR4A3 WILD-TYPE   82   30
     clus
vv    NR4A3 MUTATED NR4A3 WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NR4A3 MUTATED                                     6
  NR4A3 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NR4A3 MUTATED                                       0
  NR4A3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NR4A3 MUTATED                                                  1
  NR4A3 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NR4A3 MUTATED                                     0
  NR4A3 WILD-TYPE                                   1
D72V9, multiclass
                                                  clus
vv                                                 NR4A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NR4A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
[1] "Remove cluster labels:" "NR4A3 MUTATED"         
clus
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
D72V11, continuous
[1] "Remove cluster labels:" "NR4A3 MUTATED"         
clus
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NR4A3 MUTATED    4  2  1  0
  NR4A3 WILD-TYPE 76 33  3  2
D72V12, multiclass
    clus
vv   NR4A3 MUTATED NR4A3 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NR4A3 MUTATED       2                         0     5
  NR4A3 WILD-TYPE     4                         5   109
D72V14, multiclass
                           clus
vv                          NR4A3 MUTATED NR4A3 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                 cls
clus               0  1
  NR4A3 MUTATED    0  4
  NR4A3 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      0    4
  NR4A3 WILD-TYPE    5   87
                        clus
vv                       NR4A3 MUTATED NR4A3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(73) Variable = DPYS MUTATION ANALYSIS
D73V1, survival
                sevent
clus2             0  1
  DPYS MUTATED    5  6
  DPYS WILD-TYPE 58 56
  DPYS MUTATED DPYS WILD-TYPE 
            11            114 
  DPYS MUTATED DPYS WILD-TYPE 
             6             56 
$`DPYS MUTATED`
TCGA-F2-A44G TCGA-2J-AAB4 TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IZ TCGA-FB-A5VM 
        7.66        23.97        50.70        32.81        10.13        16.37 
TCGA-IB-7651 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-XD-AAUG 
       19.82        10.29        13.68        15.32        13.81 

$`DPYS WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 
       33.57        63.85        15.06        36.26        34.09        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T 
       75.12        71.74        19.46         3.12        17.00        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
        7.56        12.46         8.78         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        18.67        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  DPYS MUTATED DPYS WILD-TYPE 
          7.66           0.23 
  DPYS MUTATED DPYS WILD-TYPE 
         50.70          90.12 
  DPYS MUTATED DPYS WILD-TYPE 
        15.320         15.205 
[1] "7.7 - 50.7 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D73V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DPYS MUTATED         0        0        3         0         7         0
  DPYS WILD-TYPE       1        3        9        19        75         4
                vv
clus             STAGE IV
  DPYS MUTATED          1
  DPYS WILD-TYPE        2
D73V3, multiclass
           clus
vv          DPYS MUTATED DPYS WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             3              9
  STAGE IIA            0             19
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  DPYS MUTATED    0  4     7
  DPYS WILD-TYPE  5 13    95
D73V4, multiclass
       clus
vv      DPYS MUTATED DPYS WILD-TYPE
  T1               0              5
  T2               4             13
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                cls
clus              0  1
  DPYS MUTATED    3  8
  DPYS WILD-TYPE 32 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPYS MUTATED      3    8
  DPYS WILD-TYPE   32   81
   clus
vv  DPYS MUTATED DPYS WILD-TYPE
  0            3             32
  1            8             81
[1] 2 2
[1] FALSE
D73V6, binary
                cls
clus              0  1
  DPYS MUTATED    4  1
  DPYS WILD-TYPE 53  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPYS MUTATED      4    1
  DPYS WILD-TYPE   53    2
   clus
vv  DPYS MUTATED DPYS WILD-TYPE
  0            4             53
  1            1              2
[1] 2 2
[1] FALSE
D73V7, binary
                cls
clus              0  1
  DPYS MUTATED    6  5
  DPYS WILD-TYPE 45 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPYS MUTATED      6    5
  DPYS WILD-TYPE   45   70
        clus
vv       DPYS MUTATED DPYS WILD-TYPE
  FEMALE            6             45
  MALE              5             70
[1] 2 2
[1] FALSE
D73V8, binary
                cls
clus              0  1
  DPYS MUTATED    9  2
  DPYS WILD-TYPE 79 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPYS MUTATED      9    2
  DPYS WILD-TYPE   79   28
     clus
vv    DPYS MUTATED DPYS WILD-TYPE
  NO             9             79
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DPYS MUTATED                                     7
  DPYS WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DPYS MUTATED                                       4
  DPYS WILD-TYPE                                    14
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DPYS MUTATED                                                  0
  DPYS WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  DPYS MUTATED                                     0
  DPYS WILD-TYPE                                   1
D73V9, multiclass
                                                  clus
vv                                                 DPYS MUTATED DPYS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       4             14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
D73V11, continuous
                vv
clus             R0 R1 R2 RX
  DPYS MUTATED    9  2  0  0
  DPYS WILD-TYPE 71 33  4  2
D73V12, multiclass
    clus
vv   DPYS MUTATED DPYS WILD-TYPE
  R0            9             71
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DPYS MUTATED       0                         0    11
  DPYS WILD-TYPE     6                         5   103
D73V14, multiclass
                           clus
vv                          DPYS MUTATED DPYS WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               11            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                cls
clus              0  1
  DPYS MUTATED    1  9
  DPYS WILD-TYPE  4 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPYS MUTATED      1    9
  DPYS WILD-TYPE    4   82
                        clus
vv                       DPYS MUTATED DPYS WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            9             82
[1] 2 2
[1] FALSE

Clustering(74) Variable = LRIG1 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2              0  1
  LRIG1 MUTATED    6  5
  LRIG1 WILD-TYPE 57 57
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             11             114 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
              5              57 
$`LRIG1 MUTATED`
TCGA-3A-A9IJ TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-2J-AABA TCGA-3A-A9I7 TCGA-FB-AAPS 
       60.95         8.02         1.08        19.96        43.50         7.50 
TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-AAUQ TCGA-US-A77G 
       32.15        19.82        15.19         6.02         0.39 

$`LRIG1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FZ-5924 
       14.40        10.49        58.98        90.12         7.66        15.78 
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.12        12.92        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       42.31        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.33        15.95        37.15        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  LRIG1 MUTATED LRIG1 WILD-TYPE 
           0.39            0.23 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          60.95           90.12 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
          15.19           15.27 
[1] "0.4 - 61.0 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D74V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LRIG1 MUTATED         0        1        1         0         8         1
  LRIG1 WILD-TYPE       1        2       11        19        74         3
                 vv
clus              STAGE IV
  LRIG1 MUTATED          0
  LRIG1 WILD-TYPE        3
D74V3, multiclass
           clus
vv          LRIG1 MUTATED LRIG1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             8              74
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LRIG1 MUTATED    1  2     8
  LRIG1 WILD-TYPE  4 15    94
D74V4, multiclass
       clus
vv      LRIG1 MUTATED LRIG1 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                 cls
clus               0  1
  LRIG1 MUTATED    2  9
  LRIG1 WILD-TYPE 33 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      2    9
  LRIG1 WILD-TYPE   33   80
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0             2              33
  1             9              80
[1] 2 2
[1] FALSE
D74V6, binary
                 cls
clus               0  1
  LRIG1 MUTATED    5  0
  LRIG1 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      5    0
  LRIG1 WILD-TYPE   52    3
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D74V7, binary
                 cls
clus               0  1
  LRIG1 MUTATED    4  7
  LRIG1 WILD-TYPE 47 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      4    7
  LRIG1 WILD-TYPE   47   68
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  FEMALE             4              47
  MALE               7              68
[1] 2 2
[1] FALSE
D74V8, binary
                 cls
clus               0  1
  LRIG1 MUTATED    7  3
  LRIG1 WILD-TYPE 81 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      7    3
  LRIG1 WILD-TYPE   81   27
     clus
vv    LRIG1 MUTATED LRIG1 WILD-TYPE
  NO              7              81
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LRIG1 MUTATED                                     8
  LRIG1 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LRIG1 MUTATED                                       3
  LRIG1 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LRIG1 MUTATED                                                  0
  LRIG1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LRIG1 MUTATED                                     0
  LRIG1 WILD-TYPE                                   1
D74V9, multiclass
                                                  clus
vv                                                 LRIG1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LRIG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, continuous
D74V11, continuous
                 vv
clus              R0 R1 R2 RX
  LRIG1 MUTATED    8  3  0  0
  LRIG1 WILD-TYPE 72 32  4  2
D74V12, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  R0             8              72
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRIG1 MUTATED       1                         1     9
  LRIG1 WILD-TYPE     5                         4   105
D74V14, multiclass
                           clus
vv                          LRIG1 MUTATED LRIG1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                 cls
clus               0  1
  LRIG1 MUTATED    0  9
  LRIG1 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      0    9
  LRIG1 WILD-TYPE    5   82
                        clus
vv                       LRIG1 MUTATED LRIG1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(75) Variable = EPS8L3 MUTATION ANALYSIS
D75V1, survival
                  sevent
clus2               0  1
  EPS8L3 MUTATED    3  5
  EPS8L3 WILD-TYPE 60 57
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               8              117 
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               5               57 
$`EPS8L3 MUTATED`
TCGA-2J-AABV TCGA-3A-A9I7 TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-FZ-5919 TCGA-IB-7651 
       21.44        43.50        15.06        10.13        24.36        19.82 
TCGA-IB-A5ST TCGA-RB-AA9M 
       20.88         9.40 

$`EPS8L3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 
       23.54        15.55         4.04         5.03         1.02         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85         7.20        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
            9.40             0.23 
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
           43.50            90.12 
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
           20.35            15.19 
[1] "9.4 - 43.5 (20.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D75V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EPS8L3 MUTATED         0        0        0         0         8         0
  EPS8L3 WILD-TYPE       1        3       12        19        74         4
                  vv
clus               STAGE IV
  EPS8L3 MUTATED          0
  EPS8L3 WILD-TYPE        3
D75V3, multiclass
           clus
vv          EPS8L3 MUTATED EPS8L3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              8               74
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  EPS8L3 MUTATED    1  0     7
  EPS8L3 WILD-TYPE  4 17    95
D75V4, multiclass
       clus
vv      EPS8L3 MUTATED EPS8L3 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                  cls
clus                0  1
  EPS8L3 MUTATED    0  8
  EPS8L3 WILD-TYPE 35 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPS8L3 MUTATED      0    8
  EPS8L3 WILD-TYPE   35   81
   clus
vv  EPS8L3 MUTATED EPS8L3 WILD-TYPE
  0              0               35
  1              8               81
[1] 2 2
[1] FALSE
D75V6, binary
                  cls
clus                0  1
  EPS8L3 MUTATED    3  0
  EPS8L3 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPS8L3 MUTATED      3    0
  EPS8L3 WILD-TYPE   54    3
   clus
vv  EPS8L3 MUTATED EPS8L3 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D75V7, binary
                  cls
clus                0  1
  EPS8L3 MUTATED    3  5
  EPS8L3 WILD-TYPE 48 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPS8L3 MUTATED      3    5
  EPS8L3 WILD-TYPE   48   70
        clus
vv       EPS8L3 MUTATED EPS8L3 WILD-TYPE
  FEMALE              3               48
  MALE                5               70
[1] 2 2
[1] FALSE
D75V8, binary
                  cls
clus                0  1
  EPS8L3 MUTATED    6  2
  EPS8L3 WILD-TYPE 82 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPS8L3 MUTATED      6    2
  EPS8L3 WILD-TYPE   82   28
     clus
vv    EPS8L3 MUTATED EPS8L3 WILD-TYPE
  NO               6               82
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EPS8L3 MUTATED                                     8
  EPS8L3 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EPS8L3 MUTATED                                       0
  EPS8L3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EPS8L3 MUTATED                                                  0
  EPS8L3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  EPS8L3 MUTATED                                     0
  EPS8L3 WILD-TYPE                                   1
D75V9, multiclass
                                                  clus
vv                                                 EPS8L3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 EPS8L3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
[1] "Remove cluster labels:" "EPS8L3 MUTATED"        
clus
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2L-AAQA 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-YY-A8LH 
"EPS8L3 WILD-TYPE" 
D75V11, continuous
[1] "Remove cluster labels:" "EPS8L3 MUTATED"        
clus
  EPS8L3 MUTATED EPS8L3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" "EPS8L3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  EPS8L3 MUTATED    5  2  0  0
  EPS8L3 WILD-TYPE 75 33  4  2
D75V12, multiclass
    clus
vv   EPS8L3 MUTATED EPS8L3 WILD-TYPE
  R0              5               75
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPS8L3 MUTATED       0                         1     7
  EPS8L3 WILD-TYPE     6                         4   107
D75V14, multiclass
                           clus
vv                          EPS8L3 MUTATED EPS8L3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                  cls
clus                0  1
  EPS8L3 MUTATED    1  6
  EPS8L3 WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPS8L3 MUTATED      1    6
  EPS8L3 WILD-TYPE    4   85
                        clus
vv                       EPS8L3 MUTATED EPS8L3 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(76) Variable = RIOK1 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2              0  1
  RIOK1 MUTATED    5  3
  RIOK1 WILD-TYPE 58 59
  RIOK1 MUTATED RIOK1 WILD-TYPE 
              8             117 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
              3              59 
$`RIOK1 MUTATED`
TCGA-FB-AAPZ TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-AAUQ TCGA-IB-AAUV TCGA-LB-A9Q5 
       23.54        32.15        19.82         6.02        13.28        10.29 
TCGA-Q3-AA2A TCGA-YB-A89D 
        3.12        11.51 

$`RIOK1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
        7.40         8.05         7.56        12.46         8.78        13.68 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RIOK1 MUTATED RIOK1 WILD-TYPE 
           3.12            0.23 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
          32.15           90.12 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
         12.395          15.320 
[1] "3.1 - 32.1 (12.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D76V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RIOK1 MUTATED         0        0        1         0         7         0
  RIOK1 WILD-TYPE       1        3       11        19        75         4
                 vv
clus              STAGE IV
  RIOK1 MUTATED          0
  RIOK1 WILD-TYPE        3
D76V3, multiclass
           clus
vv          RIOK1 MUTATED RIOK1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RIOK1 MUTATED    0  1     7
  RIOK1 WILD-TYPE  5 16    95
D76V4, multiclass
       clus
vv      RIOK1 MUTATED RIOK1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                 cls
clus               0  1
  RIOK1 MUTATED    0  8
  RIOK1 WILD-TYPE 35 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      0    8
  RIOK1 WILD-TYPE   35   81
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0             0              35
  1             8              81
[1] 2 2
[1] FALSE
D76V6, binary
                 cls
clus               0  1
  RIOK1 MUTATED    4  0
  RIOK1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      4    0
  RIOK1 WILD-TYPE   53    3
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D76V7, binary
                 cls
clus               0  1
  RIOK1 MUTATED    3  5
  RIOK1 WILD-TYPE 48 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      3    5
  RIOK1 WILD-TYPE   48   70
        clus
vv       RIOK1 MUTATED RIOK1 WILD-TYPE
  FEMALE             3              48
  MALE               5              70
[1] 2 2
[1] FALSE
D76V8, binary
                 cls
clus               0  1
  RIOK1 MUTATED    5  3
  RIOK1 WILD-TYPE 83 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      5    3
  RIOK1 WILD-TYPE   83   27
     clus
vv    RIOK1 MUTATED RIOK1 WILD-TYPE
  NO              5              83
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RIOK1 MUTATED                                     7
  RIOK1 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RIOK1 MUTATED                                       1
  RIOK1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RIOK1 MUTATED                                                  0
  RIOK1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RIOK1 MUTATED                                     0
  RIOK1 WILD-TYPE                                   1
D76V9, multiclass
                                                  clus
vv                                                 RIOK1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RIOK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, continuous
D76V11, continuous
                 vv
clus              R0 R1 R2 RX
  RIOK1 MUTATED    6  1  0  1
  RIOK1 WILD-TYPE 74 34  4  1
D76V12, multiclass
    clus
vv   RIOK1 MUTATED RIOK1 WILD-TYPE
  R0             6              74
  R1             1              34
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIOK1 MUTATED       1                         0     7
  RIOK1 WILD-TYPE     5                         5   107
D76V14, multiclass
                           clus
vv                          RIOK1 MUTATED RIOK1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                 cls
clus               0  1
  RIOK1 MUTATED    0  7
  RIOK1 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      0    7
  RIOK1 WILD-TYPE    5   84
                        clus
vv                       RIOK1 MUTATED RIOK1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(77) Variable = RBM10 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2              0  1
  RBM10 MUTATED    6  5
  RBM10 WILD-TYPE 57 57
  RBM10 MUTATED RBM10 WILD-TYPE 
             11             114 
  RBM10 MUTATED RBM10 WILD-TYPE 
              5              57 
$`RBM10 MUTATED`
TCGA-FZ-5924 TCGA-US-A77E TCGA-2J-AAB4 TCGA-3A-A9I7 TCGA-FB-AAQ2 TCGA-HV-A7OL 
       15.78        14.14        23.97        43.50         5.03         8.28 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-US-A77G TCGA-XD-AAUH 
       19.82        36.69        15.19         0.39        12.99 

$`RBM10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
        8.02         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP 
        5.10        36.20        20.35        17.79        22.06        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-A5SO 
        5.26        10.85         0.23        19.82        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI 
        0.30        39.98        16.80        18.67        13.81        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.39            0.23 
  RBM10 MUTATED RBM10 WILD-TYPE 
          43.50           90.12 
  RBM10 MUTATED RBM10 WILD-TYPE 
          15.19           15.27 
[1] "0.4 - 43.5 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D77V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM10 MUTATED         0        0        0         2         8         1
  RBM10 WILD-TYPE       1        3       12        17        74         3
                 vv
clus              STAGE IV
  RBM10 MUTATED          0
  RBM10 WILD-TYPE        3
D77V3, multiclass
           clus
vv          RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             8              74
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM10 MUTATED    0  1    10
  RBM10 WILD-TYPE  5 16    92
D77V4, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                 cls
clus               0  1
  RBM10 MUTATED    1 10
  RBM10 WILD-TYPE 34 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      1   10
  RBM10 WILD-TYPE   34   79
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             1              34
  1            10              79
[1] 2 2
[1] FALSE
D77V6, binary
                 cls
clus               0  1
  RBM10 MUTATED    6  0
  RBM10 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      6    0
  RBM10 WILD-TYPE   51    3
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D77V7, binary
                 cls
clus               0  1
  RBM10 MUTATED    5  6
  RBM10 WILD-TYPE 46 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      5    6
  RBM10 WILD-TYPE   46   69
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             5              46
  MALE               6              69
[1] 2 2
[1] FALSE
D77V8, binary
                 cls
clus               0  1
  RBM10 MUTATED    9  2
  RBM10 WILD-TYPE 79 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      9    2
  RBM10 WILD-TYPE   79   28
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              9              79
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM10 MUTATED                                     9
  RBM10 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM10 MUTATED                                       2
  RBM10 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM10 MUTATED                                                  0
  RBM10 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM10 MUTATED                                     0
  RBM10 WILD-TYPE                                   1
D77V9, multiclass
                                                  clus
vv                                                 RBM10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RBM10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, continuous
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-YY-A8LH 
"RBM10 WILD-TYPE" 
D77V11, continuous
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RBM10 MUTATED    5  4  2  0
  RBM10 WILD-TYPE 75 31  2  2
D77V12, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             5              75
  R1             4              31
  R2             2               2
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       2                         1     8
  RBM10 WILD-TYPE     4                         4   106
D77V14, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                 cls
clus               0  1
  RBM10 MUTATED    0  9
  RBM10 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0    9
  RBM10 WILD-TYPE    5   82
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(78) Variable = USP40 MUTATION ANALYSIS
D78V1, survival
                 sevent
clus2              0  1
  USP40 MUTATED    5  5
  USP40 WILD-TYPE 58 57
  USP40 MUTATED USP40 WILD-TYPE 
             10             115 
  USP40 MUTATED USP40 WILD-TYPE 
              5              57 
$`USP40 MUTATED`
TCGA-FB-AAQ6 TCGA-2J-AABE TCGA-3A-A9IU TCGA-FB-AAQ2 TCGA-HV-AA8X TCGA-HZ-A77P 
        8.02        22.22        15.06         5.03        17.49        10.85 
TCGA-IB-7651 TCGA-IB-AAUU TCGA-XD-AAUG TCGA-YY-A8LH 
       19.82         8.05        13.81        66.28 

$`USP40 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13         5.26         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  USP40 MUTATED USP40 WILD-TYPE 
           5.03            0.23 
  USP40 MUTATED USP40 WILD-TYPE 
          66.28           90.12 
  USP40 MUTATED USP40 WILD-TYPE 
         14.435          15.320 
[1] "5.0 - 66.3 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D78V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  USP40 MUTATED         0        1        0         1         7         0
  USP40 WILD-TYPE       1        2       12        18        75         4
                 vv
clus              STAGE IV
  USP40 MUTATED          1
  USP40 WILD-TYPE        2
D78V3, multiclass
           clus
vv          USP40 MUTATED USP40 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  USP40 MUTATED    1  1     8
  USP40 WILD-TYPE  4 16    94
D78V4, multiclass
       clus
vv      USP40 MUTATED USP40 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V5, binary
                 cls
clus               0  1
  USP40 MUTATED    2  8
  USP40 WILD-TYPE 33 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP40 MUTATED      2    8
  USP40 WILD-TYPE   33   81
   clus
vv  USP40 MUTATED USP40 WILD-TYPE
  0             2              33
  1             8              81
[1] 2 2
[1] FALSE
D78V6, binary
                 cls
clus               0  1
  USP40 MUTATED    3  1
  USP40 WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP40 MUTATED      3    1
  USP40 WILD-TYPE   54    2
   clus
vv  USP40 MUTATED USP40 WILD-TYPE
  0             3              54
  1             1               2
[1] 2 2
[1] FALSE
D78V7, binary
                 cls
clus               0  1
  USP40 MUTATED    5  5
  USP40 WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP40 MUTATED      5    5
  USP40 WILD-TYPE   46   70
        clus
vv       USP40 MUTATED USP40 WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D78V8, binary
                 cls
clus               0  1
  USP40 MUTATED    8  2
  USP40 WILD-TYPE 80 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP40 MUTATED      8    2
  USP40 WILD-TYPE   80   28
     clus
vv    USP40 MUTATED USP40 WILD-TYPE
  NO              8              80
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  USP40 MUTATED                                     9
  USP40 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  USP40 MUTATED                                       1
  USP40 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  USP40 MUTATED                                                  0
  USP40 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  USP40 MUTATED                                     0
  USP40 WILD-TYPE                                   1
D78V9, multiclass
                                                  clus
vv                                                 USP40 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 USP40 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, continuous
D78V11, continuous
                 vv
clus              R0 R1 R2 RX
  USP40 MUTATED    8  1  1  0
  USP40 WILD-TYPE 72 34  3  2
D78V12, multiclass
    clus
vv   USP40 MUTATED USP40 WILD-TYPE
  R0             8              72
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP40 MUTATED       1                         0     9
  USP40 WILD-TYPE     5                         5   105
D78V14, multiclass
                           clus
vv                          USP40 MUTATED USP40 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                 cls
clus               0  1
  USP40 MUTATED    0  8
  USP40 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP40 MUTATED      0    8
  USP40 WILD-TYPE    5   83
                        clus
vv                       USP40 MUTATED USP40 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(79) Variable = NAPSA MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2              0  1
  NAPSA MUTATED    3  5
  NAPSA WILD-TYPE 60 57
  NAPSA MUTATED NAPSA WILD-TYPE 
              8             117 
  NAPSA MUTATED NAPSA WILD-TYPE 
              5              57 
$`NAPSA MUTATED`
TCGA-US-A77E TCGA-3A-A9I7 TCGA-FZ-5922 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7651 
       14.14        43.50        36.20        20.19         5.26        19.82 
TCGA-IB-A6UF TCGA-XN-A8T5 
       21.90        23.67 

$`NAPSA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        31.27        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NAPSA MUTATED NAPSA WILD-TYPE 
           5.26            0.23 
  NAPSA MUTATED NAPSA WILD-TYPE 
          43.50           90.12 
  NAPSA MUTATED NAPSA WILD-TYPE 
         21.045          15.120 
[1] "5.3 - 43.5 (21.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.1"
D79V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NAPSA MUTATED         0        0        1         1         6         0
  NAPSA WILD-TYPE       1        3       11        18        76         4
                 vv
clus              STAGE IV
  NAPSA MUTATED          0
  NAPSA WILD-TYPE        3
D79V3, multiclass
           clus
vv          NAPSA MUTATED NAPSA WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NAPSA MUTATED    0  2     6
  NAPSA WILD-TYPE  5 15    96
D79V4, multiclass
       clus
vv      NAPSA MUTATED NAPSA WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V5, binary
                 cls
clus               0  1
  NAPSA MUTATED    2  6
  NAPSA WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      2    6
  NAPSA WILD-TYPE   33   83
   clus
vv  NAPSA MUTATED NAPSA WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D79V6, binary
                 cls
clus               0  1
  NAPSA MUTATED    4  0
  NAPSA WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      4    0
  NAPSA WILD-TYPE   53    3
   clus
vv  NAPSA MUTATED NAPSA WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D79V7, binary
                 cls
clus               0  1
  NAPSA MUTATED    3  5
  NAPSA WILD-TYPE 48 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      3    5
  NAPSA WILD-TYPE   48   70
        clus
vv       NAPSA MUTATED NAPSA WILD-TYPE
  FEMALE             3              48
  MALE               5              70
[1] 2 2
[1] FALSE
D79V8, binary
                 cls
clus               0  1
  NAPSA MUTATED    6  2
  NAPSA WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      6    2
  NAPSA WILD-TYPE   82   28
     clus
vv    NAPSA MUTATED NAPSA WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAPSA MUTATED                                     6
  NAPSA WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAPSA MUTATED                                       2
  NAPSA WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAPSA MUTATED                                                  0
  NAPSA WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NAPSA MUTATED                                     0
  NAPSA WILD-TYPE                                   1
D79V9, multiclass
                                                  clus
vv                                                 NAPSA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NAPSA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, continuous
D79V11, continuous
                 vv
clus              R0 R1 R2 RX
  NAPSA MUTATED    5  3  0  0
  NAPSA WILD-TYPE 75 32  4  2
D79V12, multiclass
    clus
vv   NAPSA MUTATED NAPSA WILD-TYPE
  R0             5              75
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAPSA MUTATED       0                         1     7
  NAPSA WILD-TYPE     6                         4   107
D79V14, multiclass
                           clus
vv                          NAPSA MUTATED NAPSA WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                 cls
clus               0  1
  NAPSA MUTATED    1  7
  NAPSA WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      1    7
  NAPSA WILD-TYPE    4   84
                        clus
vv                       NAPSA MUTATED NAPSA WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(80) Variable = GPR25 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2              0  1
  GPR25 MUTATED    2  3
  GPR25 WILD-TYPE 61 59
  GPR25 MUTATED GPR25 WILD-TYPE 
              5             120 
  GPR25 MUTATED GPR25 WILD-TYPE 
              3              59 
$`GPR25 MUTATED`
TCGA-IB-A5SS TCGA-H8-A6C1 TCGA-HZ-A77O TCGA-IB-7651 TCGA-XN-A8T3 
       15.12        22.06         5.26        19.82        31.27 

$`GPR25 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        23.67        11.51        12.76        66.28        15.35 

  GPR25 MUTATED GPR25 WILD-TYPE 
           5.26            0.23 
  GPR25 MUTATED GPR25 WILD-TYPE 
          31.27           90.12 
  GPR25 MUTATED GPR25 WILD-TYPE 
         19.820          15.205 
[1] "5.3 - 31.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D80V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GPR25 MUTATED         0        0        1         1         3         0
  GPR25 WILD-TYPE       1        3       11        18        79         4
                 vv
clus              STAGE IV
  GPR25 MUTATED          0
  GPR25 WILD-TYPE        3
D80V3, multiclass
           clus
vv          GPR25 MUTATED GPR25 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  GPR25 MUTATED    0  2     3
  GPR25 WILD-TYPE  5 15    99
D80V4, multiclass
       clus
vv      GPR25 MUTATED GPR25 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V5, binary
                 cls
clus               0  1
  GPR25 MUTATED    2  3
  GPR25 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      2    3
  GPR25 WILD-TYPE   33   86
   clus
vv  GPR25 MUTATED GPR25 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D80V6, binary
                 cls
clus               0  1
  GPR25 MUTATED    3  0
  GPR25 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      3    0
  GPR25 WILD-TYPE   54    3
   clus
vv  GPR25 MUTATED GPR25 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D80V7, binary
                 cls
clus               0  1
  GPR25 MUTATED    3  2
  GPR25 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      3    2
  GPR25 WILD-TYPE   48   73
        clus
vv       GPR25 MUTATED GPR25 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D80V8, binary
                 cls
clus               0  1
  GPR25 MUTATED    4  1
  GPR25 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      4    1
  GPR25 WILD-TYPE   84   29
     clus
vv    GPR25 MUTATED GPR25 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR25 MUTATED                                     4
  GPR25 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR25 MUTATED                                       1
  GPR25 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR25 MUTATED                                                  0
  GPR25 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  GPR25 MUTATED                                     0
  GPR25 WILD-TYPE                                   1
D80V9, multiclass
                                                  clus
vv                                                 GPR25 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 GPR25 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, continuous
D80V11, continuous
                 vv
clus              R0 R1 R2 RX
  GPR25 MUTATED    4  1  0  0
  GPR25 WILD-TYPE 76 34  4  2
D80V12, multiclass
    clus
vv   GPR25 MUTATED GPR25 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR25 MUTATED       0                         0     5
  GPR25 WILD-TYPE     6                         5   109
D80V14, multiclass
                           clus
vv                          GPR25 MUTATED GPR25 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                 cls
clus               0  1
  GPR25 MUTATED    1  4
  GPR25 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      1    4
  GPR25 WILD-TYPE    4   87
                        clus
vv                       GPR25 MUTATED GPR25 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(81) Variable = SETD1A MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2               0  1
  SETD1A MUTATED    4  7
  SETD1A WILD-TYPE 59 55
  SETD1A MUTATED SETD1A WILD-TYPE 
              11              114 
  SETD1A MUTATED SETD1A WILD-TYPE 
               7               55 
$`SETD1A MUTATED`
TCGA-LB-A7SX TCGA-2J-AABA TCGA-2J-AABE TCGA-2L-AAQJ TCGA-FB-A5VM TCGA-FB-A78T 
       12.92        19.96        22.22        12.95        16.37        12.33 
TCGA-HV-AA8X TCGA-IB-AAUM TCGA-IB-AAUQ TCGA-XD-AAUH TCGA-XN-A8T3 
       17.49         0.26         6.02        12.99        31.27 

$`SETD1A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49         3.39         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22        15.88         4.73         7.86        14.17 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        23.67        11.51        12.76        66.28        15.35 

  SETD1A MUTATED SETD1A WILD-TYPE 
            0.26             0.23 
  SETD1A MUTATED SETD1A WILD-TYPE 
           31.27            90.12 
  SETD1A MUTATED SETD1A WILD-TYPE 
           12.99            15.27 
[1] "0.3 - 31.3 (13.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D81V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SETD1A MUTATED         0        0        2         1         7         1
  SETD1A WILD-TYPE       1        3       10        18        75         3
                  vv
clus               STAGE IV
  SETD1A MUTATED          0
  SETD1A WILD-TYPE        3
D81V3, multiclass
           clus
vv          SETD1A MUTATED SETD1A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              1               18
  STAGE IIB              7               75
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SETD1A MUTATED    0  4     7
  SETD1A WILD-TYPE  5 13    95
D81V4, multiclass
       clus
vv      SETD1A MUTATED SETD1A WILD-TYPE
  T1                 0                5
  T2                 4               13
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V5, binary
                  cls
clus                0  1
  SETD1A MUTATED    4  7
  SETD1A WILD-TYPE 31 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETD1A MUTATED      4    7
  SETD1A WILD-TYPE   31   82
   clus
vv  SETD1A MUTATED SETD1A WILD-TYPE
  0              4               31
  1              7               82
[1] 2 2
[1] FALSE
D81V6, binary
                  cls
clus                0  1
  SETD1A MUTATED    8  0
  SETD1A WILD-TYPE 49  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETD1A MUTATED      8    0
  SETD1A WILD-TYPE   49    3
   clus
vv  SETD1A MUTATED SETD1A WILD-TYPE
  0              8               49
  1              0                3
[1] 2 2
[1] FALSE
D81V7, binary
                  cls
clus                0  1
  SETD1A MUTATED    5  6
  SETD1A WILD-TYPE 46 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETD1A MUTATED      5    6
  SETD1A WILD-TYPE   46   69
        clus
vv       SETD1A MUTATED SETD1A WILD-TYPE
  FEMALE              5               46
  MALE                6               69
[1] 2 2
[1] FALSE
D81V8, binary
                  cls
clus                0  1
  SETD1A MUTATED    8  3
  SETD1A WILD-TYPE 80 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETD1A MUTATED      8    3
  SETD1A WILD-TYPE   80   27
     clus
vv    SETD1A MUTATED SETD1A WILD-TYPE
  NO               8               80
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SETD1A MUTATED                                    11
  SETD1A WILD-TYPE                                  94
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SETD1A MUTATED                                       0
  SETD1A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SETD1A MUTATED                                                  0
  SETD1A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SETD1A MUTATED                                     0
  SETD1A WILD-TYPE                                   1
D81V9, multiclass
                                                  clus
vv                                                 SETD1A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SETD1A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, continuous
D81V11, continuous
                  vv
clus               R0 R1 R2 RX
  SETD1A MUTATED    4  5  2  0
  SETD1A WILD-TYPE 76 30  2  2
D81V12, multiclass
    clus
vv   SETD1A MUTATED SETD1A WILD-TYPE
  R0              4               76
  R1              5               30
  R2              2                2
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETD1A MUTATED       1                         1     9
  SETD1A WILD-TYPE     5                         4   105
D81V14, multiclass
                           clus
vv                          SETD1A MUTATED SETD1A WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                  cls
clus                0  1
  SETD1A MUTATED    1  6
  SETD1A WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SETD1A MUTATED      1    6
  SETD1A WILD-TYPE    4   85
                        clus
vv                       SETD1A MUTATED SETD1A WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(82) Variable = SEC63 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2              0  1
  SEC63 MUTATED    5  3
  SEC63 WILD-TYPE 58 59
  SEC63 MUTATED SEC63 WILD-TYPE 
              8             117 
  SEC63 MUTATED SEC63 WILD-TYPE 
              3              59 
$`SEC63 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IB TCGA-F2-A8YN TCGA-IB-A6UF TCGA-IB-AAUS TCGA-IB-AAUU 
        1.08         7.36        17.00        21.90         7.40         8.05 
TCGA-US-A77G TCGA-XD-AAUI 
        0.39        12.03 

$`SEC63 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SEC63 MUTATED SEC63 WILD-TYPE 
           0.39            0.23 
  SEC63 MUTATED SEC63 WILD-TYPE 
          21.90           90.12 
  SEC63 MUTATED SEC63 WILD-TYPE 
          7.725          15.350 
[1] "0.4 - 21.9 (7.7)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D82V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SEC63 MUTATED         0        0        0         1         7         0
  SEC63 WILD-TYPE       1        3       12        18        75         4
                 vv
clus              STAGE IV
  SEC63 MUTATED          0
  SEC63 WILD-TYPE        3
D82V3, multiclass
           clus
vv          SEC63 MUTATED SEC63 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SEC63 MUTATED    0  0     8
  SEC63 WILD-TYPE  5 17    94
D82V4, multiclass
       clus
vv      SEC63 MUTATED SEC63 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V5, binary
                 cls
clus               0  1
  SEC63 MUTATED    1  7
  SEC63 WILD-TYPE 34 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      1    7
  SEC63 WILD-TYPE   34   82
   clus
vv  SEC63 MUTATED SEC63 WILD-TYPE
  0             1              34
  1             7              82
[1] 2 2
[1] FALSE
D82V6, binary
                 cls
clus               0  1
  SEC63 MUTATED    4  0
  SEC63 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      4    0
  SEC63 WILD-TYPE   53    3
   clus
vv  SEC63 MUTATED SEC63 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus               0  1
  SEC63 MUTATED    4  4
  SEC63 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      4    4
  SEC63 WILD-TYPE   47   71
        clus
vv       SEC63 MUTATED SEC63 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D82V8, binary
                 cls
clus               0  1
  SEC63 MUTATED    7  0
  SEC63 WILD-TYPE 81 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      7    0
  SEC63 WILD-TYPE   81   30
     clus
vv    SEC63 MUTATED SEC63 WILD-TYPE
  NO              7              81
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEC63 MUTATED                                     7
  SEC63 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEC63 MUTATED                                       1
  SEC63 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEC63 MUTATED                                                  0
  SEC63 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SEC63 MUTATED                                     0
  SEC63 WILD-TYPE                                   1
D82V9, multiclass
                                                  clus
vv                                                 SEC63 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SEC63 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, continuous
D82V11, continuous
                 vv
clus              R0 R1 R2 RX
  SEC63 MUTATED    4  4  0  0
  SEC63 WILD-TYPE 76 31  4  2
D82V12, multiclass
    clus
vv   SEC63 MUTATED SEC63 WILD-TYPE
  R0             4              76
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEC63 MUTATED       0                         0     8
  SEC63 WILD-TYPE     6                         5   106
D82V14, multiclass
                           clus
vv                          SEC63 MUTATED SEC63 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                 cls
clus               0  1
  SEC63 MUTATED    0  8
  SEC63 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      0    8
  SEC63 WILD-TYPE    5   83
                        clus
vv                       SEC63 MUTATED SEC63 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(83) Variable = GAS2L2 MUTATION ANALYSIS
D83V1, survival
                  sevent
clus2               0  1
  GAS2L2 MUTATED    6  6
  GAS2L2 WILD-TYPE 57 56
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
              12              113 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               6               56 
$`GAS2L2 MUTATED`
TCGA-FZ-5924 TCGA-LB-A7SX TCGA-2J-AAB9 TCGA-2J-AABO TCGA-3A-A9IH TCGA-3A-A9J0 
       15.78        12.92        20.61        14.47        33.57        24.43 
TCGA-FZ-5920 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A7LX TCGA-IB-AAUU 
        2.01        10.85        19.82        15.19         8.22         8.05 

$`GAS2L2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        15.91        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50        20.84         7.36        24.26        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       32.81        15.06        36.26        34.09        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03         1.02        24.36         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
            2.01             0.23 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
           33.57            90.12 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
           14.83            15.32 
[1] "2.0 - 33.6 (14.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D83V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GAS2L2 MUTATED         0        1        0         1         9         1
  GAS2L2 WILD-TYPE       1        2       12        18        73         3
                  vv
clus               STAGE IV
  GAS2L2 MUTATED          0
  GAS2L2 WILD-TYPE        3
D83V3, multiclass
           clus
vv          GAS2L2 MUTATED GAS2L2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              9               73
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GAS2L2 MUTATED    1  0    11
  GAS2L2 WILD-TYPE  4 17    91
D83V4, multiclass
       clus
vv      GAS2L2 MUTATED GAS2L2 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4             11               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V5, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    1 11
  GAS2L2 WILD-TYPE 34 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      1   11
  GAS2L2 WILD-TYPE   34   78
   clus
vv  GAS2L2 MUTATED GAS2L2 WILD-TYPE
  0              1               34
  1             11               78
[1] 2 2
[1] FALSE
D83V6, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    7  0
  GAS2L2 WILD-TYPE 50  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      7    0
  GAS2L2 WILD-TYPE   50    3
   clus
vv  GAS2L2 MUTATED GAS2L2 WILD-TYPE
  0              7               50
  1              0                3
[1] 2 2
[1] FALSE
D83V7, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    5  7
  GAS2L2 WILD-TYPE 46 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      5    7
  GAS2L2 WILD-TYPE   46   68
        clus
vv       GAS2L2 MUTATED GAS2L2 WILD-TYPE
  FEMALE              5               46
  MALE                7               68
[1] 2 2
[1] FALSE
D83V8, binary
                  cls
clus                0  1
  GAS2L2 MUTATED   10  2
  GAS2L2 WILD-TYPE 78 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED     10    2
  GAS2L2 WILD-TYPE   78   28
     clus
vv    GAS2L2 MUTATED GAS2L2 WILD-TYPE
  NO              10               78
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GAS2L2 MUTATED                                    11
  GAS2L2 WILD-TYPE                                  94
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GAS2L2 MUTATED                                       1
  GAS2L2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GAS2L2 MUTATED                                                  0
  GAS2L2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GAS2L2 MUTATED                                     0
  GAS2L2 WILD-TYPE                                   1
D83V9, multiclass
                                                  clus
vv                                                 GAS2L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GAS2L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, continuous
D83V11, continuous
                  vv
clus               R0 R1 R2 RX
  GAS2L2 MUTATED   10  2  0  0
  GAS2L2 WILD-TYPE 70 33  4  2
D83V12, multiclass
    clus
vv   GAS2L2 MUTATED GAS2L2 WILD-TYPE
  R0             10               70
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAS2L2 MUTATED       0                         2    10
  GAS2L2 WILD-TYPE     6                         3   104
D83V14, multiclass
                           clus
vv                          GAS2L2 MUTATED GAS2L2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V15, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    0 10
  GAS2L2 WILD-TYPE  5 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      0   10
  GAS2L2 WILD-TYPE    5   81
                        clus
vv                       GAS2L2 MUTATED GAS2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             10               81
[1] 2 2
[1] FALSE

Clustering(84) Variable = PHF8 MUTATION ANALYSIS
D84V1, survival
                sevent
clus2             0  1
  PHF8 MUTATED    6  5
  PHF8 WILD-TYPE 57 57
  PHF8 MUTATED PHF8 WILD-TYPE 
            11            114 
  PHF8 MUTATED PHF8 WILD-TYPE 
             5             57 
$`PHF8 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABP TCGA-2L-AAQI TCGA-F2-A8YN TCGA-FB-AAPZ TCGA-FZ-5922 
       12.92        15.22         3.39        17.00        23.54        36.20 
TCGA-HV-A7OP TCGA-IB-AAUO TCGA-IB-AAUS TCGA-OE-A75W TCGA-US-A776 
       32.15         7.86         7.40         8.78        39.98 

$`PHF8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
        5.10        20.35        17.79        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         4.73        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  PHF8 MUTATED PHF8 WILD-TYPE 
          3.39           0.23 
  PHF8 MUTATED PHF8 WILD-TYPE 
         39.98          90.12 
  PHF8 MUTATED PHF8 WILD-TYPE 
        15.220         15.255 
[1] "3.4 - 40.0 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D84V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHF8 MUTATED         0        0        0         4         7         0
  PHF8 WILD-TYPE       1        3       12        15        75         4
                vv
clus             STAGE IV
  PHF8 MUTATED          0
  PHF8 WILD-TYPE        3
D84V3, multiclass
           clus
vv          PHF8 MUTATED PHF8 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            4             15
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PHF8 MUTATED    0  1    10
  PHF8 WILD-TYPE  5 16    92
D84V4, multiclass
       clus
vv      PHF8 MUTATED PHF8 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4           10             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V5, binary
                cls
clus              0  1
  PHF8 MUTATED    4  7
  PHF8 WILD-TYPE 31 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      4    7
  PHF8 WILD-TYPE   31   82
   clus
vv  PHF8 MUTATED PHF8 WILD-TYPE
  0            4             31
  1            7             82
[1] 2 2
[1] FALSE
D84V6, binary
                cls
clus              0  1
  PHF8 MUTATED    7  0
  PHF8 WILD-TYPE 50  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      7    0
  PHF8 WILD-TYPE   50    3
   clus
vv  PHF8 MUTATED PHF8 WILD-TYPE
  0            7             50
  1            0              3
[1] 2 2
[1] FALSE
D84V7, binary
                cls
clus              0  1
  PHF8 MUTATED    4  7
  PHF8 WILD-TYPE 47 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      4    7
  PHF8 WILD-TYPE   47   68
        clus
vv       PHF8 MUTATED PHF8 WILD-TYPE
  FEMALE            4             47
  MALE              7             68
[1] 2 2
[1] FALSE
D84V8, binary
                cls
clus              0  1
  PHF8 MUTATED    9  2
  PHF8 WILD-TYPE 79 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      9    2
  PHF8 WILD-TYPE   79   28
     clus
vv    PHF8 MUTATED PHF8 WILD-TYPE
  NO             9             79
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF8 MUTATED                                     8
  PHF8 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF8 MUTATED                                       1
  PHF8 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF8 MUTATED                                                  1
  PHF8 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHF8 MUTATED                                     1
  PHF8 WILD-TYPE                                   0
D84V9, multiclass
                                                  clus
vv                                                 PHF8 MUTATED PHF8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         1              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V10, continuous
D84V11, continuous
                vv
clus             R0 R1 R2 RX
  PHF8 MUTATED    6  5  0  0
  PHF8 WILD-TYPE 74 30  4  2
D84V12, multiclass
    clus
vv   PHF8 MUTATED PHF8 WILD-TYPE
  R0            6             74
  R1            5             30
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF8 MUTATED       1                         1     9
  PHF8 WILD-TYPE     5                         4   105
D84V14, multiclass
                           clus
vv                          PHF8 MUTATED PHF8 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V15, binary
                cls
clus              0  1
  PHF8 MUTATED    0  8
  PHF8 WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      0    8
  PHF8 WILD-TYPE    5   83
                        clus
vv                       PHF8 MUTATED PHF8 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(85) Variable = SLC39A5 MUTATION ANALYSIS
D85V1, survival
                   sevent
clus2                0  1
  SLC39A5 MUTATED    3  5
  SLC39A5 WILD-TYPE 60 57
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                8               117 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                5                57 
$`SLC39A5 MUTATED`
TCGA-FB-AAPQ TCGA-HZ-7925 TCGA-HZ-8637 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUS 
       37.15        20.19        17.00        21.90         1.35         7.40 
TCGA-OE-A75W TCGA-Q3-AA2A 
        8.78         3.12 

$`SLC39A5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       17.49        31.86        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85         7.20        20.88         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU 
        4.73         7.86        14.17         6.02        11.11         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-RB-A7B8 
       13.28         7.56        12.46        10.29        13.68        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
             1.35              0.23 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
            37.15             90.12 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
            12.89             15.22 
[1] "1.4 - 37.1 (12.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D85V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC39A5 MUTATED         0        0        1         1         6         0
  SLC39A5 WILD-TYPE       1        3       11        18        76         4
                   vv
clus                STAGE IV
  SLC39A5 MUTATED          0
  SLC39A5 WILD-TYPE        3
D85V3, multiclass
           clus
vv          SLC39A5 MUTATED SLC39A5 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               6                76
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC39A5 MUTATED    0  0     8
  SLC39A5 WILD-TYPE  5 17    94
D85V4, multiclass
       clus
vv      SLC39A5 MUTATED SLC39A5 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               8                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V5, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    1  7
  SLC39A5 WILD-TYPE 34 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      1    7
  SLC39A5 WILD-TYPE   34   82
   clus
vv  SLC39A5 MUTATED SLC39A5 WILD-TYPE
  0               1                34
  1               7                82
[1] 2 2
[1] FALSE
D85V6, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    4  0
  SLC39A5 WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      4    0
  SLC39A5 WILD-TYPE   53    3
   clus
vv  SLC39A5 MUTATED SLC39A5 WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D85V7, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    3  5
  SLC39A5 WILD-TYPE 48 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      3    5
  SLC39A5 WILD-TYPE   48   70
        clus
vv       SLC39A5 MUTATED SLC39A5 WILD-TYPE
  FEMALE               3                48
  MALE                 5                70
[1] 2 2
[1] FALSE
D85V8, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    6  2
  SLC39A5 WILD-TYPE 82 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      6    2
  SLC39A5 WILD-TYPE   82   28
     clus
vv    SLC39A5 MUTATED SLC39A5 WILD-TYPE
  NO                6                82
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC39A5 MUTATED                                     8
  SLC39A5 WILD-TYPE                                  97
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC39A5 MUTATED                                       0
  SLC39A5 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC39A5 MUTATED                                                  0
  SLC39A5 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC39A5 MUTATED                                     0
  SLC39A5 WILD-TYPE                                   1
D85V9, multiclass
                                                  clus
vv                                                 SLC39A5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC39A5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V10, continuous
D85V11, continuous
                   vv
clus                R0 R1 R2 RX
  SLC39A5 MUTATED    4  3  0  1
  SLC39A5 WILD-TYPE 76 32  4  1
D85V12, multiclass
    clus
vv   SLC39A5 MUTATED SLC39A5 WILD-TYPE
  R0               4                76
  R1               3                32
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC39A5 MUTATED       0                         0     8
  SLC39A5 WILD-TYPE     6                         5   106
D85V14, multiclass
                           clus
vv                          SLC39A5 MUTATED SLC39A5 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   8               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V15, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    1  7
  SLC39A5 WILD-TYPE  4 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      1    7
  SLC39A5 WILD-TYPE    4   84
                        clus
vv                       SLC39A5 MUTATED SLC39A5 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               7                84
[1] 2 2
[1] FALSE

Clustering(86) Variable = FAM82A2 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                0  1
  FAM82A2 MUTATED    4  4
  FAM82A2 WILD-TYPE 59 58
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
                8               117 
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
                4                58 
$`FAM82A2 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IC TCGA-HV-A7OL TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A7M4 
       22.49        24.26         8.28        32.15        19.82        15.88 
TCGA-Q3-A5QY TCGA-US-A77J 
       13.68        18.67 

$`FAM82A2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        22.06        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
             8.28              0.23 
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
            32.15             90.12 
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
           19.245            15.120 
[1] "8.3 - 32.1 (19.2)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.2"
D86V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM82A2 MUTATED         0        0        0         1         7         0
  FAM82A2 WILD-TYPE       1        3       12        18        75         4
                   vv
clus                STAGE IV
  FAM82A2 MUTATED          0
  FAM82A2 WILD-TYPE        3
D86V3, multiclass
           clus
vv          FAM82A2 MUTATED FAM82A2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               7                75
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  FAM82A2 MUTATED    0  0     8
  FAM82A2 WILD-TYPE  5 17    94
D86V4, multiclass
       clus
vv      FAM82A2 MUTATED FAM82A2 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               8                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V5, binary
                   cls
clus                 0  1
  FAM82A2 MUTATED    1  7
  FAM82A2 WILD-TYPE 34 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A2 MUTATED      1    7
  FAM82A2 WILD-TYPE   34   82
   clus
vv  FAM82A2 MUTATED FAM82A2 WILD-TYPE
  0               1                34
  1               7                82
[1] 2 2
[1] FALSE
D86V6, binary
                   cls
clus                 0  1
  FAM82A2 MUTATED    3  0
  FAM82A2 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A2 MUTATED      3    0
  FAM82A2 WILD-TYPE   54    3
   clus
vv  FAM82A2 MUTATED FAM82A2 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D86V7, binary
                   cls
clus                 0  1
  FAM82A2 MUTATED    3  5
  FAM82A2 WILD-TYPE 48 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A2 MUTATED      3    5
  FAM82A2 WILD-TYPE   48   70
        clus
vv       FAM82A2 MUTATED FAM82A2 WILD-TYPE
  FEMALE               3                48
  MALE                 5                70
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                 0  1
  FAM82A2 MUTATED    5  2
  FAM82A2 WILD-TYPE 83 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A2 MUTATED      5    2
  FAM82A2 WILD-TYPE   83   28
     clus
vv    FAM82A2 MUTATED FAM82A2 WILD-TYPE
  NO                5                83
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM82A2 MUTATED                                     7
  FAM82A2 WILD-TYPE                                  98
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM82A2 MUTATED                                       1
  FAM82A2 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM82A2 MUTATED                                                  0
  FAM82A2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM82A2 MUTATED                                     0
  FAM82A2 WILD-TYPE                                   1
D86V9, multiclass
                                                  clus
vv                                                 FAM82A2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 FAM82A2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V10, continuous
D86V11, continuous
[1] "Remove cluster labels:" "FAM82A2 MUTATED"       
clus
  FAM82A2 MUTATED FAM82A2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-AAUQ 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" "FAM82A2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  FAM82A2 MUTATED    7  0  1  0
  FAM82A2 WILD-TYPE 73 35  3  2
D86V12, multiclass
    clus
vv   FAM82A2 MUTATED FAM82A2 WILD-TYPE
  R0               7                73
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM82A2 MUTATED       2                         0     6
  FAM82A2 WILD-TYPE     4                         5   108
D86V14, multiclass
                           clus
vv                          FAM82A2 MUTATED FAM82A2 WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V15, binary
                   cls
clus                 0  1
  FAM82A2 MUTATED    0  5
  FAM82A2 WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM82A2 MUTATED      0    5
  FAM82A2 WILD-TYPE    5   86
                        clus
vv                       FAM82A2 MUTATED FAM82A2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(87) Variable = CHGA MUTATION ANALYSIS
D87V1, survival
                sevent
clus2             0  1
  CHGA MUTATED    7  4
  CHGA WILD-TYPE 56 58
  CHGA MUTATED CHGA WILD-TYPE 
            11            114 
  CHGA MUTATED CHGA WILD-TYPE 
             4             58 
$`CHGA MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABE TCGA-2J-AABK TCGA-FB-A5VM TCGA-HZ-7918 TCGA-HZ-A77O 
        1.08        22.22        15.91        16.37        31.86         5.26 
TCGA-IB-7651 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-US-A776 
       19.82         0.26         7.86        14.17        39.98 

$`CHGA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       19.96        22.72        42.31        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        17.49        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUR 
        1.35         8.22        15.88         4.73         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CHGA MUTATED CHGA WILD-TYPE 
          0.26           0.23 
  CHGA MUTATED CHGA WILD-TYPE 
         39.98          90.12 
  CHGA MUTATED CHGA WILD-TYPE 
        15.910         15.205 
[1] "0.3 - 40.0 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D87V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CHGA MUTATED         0        0        1         2         8         0
  CHGA WILD-TYPE       1        3       11        17        74         4
                vv
clus             STAGE IV
  CHGA MUTATED          0
  CHGA WILD-TYPE        3
D87V3, multiclass
           clus
vv          CHGA MUTATED CHGA WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            2             17
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CHGA MUTATED    0  3     8
  CHGA WILD-TYPE  5 14    94
D87V4, multiclass
       clus
vv      CHGA MUTATED CHGA WILD-TYPE
  T1               0              5
  T2               3             14
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V5, binary
                cls
clus              0  1
  CHGA MUTATED    3  8
  CHGA WILD-TYPE 32 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      3    8
  CHGA WILD-TYPE   32   81
   clus
vv  CHGA MUTATED CHGA WILD-TYPE
  0            3             32
  1            8             81
[1] 2 2
[1] FALSE
D87V6, binary
                cls
clus              0  1
  CHGA MUTATED    8  0
  CHGA WILD-TYPE 49  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      8    0
  CHGA WILD-TYPE   49    3
   clus
vv  CHGA MUTATED CHGA WILD-TYPE
  0            8             49
  1            0              3
[1] 2 2
[1] FALSE
D87V7, binary
                cls
clus              0  1
  CHGA MUTATED    4  7
  CHGA WILD-TYPE 47 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      4    7
  CHGA WILD-TYPE   47   68
        clus
vv       CHGA MUTATED CHGA WILD-TYPE
  FEMALE            4             47
  MALE              7             68
[1] 2 2
[1] FALSE
D87V8, binary
                cls
clus              0  1
  CHGA MUTATED    7  3
  CHGA WILD-TYPE 81 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      7    3
  CHGA WILD-TYPE   81   27
     clus
vv    CHGA MUTATED CHGA WILD-TYPE
  NO             7             81
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHGA MUTATED                                     9
  CHGA WILD-TYPE                                  96
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHGA MUTATED                                       1
  CHGA WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHGA MUTATED                                                  1
  CHGA WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CHGA MUTATED                                     0
  CHGA WILD-TYPE                                   1
D87V9, multiclass
                                                  clus
vv                                                 CHGA MUTATED CHGA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         9             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V10, continuous
D87V11, continuous
                vv
clus             R0 R1 R2 RX
  CHGA MUTATED    8  3  0  0
  CHGA WILD-TYPE 72 32  4  2
D87V12, multiclass
    clus
vv   CHGA MUTATED CHGA WILD-TYPE
  R0            8             72
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHGA MUTATED       0                         0    11
  CHGA WILD-TYPE     6                         5   103
D87V14, multiclass
                           clus
vv                          CHGA MUTATED CHGA WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               11            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V15, binary
                cls
clus              0  1
  CHGA MUTATED    0  9
  CHGA WILD-TYPE  5 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      0    9
  CHGA WILD-TYPE    5   82
                        clus
vv                       CHGA MUTATED CHGA WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            9             82
[1] 2 2
[1] FALSE

Clustering(88) Variable = EGR1 MUTATION ANALYSIS
D88V1, survival
                sevent
clus2             0  1
  EGR1 MUTATED    4  3
  EGR1 WILD-TYPE 59 59
  EGR1 MUTATED EGR1 WILD-TYPE 
             7            118 
  EGR1 MUTATED EGR1 WILD-TYPE 
             3             59 
$`EGR1 MUTATED`
TCGA-2J-AAB8 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-LB-A9Q5 TCGA-US-A779 
        2.63        19.82        36.69        41.33        10.29        16.80 
TCGA-Z5-AAPL 
       15.35 

$`EGR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       10.85         0.23        19.82        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       23.67        11.51        12.76        66.28 

  EGR1 MUTATED EGR1 WILD-TYPE 
          2.63           0.23 
  EGR1 MUTATED EGR1 WILD-TYPE 
         41.33          90.12 
  EGR1 MUTATED EGR1 WILD-TYPE 
        16.800         15.155 
[1] "2.6 - 41.3 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D88V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EGR1 MUTATED         0        0        0         1         6         0
  EGR1 WILD-TYPE       1        3       12        18        76         4
                vv
clus             STAGE IV
  EGR1 MUTATED          0
  EGR1 WILD-TYPE        3
D88V3, multiclass
           clus
vv          EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  EGR1 MUTATED    0  0     7
  EGR1 WILD-TYPE  5 17    95
D88V4, multiclass
       clus
vv      EGR1 MUTATED EGR1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V5, binary
                cls
clus              0  1
  EGR1 MUTATED    1  6
  EGR1 WILD-TYPE 34 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      1    6
  EGR1 WILD-TYPE   34   83
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            1             34
  1            6             83
[1] 2 2
[1] FALSE
D88V6, binary
                cls
clus              0  1
  EGR1 MUTATED    5  0
  EGR1 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      5    0
  EGR1 WILD-TYPE   52    3
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D88V7, binary
                cls
clus              0  1
  EGR1 MUTATED    6  1
  EGR1 WILD-TYPE 45 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      6    1
  EGR1 WILD-TYPE   45   74
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  FEMALE            6             45
  MALE              1             74
[1] 2 2
[1] FALSE
D88V8, binary
                cls
clus              0  1
  EGR1 MUTATED    4  1
  EGR1 WILD-TYPE 84 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      4    1
  EGR1 WILD-TYPE   84   29
     clus
vv    EGR1 MUTATED EGR1 WILD-TYPE
  NO             4             84
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EGR1 MUTATED                                     7
  EGR1 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EGR1 MUTATED                                       0
  EGR1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EGR1 MUTATED                                                  0
  EGR1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EGR1 MUTATED                                     0
  EGR1 WILD-TYPE                                   1
D88V9, multiclass
                                                  clus
vv                                                 EGR1 MUTATED EGR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V10, continuous
D88V11, continuous
                vv
clus             R0 R1 R2 RX
  EGR1 MUTATED    5  2  0  0
  EGR1 WILD-TYPE 75 33  4  2
D88V12, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0            5             75
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGR1 MUTATED       1                         0     6
  EGR1 WILD-TYPE     5                         5   108
D88V14, multiclass
                           clus
vv                          EGR1 MUTATED EGR1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V15, binary
                cls
clus              0  1
  EGR1 MUTATED    0  6
  EGR1 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      0    6
  EGR1 WILD-TYPE    5   85
                        clus
vv                       EGR1 MUTATED EGR1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(89) Variable = OLIG3 MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2              0  1
  OLIG3 MUTATED    6  4
  OLIG3 WILD-TYPE 57 58
  OLIG3 MUTATED OLIG3 WILD-TYPE 
             10             115 
  OLIG3 MUTATED OLIG3 WILD-TYPE 
              4              58 
$`OLIG3 MUTATED`
TCGA-LB-A7SX TCGA-S4-A8RO TCGA-2J-AABK TCGA-2J-AABP TCGA-F2-A8YN TCGA-HZ-7925 
       12.92        17.26        15.91        15.22        17.00        20.19 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SP TCGA-IB-A7LX 
       19.82        41.33        15.85         8.22 

$`OLIG3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        15.12        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.22        22.72        42.31        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM 
       24.43        75.12        71.74        19.46         3.12        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 
        5.26        10.85         0.23        19.82        36.69        15.19 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
       12.00         7.20        20.88        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OLIG3 MUTATED OLIG3 WILD-TYPE 
           8.22            0.23 
  OLIG3 MUTATED OLIG3 WILD-TYPE 
          41.33           90.12 
  OLIG3 MUTATED OLIG3 WILD-TYPE 
         16.455          15.060 
[1] "8.2 - 41.3 (16.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.3"
D89V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OLIG3 MUTATED         0        0        0         2         8         0
  OLIG3 WILD-TYPE       1        3       12        17        74         4
                 vv
clus              STAGE IV
  OLIG3 MUTATED          0
  OLIG3 WILD-TYPE        3
D89V3, multiclass
           clus
vv          OLIG3 MUTATED OLIG3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OLIG3 MUTATED    0  0    10
  OLIG3 WILD-TYPE  5 17    92
D89V4, multiclass
       clus
vv      OLIG3 MUTATED OLIG3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V5, binary
                 cls
clus               0  1
  OLIG3 MUTATED    2  8
  OLIG3 WILD-TYPE 33 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLIG3 MUTATED      2    8
  OLIG3 WILD-TYPE   33   81
   clus
vv  OLIG3 MUTATED OLIG3 WILD-TYPE
  0             2              33
  1             8              81
[1] 2 2
[1] FALSE
D89V6, binary
                 cls
clus               0  1
  OLIG3 MUTATED    6  0
  OLIG3 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLIG3 MUTATED      6    0
  OLIG3 WILD-TYPE   51    3
   clus
vv  OLIG3 MUTATED OLIG3 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus               0  1
  OLIG3 MUTATED    5  5
  OLIG3 WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLIG3 MUTATED      5    5
  OLIG3 WILD-TYPE   46   70
        clus
vv       OLIG3 MUTATED OLIG3 WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus               0  1
  OLIG3 MUTATED    8  2
  OLIG3 WILD-TYPE 80 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLIG3 MUTATED      8    2
  OLIG3 WILD-TYPE   80   28
     clus
vv    OLIG3 MUTATED OLIG3 WILD-TYPE
  NO              8              80
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OLIG3 MUTATED                                     9
  OLIG3 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OLIG3 MUTATED                                       0
  OLIG3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OLIG3 MUTATED                                                  0
  OLIG3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OLIG3 MUTATED                                     1
  OLIG3 WILD-TYPE                                   0
D89V9, multiclass
                                                  clus
vv                                                 OLIG3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 OLIG3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V10, continuous
D89V11, continuous
                 vv
clus              R0 R1 R2 RX
  OLIG3 MUTATED    5  5  0  0
  OLIG3 WILD-TYPE 75 30  4  2
D89V12, multiclass
    clus
vv   OLIG3 MUTATED OLIG3 WILD-TYPE
  R0             5              75
  R1             5              30
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OLIG3 MUTATED       0                         1     9
  OLIG3 WILD-TYPE     6                         4   105
D89V14, multiclass
                           clus
vv                          OLIG3 MUTATED OLIG3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V15, binary
                 cls
clus               0  1
  OLIG3 MUTATED    0  7
  OLIG3 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OLIG3 MUTATED      0    7
  OLIG3 WILD-TYPE    5   84
                        clus
vv                       OLIG3 MUTATED OLIG3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(90) Variable = C14ORF49 MUTATION ANALYSIS
D90V1, survival
                    sevent
clus2                 0  1
  C14ORF49 MUTATED    4  4
  C14ORF49 WILD-TYPE 59 58
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 8                117 
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 4                 58 
$`C14ORF49 MUTATED`
TCGA-LB-A7SX TCGA-S4-A8RO TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-FB-AAPP TCGA-FB-AAQ1 
       12.92        17.26        32.81        24.43        15.95         4.04 
TCGA-HZ-8637 TCGA-IB-AAUP 
       17.00        14.17 

$`C14ORF49 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        15.12        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        12.33        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        17.49        31.86        20.19        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
              4.04               0.23 
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
             32.81              90.12 
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
            16.475             15.190 
[1] "4.0 - 32.8 (16.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D90V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C14ORF49 MUTATED         0        0        1         0         7         0
  C14ORF49 WILD-TYPE       1        3       11        19        75         4
                    vv
clus                 STAGE IV
  C14ORF49 MUTATED          0
  C14ORF49 WILD-TYPE        3
D90V3, multiclass
           clus
vv          C14ORF49 MUTATED C14ORF49 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                0                 19
  STAGE IIB                7                 75
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C14ORF49 MUTATED    0  1     7
  C14ORF49 WILD-TYPE  5 16    95
D90V4, multiclass
       clus
vv      C14ORF49 MUTATED C14ORF49 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                7                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V5, binary
                    cls
clus                  0  1
  C14ORF49 MUTATED    1  7
  C14ORF49 WILD-TYPE 34 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF49 MUTATED      1    7
  C14ORF49 WILD-TYPE   34   82
   clus
vv  C14ORF49 MUTATED C14ORF49 WILD-TYPE
  0                1                 34
  1                7                 82
[1] 2 2
[1] FALSE
D90V6, binary
                    cls
clus                  0  1
  C14ORF49 MUTATED    1  0
  C14ORF49 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF49 MUTATED      1    0
  C14ORF49 WILD-TYPE   56    3
   clus
vv  C14ORF49 MUTATED C14ORF49 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D90V7, binary
                    cls
clus                  0  1
  C14ORF49 MUTATED    3  5
  C14ORF49 WILD-TYPE 48 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF49 MUTATED      3    5
  C14ORF49 WILD-TYPE   48   70
        clus
vv       C14ORF49 MUTATED C14ORF49 WILD-TYPE
  FEMALE                3                 48
  MALE                  5                 70
[1] 2 2
[1] FALSE
D90V8, binary
                    cls
clus                  0  1
  C14ORF49 MUTATED    5  3
  C14ORF49 WILD-TYPE 83 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF49 MUTATED      5    3
  C14ORF49 WILD-TYPE   83   27
     clus
vv    C14ORF49 MUTATED C14ORF49 WILD-TYPE
  NO                 5                 83
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C14ORF49 MUTATED                                     7
  C14ORF49 WILD-TYPE                                  98
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C14ORF49 MUTATED                                       1
  C14ORF49 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C14ORF49 MUTATED                                                  0
  C14ORF49 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C14ORF49 MUTATED                                     0
  C14ORF49 WILD-TYPE                                   1
D90V9, multiclass
                                                  clus
vv                                                 C14ORF49 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C14ORF49 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V10, continuous
[1] "Remove cluster labels:" "C14ORF49 MUTATED"      
clus
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
D90V11, continuous
[1] "Remove cluster labels:" "C14ORF49 MUTATED"      
clus
  C14ORF49 MUTATED C14ORF49 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C14ORF49 WILD-TYPE" "C14ORF49 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C14ORF49 MUTATED    4  4  0  0
  C14ORF49 WILD-TYPE 76 31  4  2
D90V12, multiclass
    clus
vv   C14ORF49 MUTATED C14ORF49 WILD-TYPE
  R0                4                 76
  R1                4                 31
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF49 MUTATED       0                         1     7
  C14ORF49 WILD-TYPE     6                         4   107
D90V14, multiclass
                           clus
vv                          C14ORF49 MUTATED C14ORF49 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V15, binary
                    cls
clus                  0  1
  C14ORF49 MUTATED    1  7
  C14ORF49 WILD-TYPE  4 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF49 MUTATED      1    7
  C14ORF49 WILD-TYPE    4   84
                        clus
vv                       C14ORF49 MUTATED C14ORF49 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                7                 84
[1] 2 2
[1] FALSE

Clustering(91) Variable = TOB1 MUTATION ANALYSIS
D91V1, survival
                sevent
clus2             0  1
  TOB1 MUTATED    4  1
  TOB1 WILD-TYPE 59 61
  TOB1 MUTATED TOB1 WILD-TYPE 
             5            120 
  TOB1 MUTATED TOB1 WILD-TYPE 
             1             61 
$`TOB1 MUTATED`
TCGA-2L-AAQM TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HZ-7925 TCGA-US-A776 
       45.47        22.06         8.28        20.19        39.98 

$`TOB1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95         9.60        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79        32.15        30.25        17.49        31.86 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  TOB1 MUTATED TOB1 WILD-TYPE 
          8.28           0.23 
  TOB1 MUTATED TOB1 WILD-TYPE 
         45.47          90.12 
  TOB1 MUTATED TOB1 WILD-TYPE 
        22.060         15.155 
[1] "8.3 - 45.5 (22.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.9"
D91V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TOB1 MUTATED         0        0        0         3         3         0
  TOB1 WILD-TYPE       1        3       12        16        79         4
                vv
clus             STAGE IV
  TOB1 MUTATED          0
  TOB1 WILD-TYPE        3
D91V3, multiclass
           clus
vv          TOB1 MUTATED TOB1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            3             16
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TOB1 MUTATED    0  0     6
  TOB1 WILD-TYPE  5 17    96
D91V4, multiclass
       clus
vv      TOB1 MUTATED TOB1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V5, binary
                cls
clus              0  1
  TOB1 MUTATED    3  3
  TOB1 WILD-TYPE 32 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      3    3
  TOB1 WILD-TYPE   32   86
   clus
vv  TOB1 MUTATED TOB1 WILD-TYPE
  0            3             32
  1            3             86
[1] 2 2
[1] FALSE
D91V6, binary
                cls
clus              0  1
  TOB1 MUTATED    0  0
  TOB1 WILD-TYPE 57  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      0    0
  TOB1 WILD-TYPE   57    3
D91V7, binary
                cls
clus              0  1
  TOB1 MUTATED    0  6
  TOB1 WILD-TYPE 51 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      0    6
  TOB1 WILD-TYPE   51   69
        clus
vv       TOB1 MUTATED TOB1 WILD-TYPE
  FEMALE            0             51
  MALE              6             69
[1] 2 2
[1] FALSE
D91V8, binary
                cls
clus              0  1
  TOB1 MUTATED    5  0
  TOB1 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      5    0
  TOB1 WILD-TYPE   83   30
     clus
vv    TOB1 MUTATED TOB1 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TOB1 MUTATED                                     3
  TOB1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TOB1 MUTATED                                       2
  TOB1 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TOB1 MUTATED                                                  1
  TOB1 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TOB1 MUTATED                                     0
  TOB1 WILD-TYPE                                   1
D91V9, multiclass
                                                  clus
vv                                                 TOB1 MUTATED TOB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V10, continuous
[1] "Remove cluster labels:" "TOB1 MUTATED"          
clus
  TOB1 MUTATED TOB1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-YY-A8LH 
"TOB1 WILD-TYPE" 
D91V11, continuous
[1] "Remove cluster labels:" "TOB1 MUTATED"          
clus
  TOB1 MUTATED TOB1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"TOB1 WILD-TYPE" "TOB1 WILD-TYPE" "TOB1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TOB1 MUTATED    4  1  1  0
  TOB1 WILD-TYPE 76 34  3  2
D91V12, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  R0            4             76
  R1            1             34
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TOB1 MUTATED       1                         0     5
  TOB1 WILD-TYPE     5                         5   109
D91V14, multiclass
                           clus
vv                          TOB1 MUTATED TOB1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V15, binary
                cls
clus              0  1
  TOB1 MUTATED    0  4
  TOB1 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      0    4
  TOB1 WILD-TYPE    5   87
                        clus
vv                       TOB1 MUTATED TOB1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(92) Variable = MEPCE MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2              0  1
  MEPCE MUTATED    9  1
  MEPCE WILD-TYPE 54 61
  MEPCE MUTATED MEPCE WILD-TYPE 
             10             115 
  MEPCE MUTATED MEPCE WILD-TYPE 
              1              61 
$`MEPCE MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9IV TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HZ-A9TJ TCGA-IB-7651 
       60.95        36.26         8.28        32.15        19.82        19.82 
TCGA-IB-7885 TCGA-IB-AAUU TCGA-US-A776 TCGA-YB-A89D 
       41.33         8.05        39.98        11.51 

$`MEPCE WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        22.06        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 
       17.00        10.13         5.26        10.85         0.23        36.69 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MEPCE MUTATED MEPCE WILD-TYPE 
           8.05            0.23 
  MEPCE MUTATED MEPCE WILD-TYPE 
          60.95           90.12 
  MEPCE MUTATED MEPCE WILD-TYPE 
         25.985          15.120 
[1] "8.1 - 61.0 (26.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "7.8"
D92V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MEPCE MUTATED         0        0        2         2         5         0
  MEPCE WILD-TYPE       1        3       10        17        77         4
                 vv
clus              STAGE IV
  MEPCE MUTATED          1
  MEPCE WILD-TYPE        2
D92V3, multiclass
           clus
vv          MEPCE MUTATED MEPCE WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MEPCE MUTATED    0  2     8
  MEPCE WILD-TYPE  5 15    94
D92V4, multiclass
       clus
vv      MEPCE MUTATED MEPCE WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V5, binary
                 cls
clus               0  1
  MEPCE MUTATED    5  5
  MEPCE WILD-TYPE 30 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      5    5
  MEPCE WILD-TYPE   30   84
   clus
vv  MEPCE MUTATED MEPCE WILD-TYPE
  0             5              30
  1             5              84
[1] 2 2
[1] FALSE
D92V6, binary
                 cls
clus               0  1
  MEPCE MUTATED    4  1
  MEPCE WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      4    1
  MEPCE WILD-TYPE   53    2
   clus
vv  MEPCE MUTATED MEPCE WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D92V7, binary
                 cls
clus               0  1
  MEPCE MUTATED    3  7
  MEPCE WILD-TYPE 48 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      3    7
  MEPCE WILD-TYPE   48   68
        clus
vv       MEPCE MUTATED MEPCE WILD-TYPE
  FEMALE             3              48
  MALE               7              68
[1] 2 2
[1] FALSE
D92V8, binary
                 cls
clus               0  1
  MEPCE MUTATED    8  2
  MEPCE WILD-TYPE 80 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      8    2
  MEPCE WILD-TYPE   80   28
     clus
vv    MEPCE MUTATED MEPCE WILD-TYPE
  NO              8              80
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MEPCE MUTATED                                     5
  MEPCE WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MEPCE MUTATED                                       4
  MEPCE WILD-TYPE                                    14
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MEPCE MUTATED                                                  1
  MEPCE WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MEPCE MUTATED                                     0
  MEPCE WILD-TYPE                                   1
D92V9, multiclass
                                                  clus
vv                                                 MEPCE MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MEPCE WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V10, continuous
D92V11, continuous
                 vv
clus              R0 R1 R2 RX
  MEPCE MUTATED    9  0  1  0
  MEPCE WILD-TYPE 71 35  3  2
D92V12, multiclass
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  R0             9              71
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MEPCE MUTATED       2                         0     8
  MEPCE WILD-TYPE     4                         5   106
D92V14, multiclass
                           clus
vv                          MEPCE MUTATED MEPCE WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V15, binary
                 cls
clus               0  1
  MEPCE MUTATED    0  8
  MEPCE WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      0    8
  MEPCE WILD-TYPE    5   83
                        clus
vv                       MEPCE MUTATED MEPCE WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(93) Variable = TXLNG MUTATION ANALYSIS
D93V1, survival
                 sevent
clus2              0  1
  TXLNG MUTATED    2  5
  TXLNG WILD-TYPE 61 57
  TXLNG MUTATED TXLNG WILD-TYPE 
              7             118 
  TXLNG MUTATED TXLNG WILD-TYPE 
              5              57 
$`TXLNG MUTATED`
TCGA-US-A77E TCGA-FB-A5VM TCGA-IB-7651 TCGA-US-A77J TCGA-XD-AAUI TCGA-YB-A89D 
       14.14        16.37        19.82        18.67        12.03        11.51 
TCGA-Z5-AAPL 
       15.35 

$`TXLNG WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        12.76        66.28 

  TXLNG MUTATED TXLNG WILD-TYPE 
          11.51            0.23 
  TXLNG MUTATED TXLNG WILD-TYPE 
          19.82           90.12 
  TXLNG MUTATED TXLNG WILD-TYPE 
         15.350          15.205 
[1] "11.5 - 19.8 (15.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.7"
D93V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TXLNG MUTATED         0        0        1         1         5         0
  TXLNG WILD-TYPE       1        3       11        18        77         4
                 vv
clus              STAGE IV
  TXLNG MUTATED          0
  TXLNG WILD-TYPE        3
D93V3, multiclass
           clus
vv          TXLNG MUTATED TXLNG WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TXLNG MUTATED    0  1     6
  TXLNG WILD-TYPE  5 16    96
D93V4, multiclass
       clus
vv      TXLNG MUTATED TXLNG WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V5, binary
                 cls
clus               0  1
  TXLNG MUTATED    2  5
  TXLNG WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      2    5
  TXLNG WILD-TYPE   33   84
   clus
vv  TXLNG MUTATED TXLNG WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D93V6, binary
                 cls
clus               0  1
  TXLNG MUTATED    3  0
  TXLNG WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      3    0
  TXLNG WILD-TYPE   54    3
   clus
vv  TXLNG MUTATED TXLNG WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D93V7, binary
                 cls
clus               0  1
  TXLNG MUTATED    4  3
  TXLNG WILD-TYPE 47 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      4    3
  TXLNG WILD-TYPE   47   72
        clus
vv       TXLNG MUTATED TXLNG WILD-TYPE
  FEMALE             4              47
  MALE               3              72
[1] 2 2
[1] FALSE
D93V8, binary
                 cls
clus               0  1
  TXLNG MUTATED    5  1
  TXLNG WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      5    1
  TXLNG WILD-TYPE   83   29
     clus
vv    TXLNG MUTATED TXLNG WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TXLNG MUTATED                                     6
  TXLNG WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TXLNG MUTATED                                       1
  TXLNG WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TXLNG MUTATED                                                  0
  TXLNG WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TXLNG MUTATED                                     0
  TXLNG WILD-TYPE                                   1
D93V9, multiclass
                                                  clus
vv                                                 TXLNG MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TXLNG WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V10, continuous
[1] "Remove cluster labels:" "TXLNG MUTATED"         
clus
  TXLNG MUTATED TXLNG WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" "TXLNG WILD-TYPE" 
     TCGA-YY-A8LH 
"TXLNG WILD-TYPE" 
D93V11, continuous
                 vv
clus              R0 R1 R2 RX
  TXLNG MUTATED    5  2  0  0
  TXLNG WILD-TYPE 75 33  4  2
D93V12, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TXLNG MUTATED       0                         0     7
  TXLNG WILD-TYPE     6                         5   107
D93V14, multiclass
                           clus
vv                          TXLNG MUTATED TXLNG WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V15, binary
                 cls
clus               0  1
  TXLNG MUTATED    0  7
  TXLNG WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      0    7
  TXLNG WILD-TYPE    5   84
                        clus
vv                       TXLNG MUTATED TXLNG WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(94) Variable = TTK MUTATION ANALYSIS
D94V1, survival
               sevent
clus2            0  1
  TTK MUTATED    7  5
  TTK WILD-TYPE 56 57
  TTK MUTATED TTK WILD-TYPE 
           12           113 
  TTK MUTATED TTK WILD-TYPE 
            5            57 
$`TTK MUTATED`
TCGA-HZ-A77Q TCGA-2J-AAB9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IS TCGA-3A-A9IU 
        1.08        20.61         7.36        33.57        32.81        15.06 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-AAUM TCGA-IB-AAUP TCGA-YB-A89D 
       32.15        17.49        19.82         0.26        14.17        11.51 

$`TTK WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IO 
        9.60        45.47        43.50        20.84        24.26        63.85 
TCGA-3A-A9IR TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06         8.28        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  TTK MUTATED TTK WILD-TYPE 
         0.26          0.23 
  TTK MUTATED TTK WILD-TYPE 
        33.57         90.12 
  TTK MUTATED TTK WILD-TYPE 
       16.275        15.220 
[1] "0.3 - 33.6 (16.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D94V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TTK MUTATED         0        1        1         0        10         0
  TTK WILD-TYPE       1        2       11        19        72         4
               vv
clus            STAGE IV
  TTK MUTATED          0
  TTK WILD-TYPE        3
D94V3, multiclass
           clus
vv          TTK MUTATED TTK WILD-TYPE
  STAGE I             0             1
  STAGE IA            1             2
  STAGE IB            1            11
  STAGE IIA           0            19
  STAGE IIB          10            72
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  TTK MUTATED    1  3     8
  TTK WILD-TYPE  4 14    94
D94V4, multiclass
       clus
vv      TTK MUTATED TTK WILD-TYPE
  T1              1             4
  T2              3            14
  T3+T4           8            94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V5, binary
               cls
clus             0  1
  TTK MUTATED    2 10
  TTK WILD-TYPE 33 79
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      2   10
  TTK WILD-TYPE   33   79
   clus
vv  TTK MUTATED TTK WILD-TYPE
  0           2            33
  1          10            79
[1] 2 2
[1] FALSE
D94V6, binary
               cls
clus             0  1
  TTK MUTATED    5  0
  TTK WILD-TYPE 52  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      5    0
  TTK WILD-TYPE   52    3
   clus
vv  TTK MUTATED TTK WILD-TYPE
  0           5            52
  1           0             3
[1] 2 2
[1] FALSE
D94V7, binary
               cls
clus             0  1
  TTK MUTATED    6  6
  TTK WILD-TYPE 45 69
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      6    6
  TTK WILD-TYPE   45   69
        clus
vv       TTK MUTATED TTK WILD-TYPE
  FEMALE           6            45
  MALE             6            69
[1] 2 2
[1] FALSE
D94V8, binary
               cls
clus             0  1
  TTK MUTATED    8  3
  TTK WILD-TYPE 80 27
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      8    3
  TTK WILD-TYPE   80   27
     clus
vv    TTK MUTATED TTK WILD-TYPE
  NO            8            80
  YES           3            27
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TTK MUTATED                                     9
  TTK WILD-TYPE                                  96
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TTK MUTATED                                       3
  TTK WILD-TYPE                                    15
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TTK MUTATED                                                  0
  TTK WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  TTK MUTATED                                     0
  TTK WILD-TYPE                                   1
D94V9, multiclass
                                                  clus
vv                                                 TTK MUTATED TTK WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        9            96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      3            15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V10, continuous
D94V11, continuous
               vv
clus            R0 R1 R2 RX
  TTK MUTATED   10  1  1  0
  TTK WILD-TYPE 70 34  3  2
D94V12, multiclass
    clus
vv   TTK MUTATED TTK WILD-TYPE
  R0          10            70
  R1           1            34
  R2           1             3
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTK MUTATED       2                         0    10
  TTK WILD-TYPE     4                         5   104
D94V14, multiclass
                           clus
vv                          TTK MUTATED TTK WILD-TYPE
  ASIAN                               2             4
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                              10           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V15, binary
               cls
clus             0  1
  TTK MUTATED    0  9
  TTK WILD-TYPE  5 82
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTK MUTATED      0    9
  TTK WILD-TYPE    5   82
                        clus
vv                       TTK MUTATED TTK WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           9            82
[1] 2 2
[1] FALSE

Clustering(95) Variable = TMCO1 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2              0  1
  TMCO1 MUTATED    4  4
  TMCO1 WILD-TYPE 59 58
  TMCO1 MUTATED TMCO1 WILD-TYPE 
              8             117 
  TMCO1 MUTATED TMCO1 WILD-TYPE 
              4              58 
$`TMCO1 MUTATED`
TCGA-3A-A9IB TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-A6UF TCGA-IB-AAUQ TCGA-IB-AAUV 
        7.36         7.50        19.82        21.90         6.02        13.28 
TCGA-Q3-AA2A TCGA-RB-A7B8 
        3.12        15.32 

$`TMCO1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05         7.56        12.46        10.29         8.78        13.68 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TMCO1 MUTATED TMCO1 WILD-TYPE 
           3.12            0.23 
  TMCO1 MUTATED TMCO1 WILD-TYPE 
          21.90           90.12 
  TMCO1 MUTATED TMCO1 WILD-TYPE 
          10.39           15.35 
[1] "3.1 - 21.9 (10.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D95V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMCO1 MUTATED         0        0        1         0         7         0
  TMCO1 WILD-TYPE       1        3       11        19        75         4
                 vv
clus              STAGE IV
  TMCO1 MUTATED          0
  TMCO1 WILD-TYPE        3
D95V3, multiclass
           clus
vv          TMCO1 MUTATED TMCO1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TMCO1 MUTATED    0  1     7
  TMCO1 WILD-TYPE  5 16    95
D95V4, multiclass
       clus
vv      TMCO1 MUTATED TMCO1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V5, binary
                 cls
clus               0  1
  TMCO1 MUTATED    0  8
  TMCO1 WILD-TYPE 35 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO1 MUTATED      0    8
  TMCO1 WILD-TYPE   35   81
   clus
vv  TMCO1 MUTATED TMCO1 WILD-TYPE
  0             0              35
  1             8              81
[1] 2 2
[1] FALSE
D95V6, binary
                 cls
clus               0  1
  TMCO1 MUTATED    4  0
  TMCO1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO1 MUTATED      4    0
  TMCO1 WILD-TYPE   53    3
   clus
vv  TMCO1 MUTATED TMCO1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus               0  1
  TMCO1 MUTATED    5  3
  TMCO1 WILD-TYPE 46 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO1 MUTATED      5    3
  TMCO1 WILD-TYPE   46   72
        clus
vv       TMCO1 MUTATED TMCO1 WILD-TYPE
  FEMALE             5              46
  MALE               3              72
[1] 2 2
[1] FALSE
D95V8, binary
                 cls
clus               0  1
  TMCO1 MUTATED    7  1
  TMCO1 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO1 MUTATED      7    1
  TMCO1 WILD-TYPE   81   29
     clus
vv    TMCO1 MUTATED TMCO1 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMCO1 MUTATED                                     7
  TMCO1 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMCO1 MUTATED                                       1
  TMCO1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMCO1 MUTATED                                                  0
  TMCO1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMCO1 MUTATED                                     0
  TMCO1 WILD-TYPE                                   1
D95V9, multiclass
                                                  clus
vv                                                 TMCO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TMCO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V10, continuous
D95V11, continuous
                 vv
clus              R0 R1 R2 RX
  TMCO1 MUTATED    5  2  0  1
  TMCO1 WILD-TYPE 75 33  4  1
D95V12, multiclass
    clus
vv   TMCO1 MUTATED TMCO1 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCO1 MUTATED       0                         0     8
  TMCO1 WILD-TYPE     6                         5   106
D95V14, multiclass
                           clus
vv                          TMCO1 MUTATED TMCO1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V15, binary
                 cls
clus               0  1
  TMCO1 MUTATED    0  8
  TMCO1 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO1 MUTATED      0    8
  TMCO1 WILD-TYPE    5   83
                        clus
vv                       TMCO1 MUTATED TMCO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(96) Variable = NUDT11 MUTATION ANALYSIS
D96V1, survival
                  sevent
clus2               0  1
  NUDT11 MUTATED    3  6
  NUDT11 WILD-TYPE 60 56
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               9              116 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               6               56 
$`NUDT11 MUTATED`
TCGA-2J-AABR TCGA-FB-AAQ6 TCGA-2J-AAB9 TCGA-2J-AABK TCGA-2L-AAQE TCGA-FB-A5VM 
       14.40         8.02        20.61        15.91        22.49        16.37 
TCGA-FB-AAPP TCGA-IB-7651 TCGA-YH-A8SY 
       15.95        19.82        12.76 

$`NUDT11 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FZ-5924 
       10.49        58.98        60.95        90.12         7.66        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T 
       75.12        71.74        19.46         3.12        17.00        12.33 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            8.02             0.23 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           22.49            90.12 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
          15.950           15.155 
[1] "8.0 - 22.5 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D96V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NUDT11 MUTATED         0        1        1         1         5         1
  NUDT11 WILD-TYPE       1        2       11        18        77         3
                  vv
clus               STAGE IV
  NUDT11 MUTATED          0
  NUDT11 WILD-TYPE        3
D96V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NUDT11 MUTATED    1  1     7
  NUDT11 WILD-TYPE  4 16    95
D96V4, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V5, binary
                  cls
clus                0  1
  NUDT11 MUTATED    3  6
  NUDT11 WILD-TYPE 32 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      3    6
  NUDT11 WILD-TYPE   32   83
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              3               32
  1              6               83
[1] 2 2
[1] FALSE
D96V6, binary
                  cls
clus                0  1
  NUDT11 MUTATED    6  0
  NUDT11 WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      6    0
  NUDT11 WILD-TYPE   51    3
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D96V7, binary
                  cls
clus                0  1
  NUDT11 MUTATED    4  5
  NUDT11 WILD-TYPE 47 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      4    5
  NUDT11 WILD-TYPE   47   70
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              4               47
  MALE                5               70
[1] 2 2
[1] FALSE
D96V8, binary
                  cls
clus                0  1
  NUDT11 MUTATED    5  4
  NUDT11 WILD-TYPE 83 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      5    4
  NUDT11 WILD-TYPE   83   26
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               5               83
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NUDT11 MUTATED                                     8
  NUDT11 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NUDT11 MUTATED                                       0
  NUDT11 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NUDT11 MUTATED                                                  0
  NUDT11 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NUDT11 MUTATED                                     0
  NUDT11 WILD-TYPE                                   1
D96V9, multiclass
                                                  clus
vv                                                 NUDT11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NUDT11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V10, continuous
D96V11, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NUDT11 MUTATED    7  1  0  0
  NUDT11 WILD-TYPE 73 34  4  2
D96V12, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  R0              7               73
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED       0                         0     9
  NUDT11 WILD-TYPE     6                         5   105
D96V14, multiclass
                           clus
vv                          NUDT11 MUTATED NUDT11 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V15, binary
                  cls
clus                0  1
  NUDT11 MUTATED    0  5
  NUDT11 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    5
  NUDT11 WILD-TYPE    5   86
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(97) Variable = PTPRF MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2              0  1
  PTPRF MUTATED    4  8
  PTPRF WILD-TYPE 59 54
  PTPRF MUTATED PTPRF WILD-TYPE 
             12             113 
  PTPRF MUTATED PTPRF WILD-TYPE 
              8              54 
$`PTPRF MUTATED`
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-2J-AAB1 TCGA-FB-AAPZ TCGA-HZ-8637 TCGA-IB-7651 
       15.12        12.92         2.17        23.54        17.00        19.82 
TCGA-IB-8126 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A9Q5 
       15.19        21.90         1.35         8.05         7.56        10.29 

$`PTPRF WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        17.26        14.14        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A7LX 
       41.33        12.00        15.85         7.20        20.88         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
       11.11         7.40        13.28        12.46         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PTPRF MUTATED PTPRF WILD-TYPE 
           1.35            0.23 
  PTPRF MUTATED PTPRF WILD-TYPE 
          23.54           90.12 
  PTPRF MUTATED PTPRF WILD-TYPE 
          14.02           15.35 
[1] "1.4 - 23.5 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D97V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PTPRF MUTATED         0        0        0         0        12         1
  PTPRF WILD-TYPE       1        3       12        19        70         3
                 vv
clus              STAGE IV
  PTPRF MUTATED          0
  PTPRF WILD-TYPE        3
D97V3, multiclass
           clus
vv          PTPRF MUTATED PTPRF WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB            12              70
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PTPRF MUTATED    0  1    12
  PTPRF WILD-TYPE  5 16    90
D97V4, multiclass
       clus
vv      PTPRF MUTATED PTPRF WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            12              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V5, binary
                 cls
clus               0  1
  PTPRF MUTATED    0 13
  PTPRF WILD-TYPE 35 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      0   13
  PTPRF WILD-TYPE   35   76
   clus
vv  PTPRF MUTATED PTPRF WILD-TYPE
  0             0              35
  1            13              76
[1] 2 2
[1] FALSE
D97V6, binary
                 cls
clus               0  1
  PTPRF MUTATED    8  0
  PTPRF WILD-TYPE 49  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      8    0
  PTPRF WILD-TYPE   49    3
   clus
vv  PTPRF MUTATED PTPRF WILD-TYPE
  0             8              49
  1             0               3
[1] 2 2
[1] FALSE
D97V7, binary
                 cls
clus               0  1
  PTPRF MUTATED    7  6
  PTPRF WILD-TYPE 44 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      7    6
  PTPRF WILD-TYPE   44   69
        clus
vv       PTPRF MUTATED PTPRF WILD-TYPE
  FEMALE             7              44
  MALE               6              69
[1] 2 2
[1] FALSE
D97V8, binary
                 cls
clus               0  1
  PTPRF MUTATED   10  2
  PTPRF WILD-TYPE 78 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED     10    2
  PTPRF WILD-TYPE   78   28
     clus
vv    PTPRF MUTATED PTPRF WILD-TYPE
  NO             10              78
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPRF MUTATED                                    12
  PTPRF WILD-TYPE                                  93
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPRF MUTATED                                       1
  PTPRF WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPRF MUTATED                                                  0
  PTPRF WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PTPRF MUTATED                                     0
  PTPRF WILD-TYPE                                   1
D97V9, multiclass
                                                  clus
vv                                                 PTPRF MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PTPRF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V10, continuous
D97V11, continuous
                 vv
clus              R0 R1 R2 RX
  PTPRF MUTATED    9  4  0  0
  PTPRF WILD-TYPE 71 31  4  2
D97V12, multiclass
    clus
vv   PTPRF MUTATED PTPRF WILD-TYPE
  R0             9              71
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRF MUTATED       0                         1    12
  PTPRF WILD-TYPE     6                         4   102
D97V14, multiclass
                           clus
vv                          PTPRF MUTATED PTPRF WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                12             102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V15, binary
                 cls
clus               0  1
  PTPRF MUTATED    1 11
  PTPRF WILD-TYPE  4 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      1   11
  PTPRF WILD-TYPE    4   80
                        clus
vv                       PTPRF MUTATED PTPRF WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            11              80
[1] 2 2
[1] FALSE

Clustering(98) Variable = YTHDF1 MUTATION ANALYSIS
D98V1, survival
                  sevent
clus2               0  1
  YTHDF1 MUTATED    3  5
  YTHDF1 WILD-TYPE 60 57
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               8              117 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
               5               57 
$`YTHDF1 MUTATED`
TCGA-2J-AABP TCGA-2L-AAQI TCGA-FB-A5VM TCGA-FB-AAPS TCGA-IB-A5SQ TCGA-IB-AAUQ 
       15.22         3.39        16.37         7.50         7.20         6.02 
TCGA-IB-AAUU TCGA-LB-A9Q5 
        8.05        10.29 

$`YTHDF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       14.47         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
        3.12        17.00        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        4.73         7.86        14.17        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
            3.39             0.23 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
           16.37            90.12 
  YTHDF1 MUTATED YTHDF1 WILD-TYPE 
           7.775           15.550 
[1] "3.4 - 16.4 (7.8)"  "0.2 - 90.1 (15.6)"
[1] "hr=" "3.1"
D98V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  YTHDF1 MUTATED         0        0        2         0         6         0
  YTHDF1 WILD-TYPE       1        3       10        19        76         4
                  vv
clus               STAGE IV
  YTHDF1 MUTATED          0
  YTHDF1 WILD-TYPE        3
D98V3, multiclass
           clus
vv          YTHDF1 MUTATED YTHDF1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  YTHDF1 MUTATED    0  3     5
  YTHDF1 WILD-TYPE  5 14    97
D98V4, multiclass
       clus
vv      YTHDF1 MUTATED YTHDF1 WILD-TYPE
  T1                 0                5
  T2                 3               14
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V5, binary
                  cls
clus                0  1
  YTHDF1 MUTATED    2  6
  YTHDF1 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      2    6
  YTHDF1 WILD-TYPE   33   83
   clus
vv  YTHDF1 MUTATED YTHDF1 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D98V6, binary
                  cls
clus                0  1
  YTHDF1 MUTATED    5  0
  YTHDF1 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      5    0
  YTHDF1 WILD-TYPE   52    3
   clus
vv  YTHDF1 MUTATED YTHDF1 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D98V7, binary
                  cls
clus                0  1
  YTHDF1 MUTATED    4  4
  YTHDF1 WILD-TYPE 47 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      4    4
  YTHDF1 WILD-TYPE   47   71
        clus
vv       YTHDF1 MUTATED YTHDF1 WILD-TYPE
  FEMALE              4               47
  MALE                4               71
[1] 2 2
[1] FALSE
D98V8, binary
                  cls
clus                0  1
  YTHDF1 MUTATED    6  2
  YTHDF1 WILD-TYPE 82 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      6    2
  YTHDF1 WILD-TYPE   82   28
     clus
vv    YTHDF1 MUTATED YTHDF1 WILD-TYPE
  NO               6               82
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  YTHDF1 MUTATED                                     7
  YTHDF1 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  YTHDF1 MUTATED                                       0
  YTHDF1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  YTHDF1 MUTATED                                                  0
  YTHDF1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  YTHDF1 MUTATED                                     1
  YTHDF1 WILD-TYPE                                   0
D98V9, multiclass
                                                  clus
vv                                                 YTHDF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 YTHDF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V10, continuous
D98V11, continuous
                  vv
clus               R0 R1 R2 RX
  YTHDF1 MUTATED    6  2  0  0
  YTHDF1 WILD-TYPE 74 33  4  2
D98V12, multiclass
    clus
vv   YTHDF1 MUTATED YTHDF1 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YTHDF1 MUTATED       0                         0     8
  YTHDF1 WILD-TYPE     6                         5   106
D98V14, multiclass
                           clus
vv                          YTHDF1 MUTATED YTHDF1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V15, binary
                  cls
clus                0  1
  YTHDF1 MUTATED    0  6
  YTHDF1 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF1 MUTATED      0    6
  YTHDF1 WILD-TYPE    5   85
                        clus
vv                       YTHDF1 MUTATED YTHDF1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(99) Variable = AAMP MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  AAMP MUTATED    2  3
  AAMP WILD-TYPE 61 59
  AAMP MUTATED AAMP WILD-TYPE 
             5            120 
  AAMP MUTATED AAMP WILD-TYPE 
             3             59 
$`AAMP MUTATED`
TCGA-2J-AAB4 TCGA-2L-AAQI TCGA-FB-A78T TCGA-HZ-8637 TCGA-RB-AA9M 
       23.97         3.39        12.33        17.00         9.40 

$`AAMP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  AAMP MUTATED AAMP WILD-TYPE 
          3.39           0.23 
  AAMP MUTATED AAMP WILD-TYPE 
         23.97          90.12 
  AAMP MUTATED AAMP WILD-TYPE 
         12.33          15.27 
[1] "3.4 - 24.0 (12.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D99V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AAMP MUTATED         0        0        0         0         6         0
  AAMP WILD-TYPE       1        3       12        19        76         4
                vv
clus             STAGE IV
  AAMP MUTATED          0
  AAMP WILD-TYPE        3
D99V3, multiclass
           clus
vv          AAMP MUTATED AAMP WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  AAMP MUTATED    1  1     4
  AAMP WILD-TYPE  4 16    98
D99V4, multiclass
       clus
vv      AAMP MUTATED AAMP WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V5, binary
                cls
clus              0  1
  AAMP MUTATED    0  6
  AAMP WILD-TYPE 35 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      0    6
  AAMP WILD-TYPE   35   83
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            0             35
  1            6             83
[1] 2 2
[1] FALSE
D99V6, binary
                cls
clus              0  1
  AAMP MUTATED    2  0
  AAMP WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    0
  AAMP WILD-TYPE   55    3
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D99V7, binary
                cls
clus              0  1
  AAMP MUTATED    2  4
  AAMP WILD-TYPE 49 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    4
  AAMP WILD-TYPE   49   71
        clus
vv       AAMP MUTATED AAMP WILD-TYPE
  FEMALE            2             49
  MALE              4             71
[1] 2 2
[1] FALSE
D99V8, binary
                cls
clus              0  1
  AAMP MUTATED    3  2
  AAMP WILD-TYPE 85 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    2
  AAMP WILD-TYPE   85   28
     clus
vv    AAMP MUTATED AAMP WILD-TYPE
  NO             3             85
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AAMP MUTATED                                     5
  AAMP WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AAMP MUTATED                                       1
  AAMP WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AAMP MUTATED                                                  0
  AAMP WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  AAMP MUTATED                                     0
  AAMP WILD-TYPE                                   1
D99V9, multiclass
                                                  clus
vv                                                 AAMP MUTATED AAMP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V10, continuous
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-YY-A8LH 
"AAMP WILD-TYPE" 
D99V11, continuous
[1] "Remove cluster labels:" "AAMP MUTATED"          
clus
  AAMP MUTATED AAMP WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"AAMP WILD-TYPE" "AAMP WILD-TYPE" "AAMP WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  AAMP MUTATED    5  1  0  0
  AAMP WILD-TYPE 75 34  4  2
D99V12, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  R0            5             75
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AAMP MUTATED       0                         0     6
  AAMP WILD-TYPE     6                         5   108
D99V14, multiclass
                           clus
vv                          AAMP MUTATED AAMP WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V15, binary
                cls
clus              0  1
  AAMP MUTATED    1  3
  AAMP WILD-TYPE  4 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      1    3
  AAMP WILD-TYPE    4   88
                        clus
vv                       AAMP MUTATED AAMP WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(100) Variable = RAI1 MUTATION ANALYSIS
D100V1, survival
                sevent
clus2             0  1
  RAI1 MUTATED    3  2
  RAI1 WILD-TYPE 60 60
  RAI1 MUTATED RAI1 WILD-TYPE 
             5            120 
  RAI1 MUTATED RAI1 WILD-TYPE 
             2             60 
$`RAI1 MUTATED`
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-YB-A89D 
       19.82        36.69         1.35        12.46        11.51 

$`RAI1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 
        5.26        10.85         0.23        19.82        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  RAI1 MUTATED RAI1 WILD-TYPE 
          1.35           0.23 
  RAI1 MUTATED RAI1 WILD-TYPE 
         36.69          90.12 
  RAI1 MUTATED RAI1 WILD-TYPE 
         12.46          15.27 
[1] "1.4 - 36.7 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D100V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RAI1 MUTATED         0        0        0         1         5         0
  RAI1 WILD-TYPE       1        3       12        18        77         4
                vv
clus             STAGE IV
  RAI1 MUTATED          0
  RAI1 WILD-TYPE        3
D100V3, multiclass
           clus
vv          RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RAI1 MUTATED    0  0     6
  RAI1 WILD-TYPE  5 17    96
D100V4, multiclass
       clus
vv      RAI1 MUTATED RAI1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V5, binary
                cls
clus              0  1
  RAI1 MUTATED    1  5
  RAI1 WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      1    5
  RAI1 WILD-TYPE   34   84
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D100V6, binary
                cls
clus              0  1
  RAI1 MUTATED    3  0
  RAI1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      3    0
  RAI1 WILD-TYPE   54    3
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D100V7, binary
                cls
clus              0  1
  RAI1 MUTATED    3  3
  RAI1 WILD-TYPE 48 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      3    3
  RAI1 WILD-TYPE   48   72
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE            3             48
  MALE              3             72
[1] 2 2
[1] FALSE
D100V8, binary
                cls
clus              0  1
  RAI1 MUTATED    3  2
  RAI1 WILD-TYPE 85 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      3    2
  RAI1 WILD-TYPE   85   28
     clus
vv    RAI1 MUTATED RAI1 WILD-TYPE
  NO             3             85
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAI1 MUTATED                                     6
  RAI1 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAI1 MUTATED                                       0
  RAI1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAI1 MUTATED                                                  0
  RAI1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RAI1 MUTATED                                     0
  RAI1 WILD-TYPE                                   1
D100V9, multiclass
                                                  clus
vv                                                 RAI1 MUTATED RAI1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V10, continuous
D100V11, continuous
                vv
clus             R0 R1 R2 RX
  RAI1 MUTATED    4  2  0  0
  RAI1 WILD-TYPE 76 33  4  2
D100V12, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  R0            4             76
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAI1 MUTATED       1                         1     4
  RAI1 WILD-TYPE     5                         4   110
D100V14, multiclass
                           clus
vv                          RAI1 MUTATED RAI1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V15, binary
                cls
clus              0  1
  RAI1 MUTATED    0  6
  RAI1 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      0    6
  RAI1 WILD-TYPE    5   85
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(101) Variable = PDZD7 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2              0  1
  PDZD7 MUTATED    5  2
  PDZD7 WILD-TYPE 58 60
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              7             118 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              2              60 
$`PDZD7 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AAB8 TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-AAUP 
        1.08         2.63        19.82        15.19        12.00        14.17 
TCGA-Q3-A5QY 
       13.68 

$`PDZD7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SP TCGA-IB-A5SQ 
        0.23        19.82        36.69        41.33        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  PDZD7 MUTATED PDZD7 WILD-TYPE 
           1.08            0.23 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
          19.82           90.12 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
          13.68           15.45 
[1] "1.1 - 19.8 (13.7)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1"  
D101V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PDZD7 MUTATED         0        0        0         0         6         1
  PDZD7 WILD-TYPE       1        3       12        19        76         3
                 vv
clus              STAGE IV
  PDZD7 MUTATED          0
  PDZD7 WILD-TYPE        3
D101V3, multiclass
           clus
vv          PDZD7 MUTATED PDZD7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PDZD7 MUTATED    0  0     7
  PDZD7 WILD-TYPE  5 17    95
D101V4, multiclass
       clus
vv      PDZD7 MUTATED PDZD7 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V5, binary
                 cls
clus               0  1
  PDZD7 MUTATED    0  7
  PDZD7 WILD-TYPE 35 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      0    7
  PDZD7 WILD-TYPE   35   82
   clus
vv  PDZD7 MUTATED PDZD7 WILD-TYPE
  0             0              35
  1             7              82
[1] 2 2
[1] FALSE
D101V6, binary
                 cls
clus               0  1
  PDZD7 MUTATED    5  0
  PDZD7 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      5    0
  PDZD7 WILD-TYPE   52    3
   clus
vv  PDZD7 MUTATED PDZD7 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D101V7, binary
                 cls
clus               0  1
  PDZD7 MUTATED    3  4
  PDZD7 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      3    4
  PDZD7 WILD-TYPE   48   71
        clus
vv       PDZD7 MUTATED PDZD7 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D101V8, binary
                 cls
clus               0  1
  PDZD7 MUTATED    5  0
  PDZD7 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      5    0
  PDZD7 WILD-TYPE   83   30
     clus
vv    PDZD7 MUTATED PDZD7 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDZD7 MUTATED                                     6
  PDZD7 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDZD7 MUTATED                                       1
  PDZD7 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDZD7 MUTATED                                                  0
  PDZD7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PDZD7 MUTATED                                     0
  PDZD7 WILD-TYPE                                   1
D101V9, multiclass
                                                  clus
vv                                                 PDZD7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PDZD7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V10, continuous
D101V11, continuous
                 vv
clus              R0 R1 R2 RX
  PDZD7 MUTATED    4  3  0  0
  PDZD7 WILD-TYPE 76 32  4  2
D101V12, multiclass
    clus
vv   PDZD7 MUTATED PDZD7 WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDZD7 MUTATED       0                         0     7
  PDZD7 WILD-TYPE     6                         5   107
D101V14, multiclass
                           clus
vv                          PDZD7 MUTATED PDZD7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V15, binary
                 cls
clus               0  1
  PDZD7 MUTATED    0  5
  PDZD7 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      0    5
  PDZD7 WILD-TYPE    5   86
                        clus
vv                       PDZD7 MUTATED PDZD7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(102) Variable = F8 MUTATION ANALYSIS
D102V1, survival
              sevent
clus2           0  1
  F8 MUTATED    3  9
  F8 WILD-TYPE 60 53
  F8 MUTATED F8 WILD-TYPE 
          12          113 
  F8 MUTATED F8 WILD-TYPE 
           9           53 
$`F8 MUTATED`
TCGA-S4-A8RO TCGA-2J-AABU TCGA-2L-AAQL TCGA-FB-AAQ1 TCGA-HV-A7OL TCGA-HV-AA8V 
       17.26         9.11         9.60         4.04         8.28        30.25 
TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-AAUW TCGA-OE-A75W TCGA-US-A77G TCGA-XD-AAUI 
       17.49        19.82         7.56         8.78         0.39        12.03 

$`F8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OP TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       32.15        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 
        6.02        11.11         7.40         8.05        13.28        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 
       39.98        16.80        18.67        13.81        12.99        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  F8 MUTATED F8 WILD-TYPE 
        0.39         0.23 
  F8 MUTATED F8 WILD-TYPE 
       30.25        90.12 
  F8 MUTATED F8 WILD-TYPE 
       9.355       15.350 
[1] "0.4 - 30.2 (9.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.5"
D102V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  F8 MUTATED         0        0        0         2        10         0        0
  F8 WILD-TYPE       1        3       12        17        72         4        3
D102V3, multiclass
           clus
vv          F8 MUTATED F8 WILD-TYPE
  STAGE I            0            1
  STAGE IA           0            3
  STAGE IB           0           12
  STAGE IIA          2           17
  STAGE IIB         10           72
  STAGE III          0            4
  STAGE IV           0            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T1 T2 T3+T4
  F8 MUTATED    0  1    11
  F8 WILD-TYPE  5 16    91
D102V4, multiclass
       clus
vv      F8 MUTATED F8 WILD-TYPE
  T1             0            5
  T2             1           16
  T3+T4         11           91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V5, binary
              cls
clus            0  1
  F8 MUTATED    2 10
  F8 WILD-TYPE 33 79
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      2   10
  F8 WILD-TYPE   33   79
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0          2           33
  1         10           79
[1] 2 2
[1] FALSE
D102V6, binary
              cls
clus            0  1
  F8 MUTATED    4  0
  F8 WILD-TYPE 53  3
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      4    0
  F8 WILD-TYPE   53    3
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0          4           53
  1          0            3
[1] 2 2
[1] FALSE
D102V7, binary
              cls
clus            0  1
  F8 MUTATED    5  7
  F8 WILD-TYPE 46 68
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      5    7
  F8 WILD-TYPE   46   68
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE          5           46
  MALE            7           68
[1] 2 2
[1] FALSE
D102V8, binary
              cls
clus            0  1
  F8 MUTATED   10  2
  F8 WILD-TYPE 78 28
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     10    2
  F8 WILD-TYPE   78   28
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO          10           78
  YES          2           28
[1] 2 2
[1] FALSE
              vv
clus           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  F8 MUTATED                                    12
  F8 WILD-TYPE                                  93
              vv
clus           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  F8 MUTATED                                       0
  F8 WILD-TYPE                                    18
              vv
clus           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  F8 MUTATED                                                  0
  F8 WILD-TYPE                                                1
              vv
clus           PANCREAS-UNDIFFERENTIATED CARCINOMA
  F8 MUTATED                                     0
  F8 WILD-TYPE                                   1
D102V9, multiclass
                                                  clus
vv                                                 F8 MUTATED F8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                      12           93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                     0           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA          0            1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                       0            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V10, continuous
D102V11, continuous
              vv
clus           R0 R1 R2 RX
  F8 MUTATED    5  3  3  1
  F8 WILD-TYPE 75 32  1  1
D102V12, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0          5           75
  R1          3           32
  R2          3            1
  RX          1            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V13, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  F8 MUTATED       3                         0     9
  F8 WILD-TYPE     3                         5   105
D102V14, multiclass
                           clus
vv                          F8 MUTATED F8 WILD-TYPE
  ASIAN                              3            3
  BLACK OR AFRICAN AMERICAN          0            5
  WHITE                              9          105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V15, binary
              cls
clus            0  1
  F8 MUTATED    0  7
  F8 WILD-TYPE  5 84
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      0    7
  F8 WILD-TYPE    5   84
                        clus
vv                       F8 MUTATED F8 WILD-TYPE
  HISPANIC OR LATINO              0            5
  NOT HISPANIC OR LATINO          7           84
[1] 2 2
[1] FALSE

Clustering(103) Variable = CACNA1D MUTATION ANALYSIS
D103V1, survival
                   sevent
clus2                0  1
  CACNA1D MUTATED    7  9
  CACNA1D WILD-TYPE 56 53
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               16               109 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
                9                53 
$`CACNA1D MUTATED`
TCGA-3A-A9IL TCGA-2J-AABA TCGA-2L-AAQJ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-HV-AA8V 
       90.12        19.96        12.95        15.55         4.04        30.25 
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        5.26        19.82        21.90         1.35         8.22         0.26 
TCGA-IB-AAUP TCGA-RB-A7B8 TCGA-YH-A8SY TCGA-YY-A8LH 
       14.17        15.32        12.76        66.28 

$`CACNA1D WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49         3.39         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       12.53        23.54         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-IB-AAUN 
       12.00        15.85         7.20        20.88        15.88         4.73 
TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-Z5-AAPL 
       15.35 

  CACNA1D MUTATED CACNA1D WILD-TYPE 
             0.26              0.23 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
            90.12             75.12 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
           14.745            15.220 
[1] "0.3 - 90.1 (14.7)" "0.2 - 75.1 (15.2)"
[1] "hr=" "1.2"
D103V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CACNA1D MUTATED         1        0        0         1        12         2
  CACNA1D WILD-TYPE       0        3       12        18        70         2
                   vv
clus                STAGE IV
  CACNA1D MUTATED          0
  CACNA1D WILD-TYPE        3
D103V3, multiclass
           clus
vv          CACNA1D MUTATED CACNA1D WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB              12                70
  STAGE III               2                 2
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CACNA1D MUTATED    1  2    13
  CACNA1D WILD-TYPE  4 15    89
D103V4, multiclass
       clus
vv      CACNA1D MUTATED CACNA1D WILD-TYPE
  T1                  1                 4
  T2                  2                15
  T3+T4              13                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V5, binary
                   cls
clus                 0  1
  CACNA1D MUTATED    2 13
  CACNA1D WILD-TYPE 33 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED      2   13
  CACNA1D WILD-TYPE   33   76
   clus
vv  CACNA1D MUTATED CACNA1D WILD-TYPE
  0               2                33
  1              13                76
[1] 2 2
[1] FALSE
D103V6, binary
                   cls
clus                 0  1
  CACNA1D MUTATED    6  0
  CACNA1D WILD-TYPE 51  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED      6    0
  CACNA1D WILD-TYPE   51    3
   clus
vv  CACNA1D MUTATED CACNA1D WILD-TYPE
  0               6                51
  1               0                 3
[1] 2 2
[1] FALSE
D103V7, binary
                   cls
clus                 0  1
  CACNA1D MUTATED    7  9
  CACNA1D WILD-TYPE 44 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED      7    9
  CACNA1D WILD-TYPE   44   66
        clus
vv       CACNA1D MUTATED CACNA1D WILD-TYPE
  FEMALE               7                44
  MALE                 9                66
[1] 2 2
[1] FALSE
D103V8, binary
                   cls
clus                 0  1
  CACNA1D MUTATED   14  2
  CACNA1D WILD-TYPE 74 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     14    2
  CACNA1D WILD-TYPE   74   28
     clus
vv    CACNA1D MUTATED CACNA1D WILD-TYPE
  NO               14                74
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CACNA1D MUTATED                                    13
  CACNA1D WILD-TYPE                                  92
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CACNA1D MUTATED                                       2
  CACNA1D WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CACNA1D MUTATED                                                  0
  CACNA1D WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CACNA1D MUTATED                                     0
  CACNA1D WILD-TYPE                                   1
D103V9, multiclass
                                                  clus
vv                                                 CACNA1D MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CACNA1D WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             92
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V10, continuous
D103V11, continuous
                   vv
clus                R0 R1 R2 RX
  CACNA1D MUTATED    8  6  1  0
  CACNA1D WILD-TYPE 72 29  3  2
D103V12, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  R0               8                72
  R1               6                29
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CACNA1D MUTATED       1                         0    15
  CACNA1D WILD-TYPE     5                         5    99
D103V14, multiclass
                           clus
vv                          CACNA1D MUTATED CACNA1D WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  15                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V15, binary
                   cls
clus                 0  1
  CACNA1D MUTATED    0 13
  CACNA1D WILD-TYPE  5 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED      0   13
  CACNA1D WILD-TYPE    5   78
                        clus
vv                       CACNA1D MUTATED CACNA1D WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13                78
[1] 2 2
[1] FALSE

Clustering(104) Variable = IFNGR2 MUTATION ANALYSIS
D104V1, survival
                  sevent
clus2               0  1
  IFNGR2 MUTATED    3  3
  IFNGR2 WILD-TYPE 60 59
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               6              119 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
               3               59 
$`IFNGR2 MUTATED`
TCGA-XD-AAUL TCGA-2L-AAQL TCGA-H8-A6C1 TCGA-HZ-A77O TCGA-IB-A6UF TCGA-OE-A75W 
       16.37         9.60        22.06         5.26        21.90         8.78 

$`IFNGR2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
            5.26             0.23 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
           22.06            90.12 
  IFNGR2 MUTATED IFNGR2 WILD-TYPE 
          12.985           15.220 
[1] "5.3 - 22.1 (13.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D104V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IFNGR2 MUTATED         0        0        0         3         4         0
  IFNGR2 WILD-TYPE       1        3       12        16        78         4
                  vv
clus               STAGE IV
  IFNGR2 MUTATED          0
  IFNGR2 WILD-TYPE        3
D104V3, multiclass
           clus
vv          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              3               16
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  IFNGR2 MUTATED    0  1     6
  IFNGR2 WILD-TYPE  5 16    96
D104V4, multiclass
       clus
vv      IFNGR2 MUTATED IFNGR2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V5, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    3  4
  IFNGR2 WILD-TYPE 32 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      3    4
  IFNGR2 WILD-TYPE   32   85
   clus
vv  IFNGR2 MUTATED IFNGR2 WILD-TYPE
  0              3               32
  1              4               85
[1] 2 2
[1] FALSE
D104V6, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    2  0
  IFNGR2 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      2    0
  IFNGR2 WILD-TYPE   55    3
   clus
vv  IFNGR2 MUTATED IFNGR2 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D104V7, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    1  6
  IFNGR2 WILD-TYPE 50 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      1    6
  IFNGR2 WILD-TYPE   50   69
        clus
vv       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  FEMALE              1               50
  MALE                6               69
[1] 2 2
[1] FALSE
D104V8, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    5  1
  IFNGR2 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      5    1
  IFNGR2 WILD-TYPE   83   29
     clus
vv    IFNGR2 MUTATED IFNGR2 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IFNGR2 MUTATED                                     6
  IFNGR2 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IFNGR2 MUTATED                                       1
  IFNGR2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IFNGR2 MUTATED                                                  0
  IFNGR2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  IFNGR2 MUTATED                                     0
  IFNGR2 WILD-TYPE                                   1
D104V9, multiclass
                                                  clus
vv                                                 IFNGR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 IFNGR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V10, continuous
D104V11, continuous
                  vv
clus               R0 R1 R2 RX
  IFNGR2 MUTATED    5  1  0  1
  IFNGR2 WILD-TYPE 75 34  4  1
D104V12, multiclass
    clus
vv   IFNGR2 MUTATED IFNGR2 WILD-TYPE
  R0              5               75
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFNGR2 MUTATED       0                         0     7
  IFNGR2 WILD-TYPE     6                         5   107
D104V14, multiclass
                           clus
vv                          IFNGR2 MUTATED IFNGR2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V15, binary
                  cls
clus                0  1
  IFNGR2 MUTATED    0  6
  IFNGR2 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNGR2 MUTATED      0    6
  IFNGR2 WILD-TYPE    5   85
                        clus
vv                       IFNGR2 MUTATED IFNGR2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(105) Variable = ALS2CR11 MUTATION ANALYSIS
D105V1, survival
                    sevent
clus2                 0  1
  ALS2CR11 MUTATED    6  2
  ALS2CR11 WILD-TYPE 57 60
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 8                117 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 2                 60 
$`ALS2CR11 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SP 
       20.61        22.22        19.82        36.69        41.33        15.85 
TCGA-Q3-AA2A TCGA-Z5-AAPL 
        3.12        15.35 

$`ALS2CR11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
        0.23        19.82        15.19        12.00         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
              3.12               0.23 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
             41.33              90.12 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
            20.215             15.060 
[1] "3.1 - 41.3 (20.2)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2.7"
D105V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ALS2CR11 MUTATED         0        0        1         3         4         0
  ALS2CR11 WILD-TYPE       1        3       11        16        78         4
                    vv
clus                 STAGE IV
  ALS2CR11 MUTATED          0
  ALS2CR11 WILD-TYPE        3
D105V3, multiclass
           clus
vv          ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                3                 16
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  ALS2CR11 MUTATED    0  0     8
  ALS2CR11 WILD-TYPE  5 17    94
D105V4, multiclass
       clus
vv      ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                8                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V5, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    3  5
  ALS2CR11 WILD-TYPE 32 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      3    5
  ALS2CR11 WILD-TYPE   32   84
   clus
vv  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  0                3                 32
  1                5                 84
[1] 2 2
[1] FALSE
D105V6, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    7  0
  ALS2CR11 WILD-TYPE 50  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      7    0
  ALS2CR11 WILD-TYPE   50    3
   clus
vv  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  0                7                 50
  1                0                  3
[1] 2 2
[1] FALSE
D105V7, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    6  2
  ALS2CR11 WILD-TYPE 45 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      6    2
  ALS2CR11 WILD-TYPE   45   73
        clus
vv       ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  FEMALE                6                 45
  MALE                  2                 73
[1] 2 2
[1] FALSE
D105V8, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    6  2
  ALS2CR11 WILD-TYPE 82 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      6    2
  ALS2CR11 WILD-TYPE   82   28
     clus
vv    ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  NO                 6                 82
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ALS2CR11 MUTATED                                     8
  ALS2CR11 WILD-TYPE                                  97
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ALS2CR11 MUTATED                                       0
  ALS2CR11 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ALS2CR11 MUTATED                                                  0
  ALS2CR11 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  ALS2CR11 MUTATED                                     0
  ALS2CR11 WILD-TYPE                                   1
D105V9, multiclass
                                                  clus
vv                                                 ALS2CR11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 ALS2CR11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V10, continuous
D105V11, continuous
                    vv
clus                 R0 R1 R2 RX
  ALS2CR11 MUTATED    5  2  0  1
  ALS2CR11 WILD-TYPE 75 33  4  1
D105V12, multiclass
    clus
vv   ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  R0                5                 75
  R1                2                 33
  R2                0                  4
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALS2CR11 MUTATED       1                         0     7
  ALS2CR11 WILD-TYPE     5                         5   107
D105V14, multiclass
                           clus
vv                          ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V15, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    0  5
  ALS2CR11 WILD-TYPE  5 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      0    5
  ALS2CR11 WILD-TYPE    5   86
                        clus
vv                       ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                 86
[1] 2 2
[1] FALSE

Clustering(106) Variable = OSBPL1A MUTATION ANALYSIS
D106V1, survival
                   sevent
clus2                0  1
  OSBPL1A MUTATED    3  6
  OSBPL1A WILD-TYPE 60 56
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                9               116 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                6                56 
$`OSBPL1A MUTATED`
TCGA-FB-AAQ6 TCGA-2L-AAQE TCGA-HV-A7OP TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-A5SO 
        8.02        22.49        32.15        17.49        19.82        12.00 
TCGA-IB-AAUU TCGA-US-A77G TCGA-YB-A89D 
        8.05         0.39        11.51 

$`OSBPL1A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        22.06         8.28        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        15.19        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J 
       15.32         9.40         0.30        39.98        16.80        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
             0.39              0.23 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
            32.15             90.12 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
            12.00             15.27 
[1] "0.4 - 32.1 (12.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D106V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OSBPL1A MUTATED         0        1        0         0         8         0
  OSBPL1A WILD-TYPE       1        2       12        19        74         4
                   vv
clus                STAGE IV
  OSBPL1A MUTATED          0
  OSBPL1A WILD-TYPE        3
D106V3, multiclass
           clus
vv          OSBPL1A MUTATED OSBPL1A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               8                74
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  OSBPL1A MUTATED    1  1     7
  OSBPL1A WILD-TYPE  4 16    95
D106V4, multiclass
       clus
vv      OSBPL1A MUTATED OSBPL1A WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               7                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V5, binary
                   cls
clus                 0  1
  OSBPL1A MUTATED    1  8
  OSBPL1A WILD-TYPE 34 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      1    8
  OSBPL1A WILD-TYPE   34   81
   clus
vv  OSBPL1A MUTATED OSBPL1A WILD-TYPE
  0               1                34
  1               8                81
[1] 2 2
[1] FALSE
D106V6, binary
                   cls
clus                 0  1
  OSBPL1A MUTATED    5  0
  OSBPL1A WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      5    0
  OSBPL1A WILD-TYPE   52    3
   clus
vv  OSBPL1A MUTATED OSBPL1A WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D106V7, binary
                   cls
clus                 0  1
  OSBPL1A MUTATED    2  7
  OSBPL1A WILD-TYPE 49 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      2    7
  OSBPL1A WILD-TYPE   49   68
        clus
vv       OSBPL1A MUTATED OSBPL1A WILD-TYPE
  FEMALE               2                49
  MALE                 7                68
[1] 2 2
[1] FALSE
D106V8, binary
                   cls
clus                 0  1
  OSBPL1A MUTATED    7  2
  OSBPL1A WILD-TYPE 81 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      7    2
  OSBPL1A WILD-TYPE   81   28
     clus
vv    OSBPL1A MUTATED OSBPL1A WILD-TYPE
  NO                7                81
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OSBPL1A MUTATED                                     8
  OSBPL1A WILD-TYPE                                  97
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OSBPL1A MUTATED                                       1
  OSBPL1A WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OSBPL1A MUTATED                                                  0
  OSBPL1A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  OSBPL1A MUTATED                                     0
  OSBPL1A WILD-TYPE                                   1
D106V9, multiclass
                                                  clus
vv                                                 OSBPL1A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 OSBPL1A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V10, continuous
D106V11, continuous
[1] "Remove cluster labels:" "OSBPL1A MUTATED"       
clus
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" "OSBPL1A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  OSBPL1A MUTATED    8  0  1  0
  OSBPL1A WILD-TYPE 72 35  3  2
D106V12, multiclass
    clus
vv   OSBPL1A MUTATED OSBPL1A WILD-TYPE
  R0               8                72
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OSBPL1A MUTATED       2                         0     7
  OSBPL1A WILD-TYPE     4                         5   107
D106V14, multiclass
                           clus
vv                          OSBPL1A MUTATED OSBPL1A WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   7               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V15, binary
                   cls
clus                 0  1
  OSBPL1A MUTATED    0  5
  OSBPL1A WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      0    5
  OSBPL1A WILD-TYPE    5   86
                        clus
vv                       OSBPL1A MUTATED OSBPL1A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(107) Variable = SLC24A1 MUTATION ANALYSIS
D107V1, survival
                   sevent
clus2                0  1
  SLC24A1 MUTATED    4  2
  SLC24A1 WILD-TYPE 59 60
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                6               119 
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                2                60 
$`SLC24A1 MUTATED`
TCGA-2J-AABP TCGA-FB-AAQ0 TCGA-HV-A7OL TCGA-IB-A5SQ TCGA-US-A776 TCGA-XN-A8T5 
       15.22        15.55         8.28         7.20        39.98        23.67 

$`SLC24A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        11.51        12.76        66.28        15.35 

  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
             7.20              0.23 
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
            39.98             90.12 
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
           15.385            15.190 
[1] "7.2 - 40.0 (15.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D107V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC24A1 MUTATED         0        0        2         3         1         0
  SLC24A1 WILD-TYPE       1        3       10        16        81         4
                   vv
clus                STAGE IV
  SLC24A1 MUTATED          0
  SLC24A1 WILD-TYPE        3
D107V3, multiclass
           clus
vv          SLC24A1 MUTATED SLC24A1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               3                16
  STAGE IIB               1                81
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC24A1 MUTATED    0  2     4
  SLC24A1 WILD-TYPE  5 15    98
D107V4, multiclass
       clus
vv      SLC24A1 MUTATED SLC24A1 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V5, binary
                   cls
clus                 0  1
  SLC24A1 MUTATED    5  1
  SLC24A1 WILD-TYPE 30 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A1 MUTATED      5    1
  SLC24A1 WILD-TYPE   30   88
   clus
vv  SLC24A1 MUTATED SLC24A1 WILD-TYPE
  0               5                30
  1               1                88
[1] 2 2
[1] FALSE
D107V6, binary
                   cls
clus                 0  1
  SLC24A1 MUTATED    3  0
  SLC24A1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A1 MUTATED      3    0
  SLC24A1 WILD-TYPE   54    3
   clus
vv  SLC24A1 MUTATED SLC24A1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D107V7, binary
                   cls
clus                 0  1
  SLC24A1 MUTATED    3  3
  SLC24A1 WILD-TYPE 48 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A1 MUTATED      3    3
  SLC24A1 WILD-TYPE   48   72
        clus
vv       SLC24A1 MUTATED SLC24A1 WILD-TYPE
  FEMALE               3                48
  MALE                 3                72
[1] 2 2
[1] FALSE
D107V8, binary
                   cls
clus                 0  1
  SLC24A1 MUTATED    5  1
  SLC24A1 WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A1 MUTATED      5    1
  SLC24A1 WILD-TYPE   83   29
     clus
vv    SLC24A1 MUTATED SLC24A1 WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC24A1 MUTATED                                     3
  SLC24A1 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC24A1 MUTATED                                       1
  SLC24A1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC24A1 MUTATED                                                  1
  SLC24A1 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC24A1 MUTATED                                     1
  SLC24A1 WILD-TYPE                                   0
D107V9, multiclass
                                                  clus
vv                                                 SLC24A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 SLC24A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V10, continuous
[1] "Remove cluster labels:" "SLC24A1 MUTATED"       
clus
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-YY-A8LH 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
D107V11, continuous
[1] "Remove cluster labels:" "SLC24A1 MUTATED"       
clus
  SLC24A1 MUTATED SLC24A1 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-YY-A8LH 
"SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" "SLC24A1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC24A1 MUTATED    4  1  1  0
  SLC24A1 WILD-TYPE 76 34  3  2
D107V12, multiclass
    clus
vv   SLC24A1 MUTATED SLC24A1 WILD-TYPE
  R0               4                76
  R1               1                34
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC24A1 MUTATED       1                         0     5
  SLC24A1 WILD-TYPE     5                         5   109
D107V14, multiclass
                           clus
vv                          SLC24A1 MUTATED SLC24A1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V15, binary
                   cls
clus                 0  1
  SLC24A1 MUTATED    1  3
  SLC24A1 WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A1 MUTATED      1    3
  SLC24A1 WILD-TYPE    4   88
                        clus
vv                       SLC24A1 MUTATED SLC24A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(108) Variable = PDZD2 MUTATION ANALYSIS
D108V1, survival
                 sevent
clus2              0  1
  PDZD2 MUTATED    9  4
  PDZD2 WILD-TYPE 54 58
  PDZD2 MUTATED PDZD2 WILD-TYPE 
             13             112 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              4              58 
$`PDZD2 MUTATED`
TCGA-2J-AAB9 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-A5SQ 
       20.61        22.06        32.15        19.82        36.69         7.20 
TCGA-IB-A6UF TCGA-IB-AAUP TCGA-IB-AAUU TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
       21.90        14.17         8.05        15.32         9.40        39.98 
TCGA-YH-A8SY 
       12.76 

$`PDZD2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST 
       19.82        41.33        15.19        12.00        15.85        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RL-AAAS TCGA-US-A779 
       10.29         8.78        13.68         3.12         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  PDZD2 MUTATED PDZD2 WILD-TYPE 
           7.20            0.23 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
          39.98           90.12 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
         19.820          15.155 
[1] "7.2 - 40.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D108V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PDZD2 MUTATED         0        0        1         2         9         1
  PDZD2 WILD-TYPE       1        3       11        17        73         3
                 vv
clus              STAGE IV
  PDZD2 MUTATED          0
  PDZD2 WILD-TYPE        3
D108V3, multiclass
           clus
vv          PDZD2 MUTATED PDZD2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             9              73
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PDZD2 MUTATED    1  1    11
  PDZD2 WILD-TYPE  4 16    91
D108V4, multiclass
       clus
vv      PDZD2 MUTATED PDZD2 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V5, binary
                 cls
clus               0  1
  PDZD2 MUTATED    3 10
  PDZD2 WILD-TYPE 32 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      3   10
  PDZD2 WILD-TYPE   32   79
   clus
vv  PDZD2 MUTATED PDZD2 WILD-TYPE
  0             3              32
  1            10              79
[1] 2 2
[1] FALSE
D108V6, binary
                 cls
clus               0  1
  PDZD2 MUTATED    8  0
  PDZD2 WILD-TYPE 49  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      8    0
  PDZD2 WILD-TYPE   49    3
   clus
vv  PDZD2 MUTATED PDZD2 WILD-TYPE
  0             8              49
  1             0               3
[1] 2 2
[1] FALSE
D108V7, binary
                 cls
clus               0  1
  PDZD2 MUTATED    6  7
  PDZD2 WILD-TYPE 45 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      6    7
  PDZD2 WILD-TYPE   45   68
        clus
vv       PDZD2 MUTATED PDZD2 WILD-TYPE
  FEMALE             6              45
  MALE               7              68
[1] 2 2
[1] FALSE
D108V8, binary
                 cls
clus               0  1
  PDZD2 MUTATED    9  4
  PDZD2 WILD-TYPE 79 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      9    4
  PDZD2 WILD-TYPE   79   26
     clus
vv    PDZD2 MUTATED PDZD2 WILD-TYPE
  NO              9              79
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDZD2 MUTATED                                     8
  PDZD2 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDZD2 MUTATED                                       3
  PDZD2 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDZD2 MUTATED                                                  1
  PDZD2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PDZD2 MUTATED                                     0
  PDZD2 WILD-TYPE                                   1
D108V9, multiclass
                                                  clus
vv                                                 PDZD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PDZD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V10, continuous
D108V11, continuous
                 vv
clus              R0 R1 R2 RX
  PDZD2 MUTATED    9  3  0  0
  PDZD2 WILD-TYPE 71 32  4  2
D108V12, multiclass
    clus
vv   PDZD2 MUTATED PDZD2 WILD-TYPE
  R0             9              71
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDZD2 MUTATED       2                         0    11
  PDZD2 WILD-TYPE     4                         5   103
D108V14, multiclass
                           clus
vv                          PDZD2 MUTATED PDZD2 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V15, binary
                 cls
clus               0  1
  PDZD2 MUTATED    0 11
  PDZD2 WILD-TYPE  5 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      0   11
  PDZD2 WILD-TYPE    5   80
                        clus
vv                       PDZD2 MUTATED PDZD2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            11              80
[1] 2 2
[1] FALSE

Clustering(109) Variable = CIR1 MUTATION ANALYSIS
D109V1, survival
                sevent
clus2             0  1
  CIR1 MUTATED    1  4
  CIR1 WILD-TYPE 62 58
  CIR1 MUTATED CIR1 WILD-TYPE 
             5            120 
  CIR1 MUTATED CIR1 WILD-TYPE 
             4             58 
$`CIR1 MUTATED`
TCGA-XD-AAUL TCGA-2L-AAQJ TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7LX 
       16.37        12.95        19.82         1.35         8.22 

$`CIR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85         7.20        20.88        21.90        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CIR1 MUTATED CIR1 WILD-TYPE 
          1.35           0.23 
  CIR1 MUTATED CIR1 WILD-TYPE 
         19.82          90.12 
  CIR1 MUTATED CIR1 WILD-TYPE 
         12.95          15.27 
[1] "1.4 - 19.8 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.5"
D109V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CIR1 MUTATED         0        0        0         1         3         1
  CIR1 WILD-TYPE       1        3       12        18        79         3
                vv
clus             STAGE IV
  CIR1 MUTATED          0
  CIR1 WILD-TYPE        3
D109V3, multiclass
           clus
vv          CIR1 MUTATED CIR1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CIR1 MUTATED    0  0     5
  CIR1 WILD-TYPE  5 17    97
D109V4, multiclass
       clus
vv      CIR1 MUTATED CIR1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V5, binary
                cls
clus              0  1
  CIR1 MUTATED    2  3
  CIR1 WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    3
  CIR1 WILD-TYPE   33   86
   clus
vv  CIR1 MUTATED CIR1 WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D109V6, binary
                cls
clus              0  1
  CIR1 MUTATED    2  0
  CIR1 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    0
  CIR1 WILD-TYPE   55    3
   clus
vv  CIR1 MUTATED CIR1 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D109V7, binary
                cls
clus              0  1
  CIR1 MUTATED    2  3
  CIR1 WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    3
  CIR1 WILD-TYPE   49   72
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D109V8, binary
                cls
clus              0  1
  CIR1 MUTATED    5  0
  CIR1 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      5    0
  CIR1 WILD-TYPE   83   30
     clus
vv    CIR1 MUTATED CIR1 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CIR1 MUTATED                                     5
  CIR1 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CIR1 MUTATED                                       0
  CIR1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CIR1 MUTATED                                                  0
  CIR1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CIR1 MUTATED                                     0
  CIR1 WILD-TYPE                                   1
D109V9, multiclass
                                                  clus
vv                                                 CIR1 MUTATED CIR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V10, continuous
D109V11, continuous
                vv
clus             R0 R1 R2 RX
  CIR1 MUTATED    3  2  0  0
  CIR1 WILD-TYPE 77 33  4  2
D109V12, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  R0            3             77
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CIR1 MUTATED       0                         0     5
  CIR1 WILD-TYPE     6                         5   109
D109V14, multiclass
                           clus
vv                          CIR1 MUTATED CIR1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V15, binary
                cls
clus              0  1
  CIR1 MUTATED    0  4
  CIR1 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      0    4
  CIR1 WILD-TYPE    5   87
                        clus
vv                       CIR1 MUTATED CIR1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(110) Variable = ZNF184 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2               0  1
  ZNF184 MUTATED    4  6
  ZNF184 WILD-TYPE 59 56
  ZNF184 MUTATED ZNF184 WILD-TYPE 
              10              115 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               6               56 
$`ZNF184 MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IO TCGA-3A-A9J0 TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-A6UG 
       20.84        63.85        24.43        10.13        19.82         1.35 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-US-A776 TCGA-US-A779 
       12.46         8.78        39.98        16.80 

$`ZNF184 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       13.28         7.56        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        9.40         0.30         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF184 MUTATED ZNF184 WILD-TYPE 
            1.35             0.23 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
           63.85            90.12 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
           18.31            15.19 
[1] "1.4 - 63.9 (18.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D110V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF184 MUTATED         0        0        0         4         5         0
  ZNF184 WILD-TYPE       1        3       12        15        77         4
                  vv
clus               STAGE IV
  ZNF184 MUTATED          0
  ZNF184 WILD-TYPE        3
D110V3, multiclass
           clus
vv          ZNF184 MUTATED ZNF184 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              4               15
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF184 MUTATED    0  0     9
  ZNF184 WILD-TYPE  5 17    93
D110V4, multiclass
       clus
vv      ZNF184 MUTATED ZNF184 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              9               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V5, binary
                  cls
clus                0  1
  ZNF184 MUTATED    4  5
  ZNF184 WILD-TYPE 31 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      4    5
  ZNF184 WILD-TYPE   31   84
   clus
vv  ZNF184 MUTATED ZNF184 WILD-TYPE
  0              4               31
  1              5               84
[1] 2 2
[1] FALSE
D110V6, binary
                  cls
clus                0  1
  ZNF184 MUTATED    3  0
  ZNF184 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      3    0
  ZNF184 WILD-TYPE   54    3
   clus
vv  ZNF184 MUTATED ZNF184 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                0  1
  ZNF184 MUTATED    3  7
  ZNF184 WILD-TYPE 48 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      3    7
  ZNF184 WILD-TYPE   48   68
        clus
vv       ZNF184 MUTATED ZNF184 WILD-TYPE
  FEMALE              3               48
  MALE                7               68
[1] 2 2
[1] FALSE
D110V8, binary
                  cls
clus                0  1
  ZNF184 MUTATED    5  4
  ZNF184 WILD-TYPE 83 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      5    4
  ZNF184 WILD-TYPE   83   26
     clus
vv    ZNF184 MUTATED ZNF184 WILD-TYPE
  NO               5               83
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF184 MUTATED                                     8
  ZNF184 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF184 MUTATED                                       1
  ZNF184 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF184 MUTATED                                                  1
  ZNF184 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF184 MUTATED                                     0
  ZNF184 WILD-TYPE                                   1
D110V9, multiclass
                                                  clus
vv                                                 ZNF184 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF184 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V10, continuous
D110V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF184 MUTATED    8  2  0  0
  ZNF184 WILD-TYPE 72 33  4  2
D110V12, multiclass
    clus
vv   ZNF184 MUTATED ZNF184 WILD-TYPE
  R0              8               72
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF184 MUTATED       0                         1     9
  ZNF184 WILD-TYPE     6                         4   105
D110V14, multiclass
                           clus
vv                          ZNF184 MUTATED ZNF184 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V15, binary
                  cls
clus                0  1
  ZNF184 MUTATED    0 10
  ZNF184 WILD-TYPE  5 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      0   10
  ZNF184 WILD-TYPE    5   81
                        clus
vv                       ZNF184 MUTATED ZNF184 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             10               81
[1] 2 2
[1] FALSE

Clustering(111) Variable = RBM15B MUTATION ANALYSIS
D111V1, survival
                  sevent
clus2               0  1
  RBM15B MUTATED    5  2
  RBM15B WILD-TYPE 58 60
  RBM15B MUTATED RBM15B WILD-TYPE 
               7              118 
  RBM15B MUTATED RBM15B WILD-TYPE 
               2               60 
$`RBM15B MUTATED`
TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2L-AAQA TCGA-HV-A7OL TCGA-IB-A5ST TCGA-LB-A8F3 
       17.26        16.37         4.70         8.28        20.88        12.46 
TCGA-RB-A7B8 
       15.32 

$`RBM15B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28         7.56        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  RBM15B MUTATED RBM15B WILD-TYPE 
            4.70             0.23 
  RBM15B MUTATED RBM15B WILD-TYPE 
           20.88            90.12 
  RBM15B MUTATED RBM15B WILD-TYPE 
          15.320           15.205 
[1] "4.7 - 20.9 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D111V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM15B MUTATED         0        0        0         3         4         0
  RBM15B WILD-TYPE       1        3       12        16        78         4
                  vv
clus               STAGE IV
  RBM15B MUTATED          0
  RBM15B WILD-TYPE        3
D111V3, multiclass
           clus
vv          RBM15B MUTATED RBM15B WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              3               16
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RBM15B MUTATED    0  0     7
  RBM15B WILD-TYPE  5 17    95
D111V4, multiclass
       clus
vv      RBM15B MUTATED RBM15B WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V5, binary
                  cls
clus                0  1
  RBM15B MUTATED    3  4
  RBM15B WILD-TYPE 32 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      3    4
  RBM15B WILD-TYPE   32   85
   clus
vv  RBM15B MUTATED RBM15B WILD-TYPE
  0              3               32
  1              4               85
[1] 2 2
[1] FALSE
D111V6, binary
                  cls
clus                0  1
  RBM15B MUTATED    1  0
  RBM15B WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      1    0
  RBM15B WILD-TYPE   56    3
   clus
vv  RBM15B MUTATED RBM15B WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D111V7, binary
                  cls
clus                0  1
  RBM15B MUTATED    4  3
  RBM15B WILD-TYPE 47 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      4    3
  RBM15B WILD-TYPE   47   72
        clus
vv       RBM15B MUTATED RBM15B WILD-TYPE
  FEMALE              4               47
  MALE                3               72
[1] 2 2
[1] FALSE
D111V8, binary
                  cls
clus                0  1
  RBM15B MUTATED    5  2
  RBM15B WILD-TYPE 83 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      5    2
  RBM15B WILD-TYPE   83   28
     clus
vv    RBM15B MUTATED RBM15B WILD-TYPE
  NO               5               83
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM15B MUTATED                                     6
  RBM15B WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM15B MUTATED                                       1
  RBM15B WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM15B MUTATED                                                  0
  RBM15B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM15B MUTATED                                     0
  RBM15B WILD-TYPE                                   1
D111V9, multiclass
                                                  clus
vv                                                 RBM15B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RBM15B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V10, continuous
[1] "Remove cluster labels:" "RBM15B MUTATED"        
clus
  RBM15B MUTATED RBM15B WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQE 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-F2-A8YN 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1       TCGA-IB-7651 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-YY-A8LH 
"RBM15B WILD-TYPE" 
D111V11, continuous
[1] "Remove cluster labels:" "RBM15B MUTATED"        
clus
  RBM15B MUTATED RBM15B WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" "RBM15B WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RBM15B MUTATED    4  2  1  0
  RBM15B WILD-TYPE 76 33  3  2
D111V12, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  R0              4               76
  R1              2               33
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM15B MUTATED       1                         1     5
  RBM15B WILD-TYPE     5                         4   109
D111V14, multiclass
                           clus
vv                          RBM15B MUTATED RBM15B WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V15, binary
                  cls
clus                0  1
  RBM15B MUTATED    0  5
  RBM15B WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      0    5
  RBM15B WILD-TYPE    5   86
                        clus
vv                       RBM15B MUTATED RBM15B WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(112) Variable = ATRX MUTATION ANALYSIS
D112V1, survival
                sevent
clus2             0  1
  ATRX MUTATED    7 10
  ATRX WILD-TYPE 56 52
  ATRX MUTATED ATRX WILD-TYPE 
            17            108 
  ATRX MUTATED ATRX WILD-TYPE 
            10             52 
$`ATRX MUTATED`
TCGA-HZ-A77Q TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-3A-A9IS 
        1.08        20.61        22.22        22.49        12.95        32.81 
TCGA-3A-A9IV TCGA-3E-AAAZ TCGA-F2-7273 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 
       36.26        71.74        19.46         5.26        10.85        19.82 
TCGA-IB-A7LX TCGA-IB-AAUN TCGA-LB-A8F3 TCGA-Q3-AA2A TCGA-RB-A7B8 
        8.22         4.73        12.46         3.12        15.32 

$`ATRX WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
       21.44         4.70         3.39         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-A7TX 
       15.06        34.09        10.13        24.43        75.12         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       20.19        17.00        10.13         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
       21.90         1.35        15.88         0.26         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       10.29         8.78        13.68         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ATRX MUTATED ATRX WILD-TYPE 
          1.08           0.23 
  ATRX MUTATED ATRX WILD-TYPE 
         71.74          90.12 
  ATRX MUTATED ATRX WILD-TYPE 
        15.320         15.205 
[1] "1.1 - 71.7 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D112V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATRX MUTATED         0        0        4         3         9         1
  ATRX WILD-TYPE       1        3        8        16        73         3
                vv
clus             STAGE IV
  ATRX MUTATED          0
  ATRX WILD-TYPE        3
D112V3, multiclass
           clus
vv          ATRX MUTATED ATRX WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             4              8
  STAGE IIA            3             16
  STAGE IIB            9             73
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  ATRX MUTATED    0  4    13
  ATRX WILD-TYPE  5 13    89
D112V4, multiclass
       clus
vv      ATRX MUTATED ATRX WILD-TYPE
  T1               0              5
  T2               4             13
  T3+T4           13             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V5, binary
                cls
clus              0  1
  ATRX MUTATED    7 10
  ATRX WILD-TYPE 28 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      7   10
  ATRX WILD-TYPE   28   79
   clus
vv  ATRX MUTATED ATRX WILD-TYPE
  0            7             28
  1           10             79
[1] 2 2
[1] FALSE
D112V6, binary
                cls
clus              0  1
  ATRX MUTATED    6  0
  ATRX WILD-TYPE 51  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      6    0
  ATRX WILD-TYPE   51    3
   clus
vv  ATRX MUTATED ATRX WILD-TYPE
  0            6             51
  1            0              3
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus              0  1
  ATRX MUTATED   10  7
  ATRX WILD-TYPE 41 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     10    7
  ATRX WILD-TYPE   41   68
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           10             41
  MALE              7             68
[1] 2 2
[1] FALSE
D112V8, binary
                cls
clus              0  1
  ATRX MUTATED   11  4
  ATRX WILD-TYPE 77 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     11    4
  ATRX WILD-TYPE   77   26
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            11             77
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATRX MUTATED                                    12
  ATRX WILD-TYPE                                  93
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATRX MUTATED                                       5
  ATRX WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATRX MUTATED                                                  0
  ATRX WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATRX MUTATED                                     0
  ATRX WILD-TYPE                                   1
D112V9, multiclass
                                                  clus
vv                                                 ATRX MUTATED ATRX WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        12             93
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       5             13
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V10, continuous
D112V11, continuous
                vv
clus             R0 R1 R2 RX
  ATRX MUTATED   12  3  0  1
  ATRX WILD-TYPE 68 32  4  1
D112V12, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  R0           12             68
  R1            3             32
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATRX MUTATED       0                         2    15
  ATRX WILD-TYPE     6                         3    99
D112V14, multiclass
                           clus
vv                          ATRX MUTATED ATRX WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               15             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V15, binary
                cls
clus              0  1
  ATRX MUTATED    1 12
  ATRX WILD-TYPE  4 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      1   12
  ATRX WILD-TYPE    4   79
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           12             79
[1] 2 2
[1] FALSE

Clustering(113) Variable = SBNO1 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2              0  1
  SBNO1 MUTATED    6  5
  SBNO1 WILD-TYPE 57 57
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             11             114 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              5              57 
$`SBNO1 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AAB6 TCGA-3A-A9IX TCGA-FB-AAPP TCGA-FB-AAPS TCGA-HV-A7OL 
        1.08         9.63        34.09        15.95         7.50         8.28 
TCGA-IB-A6UF TCGA-IB-AAUP TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-RB-A7B8 
       21.90        14.17        10.29         8.78        15.32 

$`SBNO1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ 
       17.00        16.37        12.33        37.15        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP 
        5.10        36.20        20.35        17.79        22.06        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       12.46        13.68         3.12         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
           1.08            0.23 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          34.09           90.12 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          10.29           15.45 
[1] "1.1 - 34.1 (10.3)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.3"
D113V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SBNO1 MUTATED         0        1        0         3         7         0
  SBNO1 WILD-TYPE       1        2       12        16        75         4
                 vv
clus              STAGE IV
  SBNO1 MUTATED          0
  SBNO1 WILD-TYPE        3
D113V3, multiclass
           clus
vv          SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SBNO1 MUTATED    1  1     9
  SBNO1 WILD-TYPE  4 16    93
D113V4, multiclass
       clus
vv      SBNO1 MUTATED SBNO1 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V5, binary
                 cls
clus               0  1
  SBNO1 MUTATED    4  7
  SBNO1 WILD-TYPE 31 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      4    7
  SBNO1 WILD-TYPE   31   82
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0             4              31
  1             7              82
[1] 2 2
[1] FALSE
D113V6, binary
                 cls
clus               0  1
  SBNO1 MUTATED    4  0
  SBNO1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      4    0
  SBNO1 WILD-TYPE   53    3
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus               0  1
  SBNO1 MUTATED    4  7
  SBNO1 WILD-TYPE 47 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      4    7
  SBNO1 WILD-TYPE   47   68
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  FEMALE             4              47
  MALE               7              68
[1] 2 2
[1] FALSE
D113V8, binary
                 cls
clus               0  1
  SBNO1 MUTATED    5  5
  SBNO1 WILD-TYPE 83 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      5    5
  SBNO1 WILD-TYPE   83   25
     clus
vv    SBNO1 MUTATED SBNO1 WILD-TYPE
  NO              5              83
  YES             5              25
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SBNO1 MUTATED                                     9
  SBNO1 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SBNO1 MUTATED                                       2
  SBNO1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SBNO1 MUTATED                                                  0
  SBNO1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SBNO1 MUTATED                                     0
  SBNO1 WILD-TYPE                                   1
D113V9, multiclass
                                                  clus
vv                                                 SBNO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SBNO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V10, continuous
D113V11, continuous
                 vv
clus              R0 R1 R2 RX
  SBNO1 MUTATED    8  2  1  0
  SBNO1 WILD-TYPE 72 33  3  2
D113V12, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0             8              72
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SBNO1 MUTATED       1                         0    10
  SBNO1 WILD-TYPE     5                         5   104
D113V14, multiclass
                           clus
vv                          SBNO1 MUTATED SBNO1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V15, binary
                 cls
clus               0  1
  SBNO1 MUTATED    0  9
  SBNO1 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      0    9
  SBNO1 WILD-TYPE    5   82
                        clus
vv                       SBNO1 MUTATED SBNO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(114) Variable = APOBEC4 MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                0  1
  APOBEC4 MUTATED    2  4
  APOBEC4 WILD-TYPE 61 58
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                6               119 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                4                58 
$`APOBEC4 MUTATED`
TCGA-F2-A44G TCGA-2J-AABA TCGA-3A-A9J0 TCGA-HZ-A49I TCGA-HZ-A9TJ TCGA-US-A77G 
        7.66        19.96        24.43        10.13        19.82         0.39 

$`APOBEC4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 
       20.19        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
             0.39              0.23 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            24.43             90.12 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
           14.975            15.220 
[1] "0.4 - 24.4 (15.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D114V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  APOBEC4 MUTATED         0        0        0         0         5         0
  APOBEC4 WILD-TYPE       1        3       12        19        77         4
                   vv
clus                STAGE IV
  APOBEC4 MUTATED          1
  APOBEC4 WILD-TYPE        2
D114V3, multiclass
           clus
vv          APOBEC4 MUTATED APOBEC4 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  APOBEC4 MUTATED    0  0     6
  APOBEC4 WILD-TYPE  5 17    96
D114V4, multiclass
       clus
vv      APOBEC4 MUTATED APOBEC4 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V5, binary
                   cls
clus                 0  1
  APOBEC4 MUTATED    1  5
  APOBEC4 WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      1    5
  APOBEC4 WILD-TYPE   34   84
   clus
vv  APOBEC4 MUTATED APOBEC4 WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D114V6, binary
                   cls
clus                 0  1
  APOBEC4 MUTATED    2  1
  APOBEC4 WILD-TYPE 55  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      2    1
  APOBEC4 WILD-TYPE   55    2
   clus
vv  APOBEC4 MUTATED APOBEC4 WILD-TYPE
  0               2                55
  1               1                 2
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                 0  1
  APOBEC4 MUTATED    1  5
  APOBEC4 WILD-TYPE 50 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      1    5
  APOBEC4 WILD-TYPE   50   70
        clus
vv       APOBEC4 MUTATED APOBEC4 WILD-TYPE
  FEMALE               1                50
  MALE                 5                70
[1] 2 2
[1] FALSE
D114V8, binary
                   cls
clus                 0  1
  APOBEC4 MUTATED    4  2
  APOBEC4 WILD-TYPE 84 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      4    2
  APOBEC4 WILD-TYPE   84   28
     clus
vv    APOBEC4 MUTATED APOBEC4 WILD-TYPE
  NO                4                84
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  APOBEC4 MUTATED                                     5
  APOBEC4 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  APOBEC4 MUTATED                                       1
  APOBEC4 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  APOBEC4 MUTATED                                                  0
  APOBEC4 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  APOBEC4 MUTATED                                     0
  APOBEC4 WILD-TYPE                                   1
D114V9, multiclass
                                                  clus
vv                                                 APOBEC4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 APOBEC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V10, continuous
[1] "Remove cluster labels:" "APOBEC4 MUTATED"       
clus
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"APOBEC4 WILD-TYPE" "APOBEC4 WILD-TYPE" 
D114V11, continuous
                   vv
clus                R0 R1 R2 RX
  APOBEC4 MUTATED    3  3  0  0
  APOBEC4 WILD-TYPE 77 32  4  2
D114V12, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  R0               3                77
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APOBEC4 MUTATED       0                         0     6
  APOBEC4 WILD-TYPE     6                         5   108
D114V14, multiclass
                           clus
vv                          APOBEC4 MUTATED APOBEC4 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V15, binary
                   cls
clus                 0  1
  APOBEC4 MUTATED    0  5
  APOBEC4 WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      0    5
  APOBEC4 WILD-TYPE    5   86
                        clus
vv                       APOBEC4 MUTATED APOBEC4 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(115) Variable = ST6GALNAC5 MUTATION ANALYSIS
D115V1, survival
                      sevent
clus2                   0  1
  ST6GALNAC5 MUTATED    5  7
  ST6GALNAC5 WILD-TYPE 58 55
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                  12                  113 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   7                   55 
$`ST6GALNAC5 MUTATED`
TCGA-3A-A9IJ TCGA-2J-AABH TCGA-3A-A9IZ TCGA-3E-AAAZ TCGA-FB-AAQ2 TCGA-HZ-7925 
       60.95        42.31        10.13        71.74         5.03        20.19 
TCGA-IB-7651 TCGA-IB-A5ST TCGA-IB-AAUM TCGA-RB-A7B8 TCGA-US-A779 TCGA-YY-A8LH 
       19.82        20.88         0.26        15.32        16.80        66.28 

$`ST6GALNAC5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       34.09        24.43        75.12        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00        15.85         7.20        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                0.26                 0.23 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
               71.74                90.12 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
              20.005               15.060 
[1] "0.3 - 71.7 (20.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.1"
D115V2, continuous
                      vv
clus                   STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ST6GALNAC5 MUTATED         0        0        1         2         9         0
  ST6GALNAC5 WILD-TYPE       1        3       11        17        73         4
                      vv
clus                   STAGE IV
  ST6GALNAC5 MUTATED          0
  ST6GALNAC5 WILD-TYPE        3
D115V3, multiclass
           clus
vv          ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  STAGE I                    0                    1
  STAGE IA                   0                    3
  STAGE IB                   1                   11
  STAGE IIA                  2                   17
  STAGE IIB                  9                   73
  STAGE III                  0                    4
  STAGE IV                   0                    3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   T1 T2 T3+T4
  ST6GALNAC5 MUTATED    0  2    10
  ST6GALNAC5 WILD-TYPE  5 15    92
D115V4, multiclass
       clus
vv      ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  T1                     0                    5
  T2                     2                   15
  T3+T4                 10                   92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V5, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    3  9
  ST6GALNAC5 WILD-TYPE 32 80
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      3    9
  ST6GALNAC5 WILD-TYPE   32   80
   clus
vv  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  0                  3                   32
  1                  9                   80
[1] 2 2
[1] FALSE
D115V6, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    4  0
  ST6GALNAC5 WILD-TYPE 53  3
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      4    0
  ST6GALNAC5 WILD-TYPE   53    3
   clus
vv  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  0                  4                   53
  1                  0                    3
[1] 2 2
[1] FALSE
D115V7, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    6  6
  ST6GALNAC5 WILD-TYPE 45 69
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      6    6
  ST6GALNAC5 WILD-TYPE   45   69
        clus
vv       ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  FEMALE                  6                   45
  MALE                    6                   69
[1] 2 2
[1] FALSE
D115V8, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    9  1
  ST6GALNAC5 WILD-TYPE 79 29
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      9    1
  ST6GALNAC5 WILD-TYPE   79   29
     clus
vv    ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  NO                   9                   79
  YES                  1                   29
[1] 2 2
[1] FALSE
                      vv
clus                   PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ST6GALNAC5 MUTATED                                     9
  ST6GALNAC5 WILD-TYPE                                  96
                      vv
clus                   PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ST6GALNAC5 MUTATED                                       3
  ST6GALNAC5 WILD-TYPE                                    15
                      vv
clus                   PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ST6GALNAC5 MUTATED                                                  0
  ST6GALNAC5 WILD-TYPE                                                1
                      vv
clus                   PANCREAS-UNDIFFERENTIATED CARCINOMA
  ST6GALNAC5 MUTATED                                     0
  ST6GALNAC5 WILD-TYPE                                   1
D115V9, multiclass
                                                  clus
vv                                                 ST6GALNAC5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                               9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               0
                                                  clus
vv                                                 ST6GALNAC5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                              15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                    1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V10, continuous
D115V11, continuous
                      vv
clus                   R0 R1 R2 RX
  ST6GALNAC5 MUTATED    9  2  0  0
  ST6GALNAC5 WILD-TYPE 71 33  4  2
D115V12, multiclass
    clus
vv   ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  R0                  9                   71
  R1                  2                   33
  R2                  0                    4
  RX                  0                    2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V13, continuous
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ST6GALNAC5 MUTATED       0                         0    12
  ST6GALNAC5 WILD-TYPE     6                         5   102
D115V14, multiclass
                           clus
vv                          ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  ASIAN                                      0                    6
  BLACK OR AFRICAN AMERICAN                  0                    5
  WHITE                                     12                  102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V15, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    2  9
  ST6GALNAC5 WILD-TYPE  3 82
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      2    9
  ST6GALNAC5 WILD-TYPE    3   82
                        clus
vv                       ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  HISPANIC OR LATINO                      2                    3
  NOT HISPANIC OR LATINO                  9                   82
[1] 2 2
[1] FALSE

Clustering(116) Variable = OFD1 MUTATION ANALYSIS
D116V1, survival
                sevent
clus2             0  1
  OFD1 MUTATED    4  3
  OFD1 WILD-TYPE 59 59
  OFD1 MUTATED OFD1 WILD-TYPE 
             7            118 
  OFD1 MUTATED OFD1 WILD-TYPE 
             3             59 
$`OFD1 MUTATED`
TCGA-2J-AABO TCGA-3A-A9IU TCGA-HV-AA8X TCGA-IB-8126 TCGA-IB-A5ST TCGA-IB-AAUP 
       14.47        15.06        17.49        15.19        20.88        14.17 
TCGA-US-A77J 
       18.67 

$`OFD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        32.81        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 
       17.79        22.06         8.28        32.15        30.25        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  OFD1 MUTATED OFD1 WILD-TYPE 
         14.17           0.23 
  OFD1 MUTATED OFD1 WILD-TYPE 
         20.88          90.12 
  OFD1 MUTATED OFD1 WILD-TYPE 
         15.19          15.27 
[1] "14.2 - 20.9 (15.2)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.1"
D116V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OFD1 MUTATED         0        0        0         0         6         1
  OFD1 WILD-TYPE       1        3       12        19        76         3
                vv
clus             STAGE IV
  OFD1 MUTATED          0
  OFD1 WILD-TYPE        3
D116V3, multiclass
           clus
vv          OFD1 MUTATED OFD1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            6             76
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  OFD1 MUTATED    0  1     6
  OFD1 WILD-TYPE  5 16    96
D116V4, multiclass
       clus
vv      OFD1 MUTATED OFD1 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V5, binary
                cls
clus              0  1
  OFD1 MUTATED    0  7
  OFD1 WILD-TYPE 35 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      0    7
  OFD1 WILD-TYPE   35   82
   clus
vv  OFD1 MUTATED OFD1 WILD-TYPE
  0            0             35
  1            7             82
[1] 2 2
[1] FALSE
D116V6, binary
                cls
clus              0  1
  OFD1 MUTATED    4  0
  OFD1 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      4    0
  OFD1 WILD-TYPE   53    3
   clus
vv  OFD1 MUTATED OFD1 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D116V7, binary
                cls
clus              0  1
  OFD1 MUTATED    4  3
  OFD1 WILD-TYPE 47 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      4    3
  OFD1 WILD-TYPE   47   72
        clus
vv       OFD1 MUTATED OFD1 WILD-TYPE
  FEMALE            4             47
  MALE              3             72
[1] 2 2
[1] FALSE
D116V8, binary
                cls
clus              0  1
  OFD1 MUTATED    5  1
  OFD1 WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      5    1
  OFD1 WILD-TYPE   83   29
     clus
vv    OFD1 MUTATED OFD1 WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OFD1 MUTATED                                     7
  OFD1 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OFD1 MUTATED                                       0
  OFD1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OFD1 MUTATED                                                  0
  OFD1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  OFD1 MUTATED                                     0
  OFD1 WILD-TYPE                                   1
D116V9, multiclass
                                                  clus
vv                                                 OFD1 MUTATED OFD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V10, continuous
[1] "Remove cluster labels:" "OFD1 MUTATED"          
clus
  OFD1 MUTATED OFD1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABV     TCGA-2L-AAQA 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-A6UF     TCGA-IB-A6UG 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-YY-A8LH 
"OFD1 WILD-TYPE" 
D116V11, continuous
[1] "Remove cluster labels:" "OFD1 MUTATED"          
clus
  OFD1 MUTATED OFD1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"OFD1 WILD-TYPE" "OFD1 WILD-TYPE" "OFD1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  OFD1 MUTATED    4  2  1  0
  OFD1 WILD-TYPE 76 33  3  2
D116V12, multiclass
    clus
vv   OFD1 MUTATED OFD1 WILD-TYPE
  R0            4             76
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OFD1 MUTATED       1                         0     6
  OFD1 WILD-TYPE     5                         5   108
D116V14, multiclass
                           clus
vv                          OFD1 MUTATED OFD1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V15, binary
                cls
clus              0  1
  OFD1 MUTATED    0  5
  OFD1 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  OFD1 MUTATED      0    5
  OFD1 WILD-TYPE    5   86
                        clus
vv                       OFD1 MUTATED OFD1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(117) Variable = NAP1L2 MUTATION ANALYSIS
D117V1, survival
                  sevent
clus2               0  1
  NAP1L2 MUTATED    2  6
  NAP1L2 WILD-TYPE 61 56
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               8              117 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               6               56 
$`NAP1L2 MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB6 TCGA-2J-AABA TCGA-3A-A9IB TCGA-3A-A9J0 TCGA-HZ-7925 
       17.26         9.63        19.96         7.36        24.43        20.19 
TCGA-IB-7651 TCGA-RB-A7B8 
       19.82        15.32 

$`NAP1L2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
       16.37         2.17        23.97         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50        20.84        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
            7.36             0.23 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           24.43            90.12 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
           18.54            15.12 
[1] "7.4 - 24.4 (18.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.5"
D117V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NAP1L2 MUTATED         0        0        0         1         7         0
  NAP1L2 WILD-TYPE       1        3       12        18        75         4
                  vv
clus               STAGE IV
  NAP1L2 MUTATED          0
  NAP1L2 WILD-TYPE        3
D117V3, multiclass
           clus
vv          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NAP1L2 MUTATED    0  0     8
  NAP1L2 WILD-TYPE  5 17    94
D117V4, multiclass
       clus
vv      NAP1L2 MUTATED NAP1L2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V5, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    1  7
  NAP1L2 WILD-TYPE 34 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      1    7
  NAP1L2 WILD-TYPE   34   82
   clus
vv  NAP1L2 MUTATED NAP1L2 WILD-TYPE
  0              1               34
  1              7               82
[1] 2 2
[1] FALSE
D117V6, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    3  0
  NAP1L2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      3    0
  NAP1L2 WILD-TYPE   54    3
   clus
vv  NAP1L2 MUTATED NAP1L2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D117V7, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    4  4
  NAP1L2 WILD-TYPE 47 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      4    4
  NAP1L2 WILD-TYPE   47   71
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              4               47
  MALE                4               71
[1] 2 2
[1] FALSE
D117V8, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    7  1
  NAP1L2 WILD-TYPE 81 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      7    1
  NAP1L2 WILD-TYPE   81   29
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  NO               7               81
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAP1L2 MUTATED                                     7
  NAP1L2 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAP1L2 MUTATED                                       1
  NAP1L2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAP1L2 MUTATED                                                  0
  NAP1L2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NAP1L2 MUTATED                                     0
  NAP1L2 WILD-TYPE                                   1
D117V9, multiclass
                                                  clus
vv                                                 NAP1L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NAP1L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V10, continuous
D117V11, continuous
[1] "Remove cluster labels:" "NAP1L2 MUTATED"        
clus
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IR       TCGA-3A-A9IX 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NAP1L2 MUTATED    6  2  0  0
  NAP1L2 WILD-TYPE 74 33  4  2
D117V12, multiclass
    clus
vv   NAP1L2 MUTATED NAP1L2 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAP1L2 MUTATED       0                         0     8
  NAP1L2 WILD-TYPE     6                         5   106
D117V14, multiclass
                           clus
vv                          NAP1L2 MUTATED NAP1L2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V15, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    0  6
  NAP1L2 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      0    6
  NAP1L2 WILD-TYPE    5   85
                        clus
vv                       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(118) Variable = AFTPH MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2              0  1
  AFTPH MUTATED    4  5
  AFTPH WILD-TYPE 59 57
  AFTPH MUTATED AFTPH WILD-TYPE 
              9             116 
  AFTPH MUTATED AFTPH WILD-TYPE 
              5              57 
$`AFTPH MUTATED`
TCGA-3A-A9IB TCGA-3A-A9IS TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-AAUQ TCGA-OE-A75W 
        7.36        32.81        19.82        15.19         6.02         8.78 
TCGA-RB-AA9M TCGA-US-A77G TCGA-Z5-AAPL 
        9.40         0.39        15.35 

$`AFTPH WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J 
        3.12        15.32         0.30        39.98        16.80        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

  AFTPH MUTATED AFTPH WILD-TYPE 
           0.39            0.23 
  AFTPH MUTATED AFTPH WILD-TYPE 
          32.81           90.12 
  AFTPH MUTATED AFTPH WILD-TYPE 
          9.400          15.435 
[1] "0.4 - 32.8 (9.4)"  "0.2 - 90.1 (15.4)"
[1] "hr=" "1.7"
D118V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AFTPH MUTATED         0        0        1         2         5         1
  AFTPH WILD-TYPE       1        3       11        17        77         3
                 vv
clus              STAGE IV
  AFTPH MUTATED          0
  AFTPH WILD-TYPE        3
D118V3, multiclass
           clus
vv          AFTPH MUTATED AFTPH WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AFTPH MUTATED    1  1     7
  AFTPH WILD-TYPE  4 16    95
D118V4, multiclass
       clus
vv      AFTPH MUTATED AFTPH WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V5, binary
                 cls
clus               0  1
  AFTPH MUTATED    3  6
  AFTPH WILD-TYPE 32 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AFTPH MUTATED      3    6
  AFTPH WILD-TYPE   32   83
   clus
vv  AFTPH MUTATED AFTPH WILD-TYPE
  0             3              32
  1             6              83
[1] 2 2
[1] FALSE
D118V6, binary
                 cls
clus               0  1
  AFTPH MUTATED    5  0
  AFTPH WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AFTPH MUTATED      5    0
  AFTPH WILD-TYPE   52    3
   clus
vv  AFTPH MUTATED AFTPH WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus               0  1
  AFTPH MUTATED    4  5
  AFTPH WILD-TYPE 47 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AFTPH MUTATED      4    5
  AFTPH WILD-TYPE   47   70
        clus
vv       AFTPH MUTATED AFTPH WILD-TYPE
  FEMALE             4              47
  MALE               5              70
[1] 2 2
[1] FALSE
D118V8, binary
                 cls
clus               0  1
  AFTPH MUTATED    7  2
  AFTPH WILD-TYPE 81 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AFTPH MUTATED      7    2
  AFTPH WILD-TYPE   81   28
     clus
vv    AFTPH MUTATED AFTPH WILD-TYPE
  NO              7              81
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AFTPH MUTATED                                     8
  AFTPH WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AFTPH MUTATED                                       1
  AFTPH WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AFTPH MUTATED                                                  0
  AFTPH WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AFTPH MUTATED                                     0
  AFTPH WILD-TYPE                                   1
D118V9, multiclass
                                                  clus
vv                                                 AFTPH MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 AFTPH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V10, continuous
D118V11, continuous
                 vv
clus              R0 R1 R2 RX
  AFTPH MUTATED    7  2  0  0
  AFTPH WILD-TYPE 73 33  4  2
D118V12, multiclass
    clus
vv   AFTPH MUTATED AFTPH WILD-TYPE
  R0             7              73
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AFTPH MUTATED       0                         0     9
  AFTPH WILD-TYPE     6                         5   105
D118V14, multiclass
                           clus
vv                          AFTPH MUTATED AFTPH WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V15, binary
                 cls
clus               0  1
  AFTPH MUTATED    0  9
  AFTPH WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AFTPH MUTATED      0    9
  AFTPH WILD-TYPE    5   82
                        clus
vv                       AFTPH MUTATED AFTPH WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(119) Variable = SYNCRIP MUTATION ANALYSIS
D119V1, survival
                   sevent
clus2                0  1
  SYNCRIP MUTATED    2  3
  SYNCRIP WILD-TYPE 61 59
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                5               120 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                3                59 
$`SYNCRIP MUTATED`
TCGA-3A-A9J0 TCGA-FB-A5VM TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-8126 
       24.43        16.37         5.26        19.82        15.19 

$`SYNCRIP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        10.13        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             5.26              0.23 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            24.43             90.12 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            16.37             15.17 
[1] "5.3 - 24.4 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D119V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYNCRIP MUTATED         0        0        1         0         3         1
  SYNCRIP WILD-TYPE       1        3       11        19        79         3
                   vv
clus                STAGE IV
  SYNCRIP MUTATED          0
  SYNCRIP WILD-TYPE        3
D119V3, multiclass
           clus
vv          SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SYNCRIP MUTATED    0  2     3
  SYNCRIP WILD-TYPE  5 15    99
D119V4, multiclass
       clus
vv      SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V5, binary
                   cls
clus                 0  1
  SYNCRIP MUTATED    1  4
  SYNCRIP WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      1    4
  SYNCRIP WILD-TYPE   34   85
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D119V6, binary
                   cls
clus                 0  1
  SYNCRIP MUTATED    3  0
  SYNCRIP WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      3    0
  SYNCRIP WILD-TYPE   54    3
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D119V7, binary
                   cls
clus                 0  1
  SYNCRIP MUTATED    3  2
  SYNCRIP WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      3    2
  SYNCRIP WILD-TYPE   48   73
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  FEMALE               3                48
  MALE                 2                73
[1] 2 2
[1] FALSE
D119V8, binary
                   cls
clus                 0  1
  SYNCRIP MUTATED    5  0
  SYNCRIP WILD-TYPE 83 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      5    0
  SYNCRIP WILD-TYPE   83   30
     clus
vv    SYNCRIP MUTATED SYNCRIP WILD-TYPE
  NO                5                83
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYNCRIP MUTATED                                     5
  SYNCRIP WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYNCRIP MUTATED                                       0
  SYNCRIP WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYNCRIP MUTATED                                                  0
  SYNCRIP WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYNCRIP MUTATED                                     0
  SYNCRIP WILD-TYPE                                   1
D119V9, multiclass
                                                  clus
vv                                                 SYNCRIP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SYNCRIP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V10, continuous
D119V11, continuous
                   vv
clus                R0 R1 R2 RX
  SYNCRIP MUTATED    4  1  0  0
  SYNCRIP WILD-TYPE 76 34  4  2
D119V12, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  R0               4                76
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNCRIP MUTATED       0                         0     5
  SYNCRIP WILD-TYPE     6                         5   109
D119V14, multiclass
                           clus
vv                          SYNCRIP MUTATED SYNCRIP WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V15, binary
                   cls
clus                 0  1
  SYNCRIP MUTATED    0  5
  SYNCRIP WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      0    5
  SYNCRIP WILD-TYPE    5   86
                        clus
vv                       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(120) Variable = RNF43 MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2              0  1
  RNF43 MUTATED    4  5
  RNF43 WILD-TYPE 59 57
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             116 
  RNF43 MUTATED RNF43 WILD-TYPE 
              5              57 
$`RNF43 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABE TCGA-2L-AAQA TCGA-3E-AAAZ TCGA-FB-AAPP TCGA-HV-A7OL 
        1.08        22.22         4.70        71.74        15.95         8.28 
TCGA-IB-7651 TCGA-IB-AAUN TCGA-YY-A8LH 
       19.82         4.73        66.28 

$`RNF43 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        75.12        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        12.33        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP 
        5.10        36.20        20.35        17.79        22.06        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  RNF43 MUTATED RNF43 WILD-TYPE 
           1.08            0.23 
  RNF43 MUTATED RNF43 WILD-TYPE 
          71.74           90.12 
  RNF43 MUTATED RNF43 WILD-TYPE 
         15.950          15.205 
[1] "1.1 - 71.7 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D120V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RNF43 MUTATED         0        0        1         3         5         0
  RNF43 WILD-TYPE       1        3       11        16        77         4
                 vv
clus              STAGE IV
  RNF43 MUTATED          0
  RNF43 WILD-TYPE        3
D120V3, multiclass
           clus
vv          RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             3              16
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RNF43 MUTATED    0  1     8
  RNF43 WILD-TYPE  5 16    94
D120V4, multiclass
       clus
vv      RNF43 MUTATED RNF43 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V5, binary
                 cls
clus               0  1
  RNF43 MUTATED    4  5
  RNF43 WILD-TYPE 31 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    5
  RNF43 WILD-TYPE   31   84
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             4              31
  1             5              84
[1] 2 2
[1] FALSE
D120V6, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  0
  RNF43 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    0
  RNF43 WILD-TYPE   54    3
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D120V7, binary
                 cls
clus               0  1
  RNF43 MUTATED    4  5
  RNF43 WILD-TYPE 47 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    5
  RNF43 WILD-TYPE   47   70
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE             4              47
  MALE               5              70
[1] 2 2
[1] FALSE
D120V8, binary
                 cls
clus               0  1
  RNF43 MUTATED    4  3
  RNF43 WILD-TYPE 84 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    3
  RNF43 WILD-TYPE   84   27
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO              4              84
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF43 MUTATED                                     8
  RNF43 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF43 MUTATED                                       1
  RNF43 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF43 MUTATED                                                  0
  RNF43 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RNF43 MUTATED                                     0
  RNF43 WILD-TYPE                                   1
D120V9, multiclass
                                                  clus
vv                                                 RNF43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RNF43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V10, continuous
D120V11, continuous
                 vv
clus              R0 R1 R2 RX
  RNF43 MUTATED    5  2  1  0
  RNF43 WILD-TYPE 75 33  3  2
D120V12, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED       1                         0     8
  RNF43 WILD-TYPE     5                         5   106
D120V14, multiclass
                           clus
vv                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V15, binary
                 cls
clus               0  1
  RNF43 MUTATED    1  5
  RNF43 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      1    5
  RNF43 WILD-TYPE    4   86
                        clus
vv                       RNF43 MUTATED RNF43 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(121) Variable = PRRG1 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2              0  1
  PRRG1 MUTATED    4  2
  PRRG1 WILD-TYPE 59 60
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              6             119 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              2              60 
$`PRRG1 MUTATED`
TCGA-2J-AABR TCGA-LB-A7SX TCGA-2J-AABA TCGA-IB-AAUP TCGA-YB-A89D TCGA-YH-A8SY 
       14.40        12.92        19.96        14.17        11.51        12.76 

$`PRRG1 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        66.28        15.35 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
          11.51            0.23 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          19.96           90.12 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
         13.545          15.350 
[1] "11.5 - 20.0 (13.5)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.2"
D121V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRRG1 MUTATED         0        0        0         1         4         1
  PRRG1 WILD-TYPE       1        3       12        18        78         3
                 vv
clus              STAGE IV
  PRRG1 MUTATED          0
  PRRG1 WILD-TYPE        3
D121V3, multiclass
           clus
vv          PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PRRG1 MUTATED    0  0     6
  PRRG1 WILD-TYPE  5 17    96
D121V4, multiclass
       clus
vv      PRRG1 MUTATED PRRG1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V5, binary
                 cls
clus               0  1
  PRRG1 MUTATED    1  5
  PRRG1 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      1    5
  PRRG1 WILD-TYPE   34   84
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D121V6, binary
                 cls
clus               0  1
  PRRG1 MUTATED    3  0
  PRRG1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      3    0
  PRRG1 WILD-TYPE   54    3
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D121V7, binary
                 cls
clus               0  1
  PRRG1 MUTATED    3  3
  PRRG1 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      3    3
  PRRG1 WILD-TYPE   48   72
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D121V8, binary
                 cls
clus               0  1
  PRRG1 MUTATED    4  2
  PRRG1 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      4    2
  PRRG1 WILD-TYPE   84   28
     clus
vv    PRRG1 MUTATED PRRG1 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRRG1 MUTATED                                     5
  PRRG1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRRG1 MUTATED                                       0
  PRRG1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRRG1 MUTATED                                                  0
  PRRG1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRRG1 MUTATED                                     0
  PRRG1 WILD-TYPE                                   1
D121V9, multiclass
                                                  clus
vv                                                 PRRG1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRRG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V10, continuous
[1] "Remove cluster labels:" "PRRG1 MUTATED"         
clus
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-YY-A8LH 
"PRRG1 WILD-TYPE" 
D121V11, continuous
[1] "Remove cluster labels:" "PRRG1 MUTATED"         
clus
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" "PRRG1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRRG1 MUTATED    2  3  0  0
  PRRG1 WILD-TYPE 78 32  4  2
D121V12, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRRG1 MUTATED       0                         1     5
  PRRG1 WILD-TYPE     6                         4   109
D121V14, multiclass
                           clus
vv                          PRRG1 MUTATED PRRG1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V15, binary
                 cls
clus               0  1
  PRRG1 MUTATED    0  4
  PRRG1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      0    4
  PRRG1 WILD-TYPE    5   87
                        clus
vv                       PRRG1 MUTATED PRRG1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(122) Variable = HSD17B7 MUTATION ANALYSIS
D122V1, survival
                   sevent
clus2                0  1
  HSD17B7 MUTATED    6  2
  HSD17B7 WILD-TYPE 57 60
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                8               117 
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                2                60 
$`HSD17B7 MUTATED`
TCGA-2L-AAQM TCGA-FB-A5VM TCGA-HV-A7OP TCGA-IB-AAUM TCGA-IB-AAUU TCGA-Q3-AA2A 
       45.47        16.37        32.15         0.26         8.05         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M 
       15.32         9.40 

$`HSD17B7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95         9.60        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       13.68         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
             0.26              0.23 
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
            45.47             90.12 
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
            12.36             15.22 
[1] "0.3 - 45.5 (12.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D122V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HSD17B7 MUTATED         0        0        2         0         6         0
  HSD17B7 WILD-TYPE       1        3       10        19        76         4
                   vv
clus                STAGE IV
  HSD17B7 MUTATED          0
  HSD17B7 WILD-TYPE        3
D122V3, multiclass
           clus
vv          HSD17B7 MUTATED HSD17B7 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               0                19
  STAGE IIB               6                76
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  HSD17B7 MUTATED    1  2     5
  HSD17B7 WILD-TYPE  4 15    97
D122V4, multiclass
       clus
vv      HSD17B7 MUTATED HSD17B7 WILD-TYPE
  T1                  1                 4
  T2                  2                15
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V5, binary
                   cls
clus                 0  1
  HSD17B7 MUTATED    1  7
  HSD17B7 WILD-TYPE 34 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B7 MUTATED      1    7
  HSD17B7 WILD-TYPE   34   82
   clus
vv  HSD17B7 MUTATED HSD17B7 WILD-TYPE
  0               1                34
  1               7                82
[1] 2 2
[1] FALSE
D122V6, binary
                   cls
clus                 0  1
  HSD17B7 MUTATED    4  0
  HSD17B7 WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B7 MUTATED      4    0
  HSD17B7 WILD-TYPE   53    3
   clus
vv  HSD17B7 MUTATED HSD17B7 WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D122V7, binary
                   cls
clus                 0  1
  HSD17B7 MUTATED    2  6
  HSD17B7 WILD-TYPE 49 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B7 MUTATED      2    6
  HSD17B7 WILD-TYPE   49   69
        clus
vv       HSD17B7 MUTATED HSD17B7 WILD-TYPE
  FEMALE               2                49
  MALE                 6                69
[1] 2 2
[1] FALSE
D122V8, binary
                   cls
clus                 0  1
  HSD17B7 MUTATED    6  2
  HSD17B7 WILD-TYPE 82 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B7 MUTATED      6    2
  HSD17B7 WILD-TYPE   82   28
     clus
vv    HSD17B7 MUTATED HSD17B7 WILD-TYPE
  NO                6                82
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HSD17B7 MUTATED                                     5
  HSD17B7 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HSD17B7 MUTATED                                       3
  HSD17B7 WILD-TYPE                                    15
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HSD17B7 MUTATED                                                  0
  HSD17B7 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  HSD17B7 MUTATED                                     0
  HSD17B7 WILD-TYPE                                   1
D122V9, multiclass
                                                  clus
vv                                                 HSD17B7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 HSD17B7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V10, continuous
[1] "Remove cluster labels:" "HSD17B7 MUTATED"       
clus
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A78T        TCGA-FB-AAPQ 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-YY-A8LH 
"HSD17B7 WILD-TYPE" 
D122V11, continuous
[1] "Remove cluster labels:" "HSD17B7 MUTATED"       
clus
  HSD17B7 MUTATED HSD17B7 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" "HSD17B7 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  HSD17B7 MUTATED    6  1  0  1
  HSD17B7 WILD-TYPE 74 34  4  1
D122V12, multiclass
    clus
vv   HSD17B7 MUTATED HSD17B7 WILD-TYPE
  R0               6                74
  R1               1                34
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSD17B7 MUTATED       1                         0     7
  HSD17B7 WILD-TYPE     5                         5   107
D122V14, multiclass
                           clus
vv                          HSD17B7 MUTATED HSD17B7 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   7               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V15, binary
                   cls
clus                 0  1
  HSD17B7 MUTATED    0  6
  HSD17B7 WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSD17B7 MUTATED      0    6
  HSD17B7 WILD-TYPE    5   85
                        clus
vv                       HSD17B7 MUTATED HSD17B7 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(123) Variable = HTATSF1 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                0  1
  HTATSF1 MUTATED    5  4
  HTATSF1 WILD-TYPE 58 58
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
                9               116 
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
                4                58 
$`HTATSF1 MUTATED`
TCGA-3A-A9IJ TCGA-LB-A7SX TCGA-2L-AAQM TCGA-F2-A7TX TCGA-HV-A7OL TCGA-HZ-A77O 
       60.95        12.92        45.47         3.12         8.28         5.26 
TCGA-IB-7651 TCGA-LB-A8F3 TCGA-XN-A8T3 
       19.82        12.46        31.27 

$`HTATSF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN 
       10.13        24.43        75.12        71.74        19.46        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
             3.12              0.23 
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
            60.95             90.12 
  HTATSF1 MUTATED HTATSF1 WILD-TYPE 
            12.92             15.27 
[1] "3.1 - 61.0 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D123V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HTATSF1 MUTATED         0        0        2         2         5         0
  HTATSF1 WILD-TYPE       1        3       10        17        77         4
                   vv
clus                STAGE IV
  HTATSF1 MUTATED          0
  HTATSF1 WILD-TYPE        3
D123V3, multiclass
           clus
vv          HTATSF1 MUTATED HTATSF1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               2                17
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  HTATSF1 MUTATED    0  3     6
  HTATSF1 WILD-TYPE  5 14    96
D123V4, multiclass
       clus
vv      HTATSF1 MUTATED HTATSF1 WILD-TYPE
  T1                  0                 5
  T2                  3                14
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V5, binary
                   cls
clus                 0  1
  HTATSF1 MUTATED    4  5
  HTATSF1 WILD-TYPE 31 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HTATSF1 MUTATED      4    5
  HTATSF1 WILD-TYPE   31   84
   clus
vv  HTATSF1 MUTATED HTATSF1 WILD-TYPE
  0               4                31
  1               5                84
[1] 2 2
[1] FALSE
D123V6, binary
                   cls
clus                 0  1
  HTATSF1 MUTATED    3  0
  HTATSF1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HTATSF1 MUTATED      3    0
  HTATSF1 WILD-TYPE   54    3
   clus
vv  HTATSF1 MUTATED HTATSF1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D123V7, binary
                   cls
clus                 0  1
  HTATSF1 MUTATED    4  5
  HTATSF1 WILD-TYPE 47 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HTATSF1 MUTATED      4    5
  HTATSF1 WILD-TYPE   47   70
        clus
vv       HTATSF1 MUTATED HTATSF1 WILD-TYPE
  FEMALE               4                47
  MALE                 5                70
[1] 2 2
[1] FALSE
D123V8, binary
                   cls
clus                 0  1
  HTATSF1 MUTATED    7  2
  HTATSF1 WILD-TYPE 81 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HTATSF1 MUTATED      7    2
  HTATSF1 WILD-TYPE   81   28
     clus
vv    HTATSF1 MUTATED HTATSF1 WILD-TYPE
  NO                7                81
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HTATSF1 MUTATED                                     7
  HTATSF1 WILD-TYPE                                  98
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HTATSF1 MUTATED                                       2
  HTATSF1 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HTATSF1 MUTATED                                                  0
  HTATSF1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  HTATSF1 MUTATED                                     0
  HTATSF1 WILD-TYPE                                   1
D123V9, multiclass
                                                  clus
vv                                                 HTATSF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 HTATSF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V10, continuous
D123V11, continuous
                   vv
clus                R0 R1 R2 RX
  HTATSF1 MUTATED    4  4  1  0
  HTATSF1 WILD-TYPE 76 31  3  2
D123V12, multiclass
    clus
vv   HTATSF1 MUTATED HTATSF1 WILD-TYPE
  R0               4                76
  R1               4                31
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HTATSF1 MUTATED       1                         2     6
  HTATSF1 WILD-TYPE     5                         3   108
D123V14, multiclass
                           clus
vv                          HTATSF1 MUTATED HTATSF1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               2                 3
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V15, binary
                   cls
clus                 0  1
  HTATSF1 MUTATED    1  5
  HTATSF1 WILD-TYPE  4 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HTATSF1 MUTATED      1    5
  HTATSF1 WILD-TYPE    4   86
                        clus
vv                       HTATSF1 MUTATED HTATSF1 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(124) Variable = PRDM8 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2              0  1
  PRDM8 MUTATED    3  5
  PRDM8 WILD-TYPE 60 57
  PRDM8 MUTATED PRDM8 WILD-TYPE 
              8             117 
  PRDM8 MUTATED PRDM8 WILD-TYPE 
              5              57 
$`PRDM8 MUTATED`
TCGA-2J-AAB6 TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-AAUU TCGA-OE-A75W 
        9.63         5.26        19.82        36.69         8.05         8.78 
TCGA-XD-AAUI TCGA-YB-A89D 
       12.03        11.51 

$`PRDM8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        7.40        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        13.81        12.99        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PRDM8 MUTATED PRDM8 WILD-TYPE 
           5.26            0.23 
  PRDM8 MUTATED PRDM8 WILD-TYPE 
          36.69           90.12 
  PRDM8 MUTATED PRDM8 WILD-TYPE 
          10.57           15.35 
[1] "5.3 - 36.7 (10.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D124V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRDM8 MUTATED         0        0        0         2         6         0
  PRDM8 WILD-TYPE       1        3       12        17        76         4
                 vv
clus              STAGE IV
  PRDM8 MUTATED          0
  PRDM8 WILD-TYPE        3
D124V3, multiclass
           clus
vv          PRDM8 MUTATED PRDM8 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PRDM8 MUTATED    0  1     7
  PRDM8 WILD-TYPE  5 16    95
D124V4, multiclass
       clus
vv      PRDM8 MUTATED PRDM8 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V5, binary
                 cls
clus               0  1
  PRDM8 MUTATED    2  6
  PRDM8 WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM8 MUTATED      2    6
  PRDM8 WILD-TYPE   33   83
   clus
vv  PRDM8 MUTATED PRDM8 WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D124V6, binary
                 cls
clus               0  1
  PRDM8 MUTATED    5  0
  PRDM8 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM8 MUTATED      5    0
  PRDM8 WILD-TYPE   52    3
   clus
vv  PRDM8 MUTATED PRDM8 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus               0  1
  PRDM8 MUTATED    4  4
  PRDM8 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM8 MUTATED      4    4
  PRDM8 WILD-TYPE   47   71
        clus
vv       PRDM8 MUTATED PRDM8 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D124V8, binary
                 cls
clus               0  1
  PRDM8 MUTATED    6  2
  PRDM8 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM8 MUTATED      6    2
  PRDM8 WILD-TYPE   82   28
     clus
vv    PRDM8 MUTATED PRDM8 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRDM8 MUTATED                                     8
  PRDM8 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRDM8 MUTATED                                       0
  PRDM8 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRDM8 MUTATED                                                  0
  PRDM8 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRDM8 MUTATED                                     0
  PRDM8 WILD-TYPE                                   1
D124V9, multiclass
                                                  clus
vv                                                 PRDM8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRDM8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V10, continuous
D124V11, continuous
                 vv
clus              R0 R1 R2 RX
  PRDM8 MUTATED    6  2  0  0
  PRDM8 WILD-TYPE 74 33  4  2
D124V12, multiclass
    clus
vv   PRDM8 MUTATED PRDM8 WILD-TYPE
  R0             6              74
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRDM8 MUTATED       1                         0     7
  PRDM8 WILD-TYPE     5                         5   107
D124V14, multiclass
                           clus
vv                          PRDM8 MUTATED PRDM8 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V15, binary
                 cls
clus               0  1
  PRDM8 MUTATED    0  7
  PRDM8 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM8 MUTATED      0    7
  PRDM8 WILD-TYPE    5   84
                        clus
vv                       PRDM8 MUTATED PRDM8 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(125) Variable = TIGD6 MUTATION ANALYSIS
D125V1, survival
                 sevent
clus2              0  1
  TIGD6 MUTATED    3  4
  TIGD6 WILD-TYPE 60 58
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              7             118 
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              4              58 
$`TIGD6 MUTATED`
TCGA-2J-AABP TCGA-2L-AAQA TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-AAUN TCGA-YB-A89D 
       15.22         4.70         5.26        19.82         4.73        11.51 
TCGA-YH-A8SY 
       12.76 

$`TIGD6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       14.47         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        66.28        15.35 

  TIGD6 MUTATED TIGD6 WILD-TYPE 
           4.70            0.23 
  TIGD6 MUTATED TIGD6 WILD-TYPE 
          19.82           90.12 
  TIGD6 MUTATED TIGD6 WILD-TYPE 
          11.51           15.45 
[1] "4.7 - 19.8 (11.5)" "0.2 - 90.1 (15.4)"
[1] "hr=" "2.2"
D125V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TIGD6 MUTATED         0        0        1         0         5         1
  TIGD6 WILD-TYPE       1        3       11        19        77         3
                 vv
clus              STAGE IV
  TIGD6 MUTATED          0
  TIGD6 WILD-TYPE        3
D125V3, multiclass
           clus
vv          TIGD6 MUTATED TIGD6 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TIGD6 MUTATED    0  2     5
  TIGD6 WILD-TYPE  5 15    97
D125V4, multiclass
       clus
vv      TIGD6 MUTATED TIGD6 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V5, binary
                 cls
clus               0  1
  TIGD6 MUTATED    1  6
  TIGD6 WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD6 MUTATED      1    6
  TIGD6 WILD-TYPE   34   83
   clus
vv  TIGD6 MUTATED TIGD6 WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D125V6, binary
                 cls
clus               0  1
  TIGD6 MUTATED    3  0
  TIGD6 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD6 MUTATED      3    0
  TIGD6 WILD-TYPE   54    3
   clus
vv  TIGD6 MUTATED TIGD6 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D125V7, binary
                 cls
clus               0  1
  TIGD6 MUTATED    5  2
  TIGD6 WILD-TYPE 46 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD6 MUTATED      5    2
  TIGD6 WILD-TYPE   46   73
        clus
vv       TIGD6 MUTATED TIGD6 WILD-TYPE
  FEMALE             5              46
  MALE               2              73
[1] 2 2
[1] FALSE
D125V8, binary
                 cls
clus               0  1
  TIGD6 MUTATED    5  2
  TIGD6 WILD-TYPE 83 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD6 MUTATED      5    2
  TIGD6 WILD-TYPE   83   28
     clus
vv    TIGD6 MUTATED TIGD6 WILD-TYPE
  NO              5              83
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TIGD6 MUTATED                                     5
  TIGD6 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TIGD6 MUTATED                                       0
  TIGD6 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TIGD6 MUTATED                                                  0
  TIGD6 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TIGD6 MUTATED                                     1
  TIGD6 WILD-TYPE                                   0
D125V9, multiclass
                                                  clus
vv                                                 TIGD6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 TIGD6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V10, continuous
[1] "Remove cluster labels:" "TIGD6 MUTATED"         
clus
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-YY-A8LH 
"TIGD6 WILD-TYPE" 
D125V11, continuous
[1] "Remove cluster labels:" "TIGD6 MUTATED"         
clus
  TIGD6 MUTATED TIGD6 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" "TIGD6 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TIGD6 MUTATED    4  2  0  0
  TIGD6 WILD-TYPE 76 33  4  2
D125V12, multiclass
    clus
vv   TIGD6 MUTATED TIGD6 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TIGD6 MUTATED       0                         0     7
  TIGD6 WILD-TYPE     6                         5   107
D125V14, multiclass
                           clus
vv                          TIGD6 MUTATED TIGD6 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V15, binary
                 cls
clus               0  1
  TIGD6 MUTATED    0  5
  TIGD6 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIGD6 MUTATED      0    5
  TIGD6 WILD-TYPE    5   86
                        clus
vv                       TIGD6 MUTATED TIGD6 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(126) Variable = CLCC1 MUTATION ANALYSIS
D126V1, survival
                 sevent
clus2              0  1
  CLCC1 MUTATED    3  3
  CLCC1 WILD-TYPE 60 59
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              6             119 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              3              59 
$`CLCC1 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-F2-7273 TCGA-HZ-8637 TCGA-IB-7885 
        1.08        43.50        20.84        19.46        17.00        41.33 

$`CLCC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       12.95         9.60        45.47         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        75.12        71.74         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        10.85         0.23        19.82        19.82 
TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
           1.08            0.23 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          43.50           90.12 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          20.15           15.12 
[1] "1.1 - 43.5 (20.1)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.4"
D126V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CLCC1 MUTATED         0        0        0         1         5         0
  CLCC1 WILD-TYPE       1        3       12        18        77         4
                 vv
clus              STAGE IV
  CLCC1 MUTATED          0
  CLCC1 WILD-TYPE        3
D126V3, multiclass
           clus
vv          CLCC1 MUTATED CLCC1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CLCC1 MUTATED    0  0     6
  CLCC1 WILD-TYPE  5 17    96
D126V4, multiclass
       clus
vv      CLCC1 MUTATED CLCC1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V5, binary
                 cls
clus               0  1
  CLCC1 MUTATED    1  5
  CLCC1 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      1    5
  CLCC1 WILD-TYPE   34   84
   clus
vv  CLCC1 MUTATED CLCC1 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D126V6, binary
                 cls
clus               0  1
  CLCC1 MUTATED    2  0
  CLCC1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      2    0
  CLCC1 WILD-TYPE   55    3
   clus
vv  CLCC1 MUTATED CLCC1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D126V7, binary
                 cls
clus               0  1
  CLCC1 MUTATED    3  3
  CLCC1 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      3    3
  CLCC1 WILD-TYPE   48   72
        clus
vv       CLCC1 MUTATED CLCC1 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D126V8, binary
                 cls
clus               0  1
  CLCC1 MUTATED    1  4
  CLCC1 WILD-TYPE 87 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      1    4
  CLCC1 WILD-TYPE   87   26
     clus
vv    CLCC1 MUTATED CLCC1 WILD-TYPE
  NO              1              87
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CLCC1 MUTATED                                     5
  CLCC1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CLCC1 MUTATED                                       1
  CLCC1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CLCC1 MUTATED                                                  0
  CLCC1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CLCC1 MUTATED                                     0
  CLCC1 WILD-TYPE                                   1
D126V9, multiclass
                                                  clus
vv                                                 CLCC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CLCC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V10, continuous
D126V11, continuous
[1] "Remove cluster labels:" "CLCC1 MUTATED"         
clus
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-8126 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CLCC1 MUTATED    5  1  0  0
  CLCC1 WILD-TYPE 75 34  4  2
D126V12, multiclass
    clus
vv   CLCC1 MUTATED CLCC1 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCC1 MUTATED       0                         2     4
  CLCC1 WILD-TYPE     6                         3   110
D126V14, multiclass
                           clus
vv                          CLCC1 MUTATED CLCC1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V15, binary
                 cls
clus               0  1
  CLCC1 MUTATED    1  5
  CLCC1 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      1    5
  CLCC1 WILD-TYPE    4   86
                        clus
vv                       CLCC1 MUTATED CLCC1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(127) Variable = MKL1 MUTATION ANALYSIS
D127V1, survival
                sevent
clus2             0  1
  MKL1 MUTATED    4  3
  MKL1 WILD-TYPE 59 59
  MKL1 MUTATED MKL1 WILD-TYPE 
             7            118 
  MKL1 MUTATED MKL1 WILD-TYPE 
             3             59 
$`MKL1 MUTATED`
TCGA-2J-AAB9 TCGA-FB-AAPS TCGA-FZ-5920 TCGA-IB-7885 TCGA-IB-A5SQ TCGA-IB-A7M4 
       20.61         7.50         2.01        41.33         7.20        15.88 
TCGA-IB-AAUR 
       11.11 

$`MKL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86        14.17         6.02         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MKL1 MUTATED MKL1 WILD-TYPE 
          2.01           0.23 
  MKL1 MUTATED MKL1 WILD-TYPE 
         41.33          90.12 
  MKL1 MUTATED MKL1 WILD-TYPE 
         11.11          15.27 
[1] "2.0 - 41.3 (11.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D127V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MKL1 MUTATED         0        0        1         0         6         0
  MKL1 WILD-TYPE       1        3       11        19        76         4
                vv
clus             STAGE IV
  MKL1 MUTATED          0
  MKL1 WILD-TYPE        3
D127V3, multiclass
           clus
vv          MKL1 MUTATED MKL1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  MKL1 MUTATED    0  2     5
  MKL1 WILD-TYPE  5 15    97
D127V4, multiclass
       clus
vv      MKL1 MUTATED MKL1 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V5, binary
                cls
clus              0  1
  MKL1 MUTATED    1  6
  MKL1 WILD-TYPE 34 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      1    6
  MKL1 WILD-TYPE   34   83
   clus
vv  MKL1 MUTATED MKL1 WILD-TYPE
  0            1             34
  1            6             83
[1] 2 2
[1] FALSE
D127V6, binary
                cls
clus              0  1
  MKL1 MUTATED    5  0
  MKL1 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      5    0
  MKL1 WILD-TYPE   52    3
   clus
vv  MKL1 MUTATED MKL1 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D127V7, binary
                cls
clus              0  1
  MKL1 MUTATED    4  3
  MKL1 WILD-TYPE 47 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      4    3
  MKL1 WILD-TYPE   47   72
        clus
vv       MKL1 MUTATED MKL1 WILD-TYPE
  FEMALE            4             47
  MALE              3             72
[1] 2 2
[1] FALSE
D127V8, binary
                cls
clus              0  1
  MKL1 MUTATED    5  2
  MKL1 WILD-TYPE 83 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      5    2
  MKL1 WILD-TYPE   83   28
     clus
vv    MKL1 MUTATED MKL1 WILD-TYPE
  NO             5             83
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MKL1 MUTATED                                     7
  MKL1 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MKL1 MUTATED                                       0
  MKL1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MKL1 MUTATED                                                  0
  MKL1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MKL1 MUTATED                                     0
  MKL1 WILD-TYPE                                   1
D127V9, multiclass
                                                  clus
vv                                                 MKL1 MUTATED MKL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V10, continuous
D127V11, continuous
                vv
clus             R0 R1 R2 RX
  MKL1 MUTATED    6  1  0  0
  MKL1 WILD-TYPE 74 34  4  2
D127V12, multiclass
    clus
vv   MKL1 MUTATED MKL1 WILD-TYPE
  R0            6             74
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MKL1 MUTATED       0                         1     6
  MKL1 WILD-TYPE     6                         4   108
D127V14, multiclass
                           clus
vv                          MKL1 MUTATED MKL1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V15, binary
                cls
clus              0  1
  MKL1 MUTATED    0  6
  MKL1 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL1 MUTATED      0    6
  MKL1 WILD-TYPE    5   85
                        clus
vv                       MKL1 MUTATED MKL1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(128) Variable = SFRS2IP MUTATION ANALYSIS
D128V1, survival
                   sevent
clus2                0  1
  SFRS2IP MUTATED    6  5
  SFRS2IP WILD-TYPE 57 57
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               11               114 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5                57 
$`SFRS2IP MUTATED`
TCGA-3A-A9IJ TCGA-US-A77E TCGA-FZ-5920 TCGA-HV-A7OL TCGA-HZ-A77O TCGA-IB-7651 
       60.95        14.14         2.01         8.28         5.26        19.82 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YY-A8LH 
       15.85         7.20        31.27        11.51        66.28 

$`SFRS2IP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       41.33        15.19        12.00        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       13.81        12.99        12.03        23.67        12.76        15.35 

  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
             2.01              0.23 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
            66.28             90.12 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
            14.14             15.27 
[1] "2.0 - 66.3 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D128V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SFRS2IP MUTATED         0        0        3         2         6         0
  SFRS2IP WILD-TYPE       1        3        9        17        76         4
                   vv
clus                STAGE IV
  SFRS2IP MUTATED          0
  SFRS2IP WILD-TYPE        3
D128V3, multiclass
           clus
vv          SFRS2IP MUTATED SFRS2IP WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                3                 9
  STAGE IIA               2                17
  STAGE IIB               6                76
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SFRS2IP MUTATED    0  4     7
  SFRS2IP WILD-TYPE  5 13    95
D128V4, multiclass
       clus
vv      SFRS2IP MUTATED SFRS2IP WILD-TYPE
  T1                  0                 5
  T2                  4                13
  T3+T4               7                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V5, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    5  6
  SFRS2IP WILD-TYPE 30 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      5    6
  SFRS2IP WILD-TYPE   30   83
   clus
vv  SFRS2IP MUTATED SFRS2IP WILD-TYPE
  0               5                30
  1               6                83
[1] 2 2
[1] FALSE
D128V6, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    5  0
  SFRS2IP WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      5    0
  SFRS2IP WILD-TYPE   52    3
   clus
vv  SFRS2IP MUTATED SFRS2IP WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D128V7, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    4  7
  SFRS2IP WILD-TYPE 47 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      4    7
  SFRS2IP WILD-TYPE   47   68
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  FEMALE               4                47
  MALE                 7                68
[1] 2 2
[1] FALSE
D128V8, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    8  3
  SFRS2IP WILD-TYPE 80 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      8    3
  SFRS2IP WILD-TYPE   80   27
     clus
vv    SFRS2IP MUTATED SFRS2IP WILD-TYPE
  NO                8                80
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SFRS2IP MUTATED                                     9
  SFRS2IP WILD-TYPE                                  96
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SFRS2IP MUTATED                                       2
  SFRS2IP WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SFRS2IP MUTATED                                                  0
  SFRS2IP WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SFRS2IP MUTATED                                     0
  SFRS2IP WILD-TYPE                                   1
D128V9, multiclass
                                                  clus
vv                                                 SFRS2IP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SFRS2IP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V10, continuous
D128V11, continuous
                   vv
clus                R0 R1 R2 RX
  SFRS2IP MUTATED    7  3  1  0
  SFRS2IP WILD-TYPE 73 32  3  2
D128V12, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  R0               7                73
  R1               3                32
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SFRS2IP MUTATED       1                         1     9
  SFRS2IP WILD-TYPE     5                         4   105
D128V14, multiclass
                           clus
vv                          SFRS2IP MUTATED SFRS2IP WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   9               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V15, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    1  8
  SFRS2IP WILD-TYPE  4 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      1    8
  SFRS2IP WILD-TYPE    4   83
                        clus
vv                       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               8                83
[1] 2 2
[1] FALSE

Clustering(129) Variable = PAK3 MUTATION ANALYSIS
D129V1, survival
                sevent
clus2             0  1
  PAK3 MUTATED    9  2
  PAK3 WILD-TYPE 54 60
  PAK3 MUTATED PAK3 WILD-TYPE 
            11            114 
  PAK3 MUTATED PAK3 WILD-TYPE 
             2             60 
$`PAK3 MUTATED`
TCGA-3A-A9I5 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-2L-AAQM TCGA-3A-A9IV TCGA-HZ-A77O 
       58.98        12.92        17.26        45.47        36.26         5.26 
TCGA-HZ-A77P TCGA-IB-AAUU TCGA-XN-A8T5 TCGA-YY-A8LH TCGA-Z5-AAPL 
       10.85         8.05        23.67        66.28        15.35 

$`PAK3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        15.12        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.13         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 

  PAK3 MUTATED PAK3 WILD-TYPE 
          5.26           0.23 
  PAK3 MUTATED PAK3 WILD-TYPE 
         66.28          90.12 
  PAK3 MUTATED PAK3 WILD-TYPE 
        17.260         15.155 
[1] "5.3 - 66.3 (17.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.7"
D129V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PAK3 MUTATED         0        0        2         1         8         0
  PAK3 WILD-TYPE       1        3       10        18        74         4
                vv
clus             STAGE IV
  PAK3 MUTATED          0
  PAK3 WILD-TYPE        3
D129V3, multiclass
           clus
vv          PAK3 MUTATED PAK3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            1             18
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PAK3 MUTATED    0  3     8
  PAK3 WILD-TYPE  5 14    94
D129V4, multiclass
       clus
vv      PAK3 MUTATED PAK3 WILD-TYPE
  T1               0              5
  T2               3             14
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V5, binary
                cls
clus              0  1
  PAK3 MUTATED    4  8
  PAK3 WILD-TYPE 31 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      4    8
  PAK3 WILD-TYPE   31   81
   clus
vv  PAK3 MUTATED PAK3 WILD-TYPE
  0            4             31
  1            8             81
[1] 2 2
[1] FALSE
D129V6, binary
                cls
clus              0  1
  PAK3 MUTATED    3  0
  PAK3 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      3    0
  PAK3 WILD-TYPE   54    3
   clus
vv  PAK3 MUTATED PAK3 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D129V7, binary
                cls
clus              0  1
  PAK3 MUTATED    7  5
  PAK3 WILD-TYPE 44 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      7    5
  PAK3 WILD-TYPE   44   70
        clus
vv       PAK3 MUTATED PAK3 WILD-TYPE
  FEMALE            7             44
  MALE              5             70
[1] 2 2
[1] FALSE
D129V8, binary
                cls
clus              0  1
  PAK3 MUTATED    7  4
  PAK3 WILD-TYPE 81 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      7    4
  PAK3 WILD-TYPE   81   26
     clus
vv    PAK3 MUTATED PAK3 WILD-TYPE
  NO             7             81
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PAK3 MUTATED                                     8
  PAK3 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PAK3 MUTATED                                       4
  PAK3 WILD-TYPE                                    14
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PAK3 MUTATED                                                  0
  PAK3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PAK3 MUTATED                                     0
  PAK3 WILD-TYPE                                   1
D129V9, multiclass
                                                  clus
vv                                                 PAK3 MUTATED PAK3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       4             14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V10, continuous
D129V11, continuous
                vv
clus             R0 R1 R2 RX
  PAK3 MUTATED    8  4  0  0
  PAK3 WILD-TYPE 72 31  4  2
D129V12, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  R0            8             72
  R1            4             31
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAK3 MUTATED       0                         1    11
  PAK3 WILD-TYPE     6                         4   103
D129V14, multiclass
                           clus
vv                          PAK3 MUTATED PAK3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               11            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V15, binary
                cls
clus              0  1
  PAK3 MUTATED    1 10
  PAK3 WILD-TYPE  4 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      1   10
  PAK3 WILD-TYPE    4   81
                        clus
vv                       PAK3 MUTATED PAK3 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           10             81
[1] 2 2
[1] FALSE

Clustering(130) Variable = RTKN2 MUTATION ANALYSIS
D130V1, survival
                 sevent
clus2              0  1
  RTKN2 MUTATED    3  5
  RTKN2 WILD-TYPE 60 57
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              8             117 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              5              57 
$`RTKN2 MUTATED`
TCGA-S4-A8RO TCGA-XD-AAUL TCGA-3A-A9I9 TCGA-3E-AAAY TCGA-HZ-7925 TCGA-IB-A5SO 
       17.26        16.37        20.84        75.12        20.19        12.00 
TCGA-IB-A5SQ TCGA-IB-AAUO 
        7.20         7.86 

$`RTKN2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 
        8.28        32.15        30.25        17.49        31.86        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        10.85         0.23        19.82        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       36.69        41.33        15.19        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         4.73        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RTKN2 MUTATED RTKN2 WILD-TYPE 
           7.20            0.23 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
          75.12           90.12 
  RTKN2 MUTATED RTKN2 WILD-TYPE 
         16.815          15.190 
[1] "7.2 - 75.1 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D130V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RTKN2 MUTATED         0        0        1         2         5         0
  RTKN2 WILD-TYPE       1        3       11        17        77         4
                 vv
clus              STAGE IV
  RTKN2 MUTATED          0
  RTKN2 WILD-TYPE        3
D130V3, multiclass
           clus
vv          RTKN2 MUTATED RTKN2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RTKN2 MUTATED    0  1     7
  RTKN2 WILD-TYPE  5 16    95
D130V4, multiclass
       clus
vv      RTKN2 MUTATED RTKN2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V5, binary
                 cls
clus               0  1
  RTKN2 MUTATED    3  5
  RTKN2 WILD-TYPE 32 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      3    5
  RTKN2 WILD-TYPE   32   84
   clus
vv  RTKN2 MUTATED RTKN2 WILD-TYPE
  0             3              32
  1             5              84
[1] 2 2
[1] FALSE
D130V6, binary
                 cls
clus               0  1
  RTKN2 MUTATED    3  0
  RTKN2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      3    0
  RTKN2 WILD-TYPE   54    3
   clus
vv  RTKN2 MUTATED RTKN2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D130V7, binary
                 cls
clus               0  1
  RTKN2 MUTATED    3  5
  RTKN2 WILD-TYPE 48 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      3    5
  RTKN2 WILD-TYPE   48   70
        clus
vv       RTKN2 MUTATED RTKN2 WILD-TYPE
  FEMALE             3              48
  MALE               5              70
[1] 2 2
[1] FALSE
D130V8, binary
                 cls
clus               0  1
  RTKN2 MUTATED    6  2
  RTKN2 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      6    2
  RTKN2 WILD-TYPE   82   28
     clus
vv    RTKN2 MUTATED RTKN2 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RTKN2 MUTATED                                     8
  RTKN2 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RTKN2 MUTATED                                       0
  RTKN2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RTKN2 MUTATED                                                  0
  RTKN2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RTKN2 MUTATED                                     0
  RTKN2 WILD-TYPE                                   1
D130V9, multiclass
                                                  clus
vv                                                 RTKN2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RTKN2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V10, continuous
[1] "Remove cluster labels:" "RTKN2 MUTATED"         
clus
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-YY-A8LH 
"RTKN2 WILD-TYPE" 
D130V11, continuous
[1] "Remove cluster labels:" "RTKN2 MUTATED"         
clus
  RTKN2 MUTATED RTKN2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" "RTKN2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RTKN2 MUTATED    5  2  0  0
  RTKN2 WILD-TYPE 75 33  4  2
D130V12, multiclass
    clus
vv   RTKN2 MUTATED RTKN2 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RTKN2 MUTATED       0                         0     8
  RTKN2 WILD-TYPE     6                         5   106
D130V14, multiclass
                           clus
vv                          RTKN2 MUTATED RTKN2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V15, binary
                 cls
clus               0  1
  RTKN2 MUTATED    0  7
  RTKN2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTKN2 MUTATED      0    7
  RTKN2 WILD-TYPE    5   84
                        clus
vv                       RTKN2 MUTATED RTKN2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(131) Variable = TEX2 MUTATION ANALYSIS
D131V1, survival
                sevent
clus2             0  1
  TEX2 MUTATED    2  7
  TEX2 WILD-TYPE 61 55
  TEX2 MUTATED TEX2 WILD-TYPE 
             9            116 
  TEX2 MUTATED TEX2 WILD-TYPE 
             7             55 
$`TEX2 MUTATED`
TCGA-3A-A9I5 TCGA-F2-A44G TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-FB-AAPU TCGA-HZ-8637 
       58.98         7.66         3.39        12.95        12.53        17.00 
TCGA-IB-7651 TCGA-IB-8126 TCGA-RB-A7B8 
       19.82        15.19        15.32 

$`TEX2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        60.95        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM 
        9.11        21.44         4.70        22.49         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ 
       16.37        12.33        15.95        37.15         7.50        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
       32.15        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TEX2 MUTATED TEX2 WILD-TYPE 
          3.39           0.23 
  TEX2 MUTATED TEX2 WILD-TYPE 
         58.98          90.12 
  TEX2 MUTATED TEX2 WILD-TYPE 
        15.190         15.285 
[1] "3.4 - 59.0 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D131V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TEX2 MUTATED         0        0        0         1         5         2
  TEX2 WILD-TYPE       1        3       12        18        77         2
                vv
clus             STAGE IV
  TEX2 MUTATED          0
  TEX2 WILD-TYPE        3
D131V3, multiclass
           clus
vv          TEX2 MUTATED TEX2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            2              2
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TEX2 MUTATED    0  0     8
  TEX2 WILD-TYPE  5 17    94
D131V4, multiclass
       clus
vv      TEX2 MUTATED TEX2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V5, binary
                cls
clus              0  1
  TEX2 MUTATED    3  6
  TEX2 WILD-TYPE 32 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      3    6
  TEX2 WILD-TYPE   32   83
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0            3             32
  1            6             83
[1] 2 2
[1] FALSE
D131V6, binary
                cls
clus              0  1
  TEX2 MUTATED    3  0
  TEX2 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      3    0
  TEX2 WILD-TYPE   54    3
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D131V7, binary
                cls
clus              0  1
  TEX2 MUTATED    7  2
  TEX2 WILD-TYPE 44 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      7    2
  TEX2 WILD-TYPE   44   73
        clus
vv       TEX2 MUTATED TEX2 WILD-TYPE
  FEMALE            7             44
  MALE              2             73
[1] 2 2
[1] FALSE
D131V8, binary
                cls
clus              0  1
  TEX2 MUTATED    6  3
  TEX2 WILD-TYPE 82 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      6    3
  TEX2 WILD-TYPE   82   27
     clus
vv    TEX2 MUTATED TEX2 WILD-TYPE
  NO             6             82
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEX2 MUTATED                                     8
  TEX2 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEX2 MUTATED                                       1
  TEX2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEX2 MUTATED                                                  0
  TEX2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TEX2 MUTATED                                     0
  TEX2 WILD-TYPE                                   1
D131V9, multiclass
                                                  clus
vv                                                 TEX2 MUTATED TEX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V10, continuous
[1] "Remove cluster labels:" "TEX2 MUTATED"          
clus
  TEX2 MUTATED TEX2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-A6UF     TCGA-IB-A6UG 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-YY-A8LH 
"TEX2 WILD-TYPE" 
D131V11, continuous
[1] "Remove cluster labels:" "TEX2 MUTATED"          
clus
  TEX2 MUTATED TEX2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TEX2 MUTATED    4  5  0  0
  TEX2 WILD-TYPE 76 30  4  2
D131V12, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  R0            4             76
  R1            5             30
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEX2 MUTATED       1                         0     8
  TEX2 WILD-TYPE     5                         5   106
D131V14, multiclass
                           clus
vv                          TEX2 MUTATED TEX2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V15, binary
                cls
clus              0  1
  TEX2 MUTATED    1  6
  TEX2 WILD-TYPE  4 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      1    6
  TEX2 WILD-TYPE    4   85
                        clus
vv                       TEX2 MUTATED TEX2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(132) Variable = TMEM41A MUTATION ANALYSIS
D132V1, survival
                   sevent
clus2                0  1
  TMEM41A MUTATED    3  3
  TMEM41A WILD-TYPE 60 59
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                6               119 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                3                59 
$`TMEM41A MUTATED`
TCGA-2J-AAB6 TCGA-3A-A9IS TCGA-FB-AAQ3 TCGA-HV-A7OL TCGA-IB-7651 TCGA-YB-A89D 
        9.63        32.81         1.02         8.28        19.82        11.51 

$`TMEM41A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  TMEM41A MUTATED TMEM41A WILD-TYPE 
             1.02              0.23 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
            32.81             90.12 
  TMEM41A MUTATED TMEM41A WILD-TYPE 
            10.57             15.32 
[1] "1.0 - 32.8 (10.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D132V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM41A MUTATED         0        0        1         2         3         0
  TMEM41A WILD-TYPE       1        3       11        17        79         4
                   vv
clus                STAGE IV
  TMEM41A MUTATED          0
  TMEM41A WILD-TYPE        3
D132V3, multiclass
           clus
vv          TMEM41A MUTATED TMEM41A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               2                17
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TMEM41A MUTATED    0  1     5
  TMEM41A WILD-TYPE  5 16    97
D132V4, multiclass
       clus
vv      TMEM41A MUTATED TMEM41A WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V5, binary
                   cls
clus                 0  1
  TMEM41A MUTATED    3  3
  TMEM41A WILD-TYPE 32 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      3    3
  TMEM41A WILD-TYPE   32   86
   clus
vv  TMEM41A MUTATED TMEM41A WILD-TYPE
  0               3                32
  1               3                86
[1] 2 2
[1] FALSE
D132V6, binary
                   cls
clus                 0  1
  TMEM41A MUTATED    2  0
  TMEM41A WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      2    0
  TMEM41A WILD-TYPE   55    3
   clus
vv  TMEM41A MUTATED TMEM41A WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D132V7, binary
                   cls
clus                 0  1
  TMEM41A MUTATED    2  4
  TMEM41A WILD-TYPE 49 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      2    4
  TMEM41A WILD-TYPE   49   71
        clus
vv       TMEM41A MUTATED TMEM41A WILD-TYPE
  FEMALE               2                49
  MALE                 4                71
[1] 2 2
[1] FALSE
D132V8, binary
                   cls
clus                 0  1
  TMEM41A MUTATED    5  1
  TMEM41A WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      5    1
  TMEM41A WILD-TYPE   83   29
     clus
vv    TMEM41A MUTATED TMEM41A WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM41A MUTATED                                     5
  TMEM41A WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM41A MUTATED                                       1
  TMEM41A WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM41A MUTATED                                                  0
  TMEM41A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM41A MUTATED                                     0
  TMEM41A WILD-TYPE                                   1
D132V9, multiclass
                                                  clus
vv                                                 TMEM41A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TMEM41A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V10, continuous
[1] "Remove cluster labels:" "TMEM41A MUTATED"       
clus
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
D132V11, continuous
[1] "Remove cluster labels:" "TMEM41A MUTATED"       
clus
  TMEM41A MUTATED TMEM41A WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" "TMEM41A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TMEM41A MUTATED    5  0  1  0
  TMEM41A WILD-TYPE 75 35  3  2
D132V12, multiclass
    clus
vv   TMEM41A MUTATED TMEM41A WILD-TYPE
  R0               5                75
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM41A MUTATED       1                         0     5
  TMEM41A WILD-TYPE     5                         5   109
D132V14, multiclass
                           clus
vv                          TMEM41A MUTATED TMEM41A WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V15, binary
                   cls
clus                 0  1
  TMEM41A MUTATED    0  4
  TMEM41A WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41A MUTATED      0    4
  TMEM41A WILD-TYPE    5   87
                        clus
vv                       TMEM41A MUTATED TMEM41A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(133) Variable = DHX57 MUTATION ANALYSIS
D133V1, survival
                 sevent
clus2              0  1
  DHX57 MUTATED    6  5
  DHX57 WILD-TYPE 57 57
  DHX57 MUTATED DHX57 WILD-TYPE 
             11             114 
  DHX57 MUTATED DHX57 WILD-TYPE 
              5              57 
$`DHX57 MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9IH TCGA-FB-A78T TCGA-HV-A7OL TCGA-HV-A7OP TCGA-IB-7651 
       12.95        33.57        12.33         8.28        32.15        19.82 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-AAUU TCGA-US-A779 
        7.20        20.88        21.90         8.05        16.80 

$`DHX57 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       22.06        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7LX 
       41.33        15.19        12.00        15.85         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  DHX57 MUTATED DHX57 WILD-TYPE 
           7.20            0.23 
  DHX57 MUTATED DHX57 WILD-TYPE 
          33.57           90.12 
  DHX57 MUTATED DHX57 WILD-TYPE 
         16.800          15.205 
[1] "7.2 - 33.6 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D133V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DHX57 MUTATED         0        1        1         1         7         1
  DHX57 WILD-TYPE       1        2       11        18        75         3
                 vv
clus              STAGE IV
  DHX57 MUTATED          0
  DHX57 WILD-TYPE        3
D133V3, multiclass
           clus
vv          DHX57 MUTATED DHX57 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DHX57 MUTATED    1  1     9
  DHX57 WILD-TYPE  4 16    93
D133V4, multiclass
       clus
vv      DHX57 MUTATED DHX57 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V5, binary
                 cls
clus               0  1
  DHX57 MUTATED    4  7
  DHX57 WILD-TYPE 31 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX57 MUTATED      4    7
  DHX57 WILD-TYPE   31   82
   clus
vv  DHX57 MUTATED DHX57 WILD-TYPE
  0             4              31
  1             7              82
[1] 2 2
[1] FALSE
D133V6, binary
                 cls
clus               0  1
  DHX57 MUTATED    7  0
  DHX57 WILD-TYPE 50  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX57 MUTATED      7    0
  DHX57 WILD-TYPE   50    3
   clus
vv  DHX57 MUTATED DHX57 WILD-TYPE
  0             7              50
  1             0               3
[1] 2 2
[1] FALSE
D133V7, binary
                 cls
clus               0  1
  DHX57 MUTATED    7  4
  DHX57 WILD-TYPE 44 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX57 MUTATED      7    4
  DHX57 WILD-TYPE   44   71
        clus
vv       DHX57 MUTATED DHX57 WILD-TYPE
  FEMALE             7              44
  MALE               4              71
[1] 2 2
[1] FALSE
D133V8, binary
                 cls
clus               0  1
  DHX57 MUTATED    9  1
  DHX57 WILD-TYPE 79 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX57 MUTATED      9    1
  DHX57 WILD-TYPE   79   29
     clus
vv    DHX57 MUTATED DHX57 WILD-TYPE
  NO              9              79
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DHX57 MUTATED                                    10
  DHX57 WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DHX57 MUTATED                                       1
  DHX57 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DHX57 MUTATED                                                  0
  DHX57 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DHX57 MUTATED                                     0
  DHX57 WILD-TYPE                                   1
D133V9, multiclass
                                                  clus
vv                                                 DHX57 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DHX57 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V10, continuous
D133V11, continuous
                 vv
clus              R0 R1 R2 RX
  DHX57 MUTATED    8  2  1  0
  DHX57 WILD-TYPE 72 33  3  2
D133V12, multiclass
    clus
vv   DHX57 MUTATED DHX57 WILD-TYPE
  R0             8              72
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHX57 MUTATED       2                         0     9
  DHX57 WILD-TYPE     4                         5   105
D133V14, multiclass
                           clus
vv                          DHX57 MUTATED DHX57 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V15, binary
                 cls
clus               0  1
  DHX57 MUTATED    0  8
  DHX57 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX57 MUTATED      0    8
  DHX57 WILD-TYPE    5   83
                        clus
vv                       DHX57 MUTATED DHX57 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(134) Variable = UHRF1BP1 MUTATION ANALYSIS
D134V1, survival
                    sevent
clus2                 0  1
  UHRF1BP1 MUTATED    4  3
  UHRF1BP1 WILD-TYPE 59 59
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 7                118 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 3                 59 
$`UHRF1BP1 MUTATED`
TCGA-2J-AABR TCGA-3A-A9IO TCGA-HZ-8637 TCGA-HZ-A49I TCGA-IB-7651 TCGA-Q3-A5QY 
       14.40        63.85        17.00        10.13        19.82        13.68 
TCGA-XN-A8T3 
       31.27 

$`UHRF1BP1 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        20.19         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
        0.39        18.67        13.81        12.99        12.03        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
             10.13               0.23 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
             63.85              90.12 
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
            17.000             15.205 
[1] "10.1 - 63.9 (17.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D134V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UHRF1BP1 MUTATED         0        0        1         1         4         0
  UHRF1BP1 WILD-TYPE       1        3       11        18        78         4
                    vv
clus                 STAGE IV
  UHRF1BP1 MUTATED          0
  UHRF1BP1 WILD-TYPE        3
D134V3, multiclass
           clus
vv          UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  UHRF1BP1 MUTATED    0  1     5
  UHRF1BP1 WILD-TYPE  5 16    97
D134V4, multiclass
       clus
vv      UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V5, binary
                    cls
clus                  0  1
  UHRF1BP1 MUTATED    2  4
  UHRF1BP1 WILD-TYPE 33 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      2    4
  UHRF1BP1 WILD-TYPE   33   85
   clus
vv  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  0                2                 33
  1                4                 85
[1] 2 2
[1] FALSE
D134V6, binary
                    cls
clus                  0  1
  UHRF1BP1 MUTATED    3  0
  UHRF1BP1 WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      3    0
  UHRF1BP1 WILD-TYPE   54    3
   clus
vv  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D134V7, binary
                    cls
clus                  0  1
  UHRF1BP1 MUTATED    3  4
  UHRF1BP1 WILD-TYPE 48 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      3    4
  UHRF1BP1 WILD-TYPE   48   71
        clus
vv       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  FEMALE                3                 48
  MALE                  4                 71
[1] 2 2
[1] FALSE
D134V8, binary
                    cls
clus                  0  1
  UHRF1BP1 MUTATED    4  3
  UHRF1BP1 WILD-TYPE 84 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      4    3
  UHRF1BP1 WILD-TYPE   84   27
     clus
vv    UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  NO                 4                 84
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UHRF1BP1 MUTATED                                     6
  UHRF1BP1 WILD-TYPE                                  99
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UHRF1BP1 MUTATED                                       1
  UHRF1BP1 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UHRF1BP1 MUTATED                                                  0
  UHRF1BP1 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  UHRF1BP1 MUTATED                                     0
  UHRF1BP1 WILD-TYPE                                   1
D134V9, multiclass
                                                  clus
vv                                                 UHRF1BP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 UHRF1BP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V10, continuous
[1] "Remove cluster labels:" "UHRF1BP1 MUTATED"      
clus
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
D134V11, continuous
[1] "Remove cluster labels:" "UHRF1BP1 MUTATED"      
clus
  UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"UHRF1BP1 WILD-TYPE" "UHRF1BP1 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  UHRF1BP1 MUTATED    5  2  0  0
  UHRF1BP1 WILD-TYPE 75 33  4  2
D134V12, multiclass
    clus
vv   UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  R0                5                 75
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UHRF1BP1 MUTATED       0                         0     7
  UHRF1BP1 WILD-TYPE     6                         5   107
D134V14, multiclass
                           clus
vv                          UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V15, binary
                    cls
clus                  0  1
  UHRF1BP1 MUTATED    2  4
  UHRF1BP1 WILD-TYPE  3 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  UHRF1BP1 MUTATED      2    4
  UHRF1BP1 WILD-TYPE    3   87
                        clus
vv                       UHRF1BP1 MUTATED UHRF1BP1 WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(135) Variable = NEDD4L MUTATION ANALYSIS
D135V1, survival
                  sevent
clus2               0  1
  NEDD4L MUTATED    6  4
  NEDD4L WILD-TYPE 57 58
  NEDD4L MUTATED NEDD4L WILD-TYPE 
              10              115 
  NEDD4L MUTATED NEDD4L WILD-TYPE 
               4               58 
$`NEDD4L MUTATED`
TCGA-3A-A9I5 TCGA-2J-AABA TCGA-2J-AABK TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9J0 
       58.98        19.96        15.91         9.11        22.49        24.43 
TCGA-F2-A8YN TCGA-IB-7651 TCGA-RB-AA9M TCGA-YH-A8SY 
       17.00        19.82         9.40        12.76 

$`NEDD4L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV 
       22.22        22.72        42.31        14.47        15.22        21.44 
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
        4.70         3.39        12.95         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY 
       32.81        15.06        36.26        34.09        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  NEDD4L MUTATED NEDD4L WILD-TYPE 
            9.11             0.23 
  NEDD4L MUTATED NEDD4L WILD-TYPE 
           58.98            90.12 
  NEDD4L MUTATED NEDD4L WILD-TYPE 
           18.41            15.12 
[1] "9.1 - 59.0 (18.4)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.5"
D135V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NEDD4L MUTATED         0        0        0         1         7         1
  NEDD4L WILD-TYPE       1        3       12        18        75         3
                  vv
clus               STAGE IV
  NEDD4L MUTATED          0
  NEDD4L WILD-TYPE        3
D135V3, multiclass
           clus
vv          NEDD4L MUTATED NEDD4L WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              7               75
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NEDD4L MUTATED    1  0     8
  NEDD4L WILD-TYPE  4 17    94
D135V4, multiclass
       clus
vv      NEDD4L MUTATED NEDD4L WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V5, binary
                  cls
clus                0  1
  NEDD4L MUTATED    2  8
  NEDD4L WILD-TYPE 33 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NEDD4L MUTATED      2    8
  NEDD4L WILD-TYPE   33   81
   clus
vv  NEDD4L MUTATED NEDD4L WILD-TYPE
  0              2               33
  1              8               81
[1] 2 2
[1] FALSE
D135V6, binary
                  cls
clus                0  1
  NEDD4L MUTATED    6  0
  NEDD4L WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NEDD4L MUTATED      6    0
  NEDD4L WILD-TYPE   51    3
   clus
vv  NEDD4L MUTATED NEDD4L WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D135V7, binary
                  cls
clus                0  1
  NEDD4L MUTATED    2  8
  NEDD4L WILD-TYPE 49 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NEDD4L MUTATED      2    8
  NEDD4L WILD-TYPE   49   67
        clus
vv       NEDD4L MUTATED NEDD4L WILD-TYPE
  FEMALE              2               49
  MALE                8               67
[1] 2 2
[1] FALSE
D135V8, binary
                  cls
clus                0  1
  NEDD4L MUTATED    6  4
  NEDD4L WILD-TYPE 82 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NEDD4L MUTATED      6    4
  NEDD4L WILD-TYPE   82   26
     clus
vv    NEDD4L MUTATED NEDD4L WILD-TYPE
  NO               6               82
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NEDD4L MUTATED                                     9
  NEDD4L WILD-TYPE                                  96
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NEDD4L MUTATED                                       0
  NEDD4L WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NEDD4L MUTATED                                                  0
  NEDD4L WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NEDD4L MUTATED                                     0
  NEDD4L WILD-TYPE                                   1
D135V9, multiclass
                                                  clus
vv                                                 NEDD4L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NEDD4L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V10, continuous
D135V11, continuous
[1] "Remove cluster labels:" "NEDD4L MUTATED"        
clus
  NEDD4L MUTATED NEDD4L WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" "NEDD4L WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NEDD4L MUTATED    6  3  0  0
  NEDD4L WILD-TYPE 74 32  4  2
D135V12, multiclass
    clus
vv   NEDD4L MUTATED NEDD4L WILD-TYPE
  R0              6               74
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEDD4L MUTATED       0                         0    10
  NEDD4L WILD-TYPE     6                         5   104
D135V14, multiclass
                           clus
vv                          NEDD4L MUTATED NEDD4L WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 10              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V15, binary
                  cls
clus                0  1
  NEDD4L MUTATED    0  6
  NEDD4L WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NEDD4L MUTATED      0    6
  NEDD4L WILD-TYPE    5   85
                        clus
vv                       NEDD4L MUTATED NEDD4L WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(136) Variable = SMCR7 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2              0  1
  SMCR7 MUTATED    4  3
  SMCR7 WILD-TYPE 59 59
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              7             118 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              3              59 
$`SMCR7 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-3A-A9IV TCGA-HZ-7925 TCGA-Q3-AA2A TCGA-US-A77G 
        9.63         2.63        36.26        20.19         3.12         0.39 
TCGA-XN-A8T3 
       31.27 

$`SMCR7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14        16.37         2.17        23.97        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       16.80        18.67        13.81        12.99        12.03        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  SMCR7 MUTATED SMCR7 WILD-TYPE 
           0.39            0.23 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
          36.26           90.12 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
           9.63           15.27 
[1] "0.4 - 36.3 (9.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D136V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMCR7 MUTATED         0        0        3         1         3         0
  SMCR7 WILD-TYPE       1        3        9        18        79         4
                 vv
clus              STAGE IV
  SMCR7 MUTATED          0
  SMCR7 WILD-TYPE        3
D136V3, multiclass
           clus
vv          SMCR7 MUTATED SMCR7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              3               9
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SMCR7 MUTATED    0  2     5
  SMCR7 WILD-TYPE  5 15    97
D136V4, multiclass
       clus
vv      SMCR7 MUTATED SMCR7 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V5, binary
                 cls
clus               0  1
  SMCR7 MUTATED    3  4
  SMCR7 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      3    4
  SMCR7 WILD-TYPE   32   85
   clus
vv  SMCR7 MUTATED SMCR7 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D136V6, binary
                 cls
clus               0  1
  SMCR7 MUTATED    3  0
  SMCR7 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      3    0
  SMCR7 WILD-TYPE   54    3
   clus
vv  SMCR7 MUTATED SMCR7 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D136V7, binary
                 cls
clus               0  1
  SMCR7 MUTATED    2  5
  SMCR7 WILD-TYPE 49 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      2    5
  SMCR7 WILD-TYPE   49   70
        clus
vv       SMCR7 MUTATED SMCR7 WILD-TYPE
  FEMALE             2              49
  MALE               5              70
[1] 2 2
[1] FALSE
D136V8, binary
                 cls
clus               0  1
  SMCR7 MUTATED    5  1
  SMCR7 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      5    1
  SMCR7 WILD-TYPE   83   29
     clus
vv    SMCR7 MUTATED SMCR7 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMCR7 MUTATED                                     6
  SMCR7 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMCR7 MUTATED                                       1
  SMCR7 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMCR7 MUTATED                                                  0
  SMCR7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMCR7 MUTATED                                     0
  SMCR7 WILD-TYPE                                   1
D136V9, multiclass
                                                  clus
vv                                                 SMCR7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SMCR7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V10, continuous
D136V11, continuous
                 vv
clus              R0 R1 R2 RX
  SMCR7 MUTATED    4  2  0  1
  SMCR7 WILD-TYPE 76 33  4  1
D136V12, multiclass
    clus
vv   SMCR7 MUTATED SMCR7 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMCR7 MUTATED       0                         0     7
  SMCR7 WILD-TYPE     6                         5   107
D136V14, multiclass
                           clus
vv                          SMCR7 MUTATED SMCR7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V15, binary
                 cls
clus               0  1
  SMCR7 MUTATED    1  4
  SMCR7 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      1    4
  SMCR7 WILD-TYPE    4   87
                        clus
vv                       SMCR7 MUTATED SMCR7 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(137) Variable = PUM2 MUTATION ANALYSIS
D137V1, survival
                sevent
clus2             0  1
  PUM2 MUTATED    3  4
  PUM2 WILD-TYPE 60 58
  PUM2 MUTATED PUM2 WILD-TYPE 
             7            118 
  PUM2 MUTATED PUM2 WILD-TYPE 
             4             58 
$`PUM2 MUTATED`
TCGA-3A-A9IJ TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-HV-A7OP TCGA-HZ-8637 TCGA-IB-7651 
       60.95         9.60        20.84        32.15        17.00        19.82 
TCGA-IB-AAUU 
        8.05 

$`PUM2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       12.95        45.47        43.50         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  PUM2 MUTATED PUM2 WILD-TYPE 
          8.05           0.23 
  PUM2 MUTATED PUM2 WILD-TYPE 
         60.95          90.12 
  PUM2 MUTATED PUM2 WILD-TYPE 
        19.820         15.155 
[1] "8.1 - 61.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D137V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PUM2 MUTATED         0        0        1         1         5         0
  PUM2 WILD-TYPE       1        3       11        18        77         4
                vv
clus             STAGE IV
  PUM2 MUTATED          0
  PUM2 WILD-TYPE        3
D137V3, multiclass
           clus
vv          PUM2 MUTATED PUM2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PUM2 MUTATED    0  1     6
  PUM2 WILD-TYPE  5 16    96
D137V4, multiclass
       clus
vv      PUM2 MUTATED PUM2 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V5, binary
                cls
clus              0  1
  PUM2 MUTATED    2  5
  PUM2 WILD-TYPE 33 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      2    5
  PUM2 WILD-TYPE   33   84
   clus
vv  PUM2 MUTATED PUM2 WILD-TYPE
  0            2             33
  1            5             84
[1] 2 2
[1] FALSE
D137V6, binary
                cls
clus              0  1
  PUM2 MUTATED    3  0
  PUM2 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      3    0
  PUM2 WILD-TYPE   54    3
   clus
vv  PUM2 MUTATED PUM2 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D137V7, binary
                cls
clus              0  1
  PUM2 MUTATED    2  5
  PUM2 WILD-TYPE 49 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      2    5
  PUM2 WILD-TYPE   49   70
        clus
vv       PUM2 MUTATED PUM2 WILD-TYPE
  FEMALE            2             49
  MALE              5             70
[1] 2 2
[1] FALSE
D137V8, binary
                cls
clus              0  1
  PUM2 MUTATED    4  3
  PUM2 WILD-TYPE 84 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      4    3
  PUM2 WILD-TYPE   84   27
     clus
vv    PUM2 MUTATED PUM2 WILD-TYPE
  NO             4             84
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PUM2 MUTATED                                     5
  PUM2 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PUM2 MUTATED                                       2
  PUM2 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PUM2 MUTATED                                                  0
  PUM2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PUM2 MUTATED                                     0
  PUM2 WILD-TYPE                                   1
D137V9, multiclass
                                                  clus
vv                                                 PUM2 MUTATED PUM2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V10, continuous
D137V11, continuous
[1] "Remove cluster labels:" "PUM2 MUTATED"          
clus
  PUM2 MUTATED PUM2 WILD-TYPE 
             2             31 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PUM2 WILD-TYPE" "PUM2 WILD-TYPE" "PUM2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PUM2 MUTATED    6  0  0  1
  PUM2 WILD-TYPE 74 35  4  1
D137V12, multiclass
    clus
vv   PUM2 MUTATED PUM2 WILD-TYPE
  R0            6             74
  R1            0             35
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PUM2 MUTATED       1                         0     6
  PUM2 WILD-TYPE     5                         5   108
D137V14, multiclass
                           clus
vv                          PUM2 MUTATED PUM2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V15, binary
                cls
clus              0  1
  PUM2 MUTATED    1  4
  PUM2 WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  PUM2 MUTATED      1    4
  PUM2 WILD-TYPE    4   87
                        clus
vv                       PUM2 MUTATED PUM2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(138) Variable = IL1R2 MUTATION ANALYSIS
D138V1, survival
                 sevent
clus2              0  1
  IL1R2 MUTATED    3  3
  IL1R2 WILD-TYPE 60 59
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              6             119 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              3              59 
$`IL1R2 MUTATED`
TCGA-3A-A9IH TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-IB-AAUU TCGA-US-A77G TCGA-YH-A8SY 
       33.57         5.03        19.82         8.05         0.39        12.76 

$`IL1R2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        66.28        15.35 

  IL1R2 MUTATED IL1R2 WILD-TYPE 
           0.39            0.23 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
          33.57           90.12 
  IL1R2 MUTATED IL1R2 WILD-TYPE 
         10.405          15.320 
[1] "0.4 - 33.6 (10.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D138V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IL1R2 MUTATED         0        1        0         0         4         1
  IL1R2 WILD-TYPE       1        2       12        19        78         3
                 vv
clus              STAGE IV
  IL1R2 MUTATED          0
  IL1R2 WILD-TYPE        3
D138V3, multiclass
           clus
vv          IL1R2 MUTATED IL1R2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  IL1R2 MUTATED    1  0     5
  IL1R2 WILD-TYPE  4 17    97
D138V4, multiclass
       clus
vv      IL1R2 MUTATED IL1R2 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V5, binary
                 cls
clus               0  1
  IL1R2 MUTATED    1  5
  IL1R2 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      1    5
  IL1R2 WILD-TYPE   34   84
   clus
vv  IL1R2 MUTATED IL1R2 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D138V6, binary
                 cls
clus               0  1
  IL1R2 MUTATED    2  0
  IL1R2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      2    0
  IL1R2 WILD-TYPE   55    3
   clus
vv  IL1R2 MUTATED IL1R2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D138V7, binary
                 cls
clus               0  1
  IL1R2 MUTATED    4  2
  IL1R2 WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      4    2
  IL1R2 WILD-TYPE   47   73
        clus
vv       IL1R2 MUTATED IL1R2 WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D138V8, binary
                 cls
clus               0  1
  IL1R2 MUTATED    5  1
  IL1R2 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      5    1
  IL1R2 WILD-TYPE   83   29
     clus
vv    IL1R2 MUTATED IL1R2 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IL1R2 MUTATED                                     5
  IL1R2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IL1R2 MUTATED                                       0
  IL1R2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IL1R2 MUTATED                                                  0
  IL1R2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  IL1R2 MUTATED                                     0
  IL1R2 WILD-TYPE                                   1
D138V9, multiclass
                                                  clus
vv                                                 IL1R2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 IL1R2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V10, continuous
[1] "Remove cluster labels:" "IL1R2 MUTATED"         
clus
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-YY-A8LH 
"IL1R2 WILD-TYPE" 
D138V11, continuous
[1] "Remove cluster labels:" "IL1R2 MUTATED"         
clus
  IL1R2 MUTATED IL1R2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" "IL1R2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  IL1R2 MUTATED    4  1  0  0
  IL1R2 WILD-TYPE 76 34  4  2
D138V12, multiclass
    clus
vv   IL1R2 MUTATED IL1R2 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL1R2 MUTATED       0                         0     6
  IL1R2 WILD-TYPE     6                         5   108
D138V14, multiclass
                           clus
vv                          IL1R2 MUTATED IL1R2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V15, binary
                 cls
clus               0  1
  IL1R2 MUTATED    0  6
  IL1R2 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1R2 MUTATED      0    6
  IL1R2 WILD-TYPE    5   85
                        clus
vv                       IL1R2 MUTATED IL1R2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(139) Variable = SLC22A9 MUTATION ANALYSIS
D139V1, survival
                   sevent
clus2                0  1
  SLC22A9 MUTATED    7  1
  SLC22A9 WILD-TYPE 56 61
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               117 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                1                61 
$`SLC22A9 MUTATED`
TCGA-3A-A9I5 TCGA-F2-A44G TCGA-3A-A9IS TCGA-IB-AAUP TCGA-IB-AAUU TCGA-Q3-A5QY 
       58.98         7.66        32.81        14.17         8.05        13.68 
TCGA-XN-A8T3 TCGA-XN-A8T5 
       31.27        23.67 

$`SLC22A9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        60.95        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YB-A89D 
        0.39        18.67        13.81        12.99        12.03        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
             7.66              0.23 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            58.98             90.12 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            18.92             15.22 
[1] "7.7 - 59.0 (18.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "5.1"
D139V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC22A9 MUTATED         0        0        3         0         4         0
  SLC22A9 WILD-TYPE       1        3        9        19        78         4
                   vv
clus                STAGE IV
  SLC22A9 MUTATED          0
  SLC22A9 WILD-TYPE        3
D139V3, multiclass
           clus
vv          SLC22A9 MUTATED SLC22A9 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                3                 9
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC22A9 MUTATED    0  3     4
  SLC22A9 WILD-TYPE  5 14    98
D139V4, multiclass
       clus
vv      SLC22A9 MUTATED SLC22A9 WILD-TYPE
  T1                  0                 5
  T2                  3                14
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V5, binary
                   cls
clus                 0  1
  SLC22A9 MUTATED    4  4
  SLC22A9 WILD-TYPE 31 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      4    4
  SLC22A9 WILD-TYPE   31   85
   clus
vv  SLC22A9 MUTATED SLC22A9 WILD-TYPE
  0               4                31
  1               4                85
[1] 2 2
[1] FALSE
D139V6, binary
                   cls
clus                 0  1
  SLC22A9 MUTATED    5  0
  SLC22A9 WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      5    0
  SLC22A9 WILD-TYPE   52    3
   clus
vv  SLC22A9 MUTATED SLC22A9 WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D139V7, binary
                   cls
clus                 0  1
  SLC22A9 MUTATED    2  6
  SLC22A9 WILD-TYPE 49 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      2    6
  SLC22A9 WILD-TYPE   49   69
        clus
vv       SLC22A9 MUTATED SLC22A9 WILD-TYPE
  FEMALE               2                49
  MALE                 6                69
[1] 2 2
[1] FALSE
D139V8, binary
                   cls
clus                 0  1
  SLC22A9 MUTATED    4  4
  SLC22A9 WILD-TYPE 84 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      4    4
  SLC22A9 WILD-TYPE   84   26
     clus
vv    SLC22A9 MUTATED SLC22A9 WILD-TYPE
  NO                4                84
  YES               4                26
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC22A9 MUTATED                                     6
  SLC22A9 WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC22A9 MUTATED                                       2
  SLC22A9 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC22A9 MUTATED                                                  0
  SLC22A9 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC22A9 MUTATED                                     0
  SLC22A9 WILD-TYPE                                   1
D139V9, multiclass
                                                  clus
vv                                                 SLC22A9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC22A9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V10, continuous
[1] "Remove cluster labels:" "SLC22A9 MUTATED"       
clus
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC22A9 WILD-TYPE" 
D139V11, continuous
[1] "Remove cluster labels:" "SLC22A9 MUTATED"       
clus
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-YY-A8LH 
"SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" "SLC22A9 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC22A9 MUTATED    4  4  0  0
  SLC22A9 WILD-TYPE 76 31  4  2
D139V12, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  R0               4                76
  R1               4                31
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC22A9 MUTATED       0                         0     8
  SLC22A9 WILD-TYPE     6                         5   106
D139V14, multiclass
                           clus
vv                          SLC22A9 MUTATED SLC22A9 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   8               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V15, binary
                   cls
clus                 0  1
  SLC22A9 MUTATED    2  6
  SLC22A9 WILD-TYPE  3 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      2    6
  SLC22A9 WILD-TYPE    3   85
                        clus
vv                       SLC22A9 MUTATED SLC22A9 WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(140) Variable = MAGEA10 MUTATION ANALYSIS
D140V1, survival
                   sevent
clus2                0  1
  MAGEA10 MUTATED    4  2
  MAGEA10 WILD-TYPE 59 60
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                6               119 
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                2                60 
$`MAGEA10 MUTATED`
TCGA-2J-AABR TCGA-2L-AAQJ TCGA-3A-A9I7 TCGA-H8-A6C1 TCGA-IB-A6UG TCGA-Q3-AA2A 
       14.40        12.95        43.50        22.06         1.35         3.12 

$`MAGEA10 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
             1.35              0.23 
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
            43.50             90.12 
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
           13.675            15.320 
[1] "1.4 - 43.5 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D140V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAGEA10 MUTATED         0        0        1         2         2         1
  MAGEA10 WILD-TYPE       1        3       11        17        80         3
                   vv
clus                STAGE IV
  MAGEA10 MUTATED          0
  MAGEA10 WILD-TYPE        3
D140V3, multiclass
           clus
vv          MAGEA10 MUTATED MAGEA10 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               2                17
  STAGE IIB               2                80
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  MAGEA10 MUTATED    0  0     6
  MAGEA10 WILD-TYPE  5 17    96
D140V4, multiclass
       clus
vv      MAGEA10 MUTATED MAGEA10 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V5, binary
                   cls
clus                 0  1
  MAGEA10 MUTATED    3  3
  MAGEA10 WILD-TYPE 32 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAGEA10 MUTATED      3    3
  MAGEA10 WILD-TYPE   32   86
   clus
vv  MAGEA10 MUTATED MAGEA10 WILD-TYPE
  0               3                32
  1               3                86
[1] 2 2
[1] FALSE
D140V6, binary
                   cls
clus                 0  1
  MAGEA10 MUTATED    2  0
  MAGEA10 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAGEA10 MUTATED      2    0
  MAGEA10 WILD-TYPE   55    3
   clus
vv  MAGEA10 MUTATED MAGEA10 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D140V7, binary
                   cls
clus                 0  1
  MAGEA10 MUTATED    3  3
  MAGEA10 WILD-TYPE 48 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAGEA10 MUTATED      3    3
  MAGEA10 WILD-TYPE   48   72
        clus
vv       MAGEA10 MUTATED MAGEA10 WILD-TYPE
  FEMALE               3                48
  MALE                 3                72
[1] 2 2
[1] FALSE
D140V8, binary
                   cls
clus                 0  1
  MAGEA10 MUTATED    5  1
  MAGEA10 WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAGEA10 MUTATED      5    1
  MAGEA10 WILD-TYPE   83   29
     clus
vv    MAGEA10 MUTATED MAGEA10 WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAGEA10 MUTATED                                     5
  MAGEA10 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAGEA10 MUTATED                                       1
  MAGEA10 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAGEA10 MUTATED                                                  0
  MAGEA10 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAGEA10 MUTATED                                     0
  MAGEA10 WILD-TYPE                                   1
D140V9, multiclass
                                                  clus
vv                                                 MAGEA10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 MAGEA10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V10, continuous
[1] "Remove cluster labels:" "MAGEA10 MUTATED"       
clus
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-YY-A8LH 
"MAGEA10 WILD-TYPE" 
D140V11, continuous
[1] "Remove cluster labels:" "MAGEA10 MUTATED"       
clus
  MAGEA10 MUTATED MAGEA10 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" "MAGEA10 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  MAGEA10 MUTATED    3  2  0  1
  MAGEA10 WILD-TYPE 77 33  4  1
D140V12, multiclass
    clus
vv   MAGEA10 MUTATED MAGEA10 WILD-TYPE
  R0               3                77
  R1               2                33
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAGEA10 MUTATED       0                         1     5
  MAGEA10 WILD-TYPE     6                         4   109
D140V14, multiclass
                           clus
vv                          MAGEA10 MUTATED MAGEA10 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V15, binary
                   cls
clus                 0  1
  MAGEA10 MUTATED    0  4
  MAGEA10 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAGEA10 MUTATED      0    4
  MAGEA10 WILD-TYPE    5   87
                        clus
vv                       MAGEA10 MUTATED MAGEA10 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(141) Variable = PTPLAD2 MUTATION ANALYSIS
D141V1, survival
                   sevent
clus2                0  1
  PTPLAD2 MUTATED    2  4
  PTPLAD2 WILD-TYPE 61 58
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
                6               119 
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
                4                58 
$`PTPLAD2 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9I9 TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-IB-AAUP 
        1.08        20.84        12.53        15.55        19.82        14.17 

$`PTPLAD2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
        7.50        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
             1.08              0.23 
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
            20.84             90.12 
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
            14.86             15.22 
[1] "1.1 - 20.8 (14.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D141V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PTPLAD2 MUTATED         0        0        0         3         3         0
  PTPLAD2 WILD-TYPE       1        3       12        16        79         4
                   vv
clus                STAGE IV
  PTPLAD2 MUTATED          0
  PTPLAD2 WILD-TYPE        3
D141V3, multiclass
           clus
vv          PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               3                16
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  PTPLAD2 MUTATED    0  0     6
  PTPLAD2 WILD-TYPE  5 17    96
D141V4, multiclass
       clus
vv      PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V5, binary
                   cls
clus                 0  1
  PTPLAD2 MUTATED    3  3
  PTPLAD2 WILD-TYPE 32 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTPLAD2 MUTATED      3    3
  PTPLAD2 WILD-TYPE   32   86
   clus
vv  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  0               3                32
  1               3                86
[1] 2 2
[1] FALSE
D141V6, binary
                   cls
clus                 0  1
  PTPLAD2 MUTATED    2  0
  PTPLAD2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTPLAD2 MUTATED      2    0
  PTPLAD2 WILD-TYPE   55    3
   clus
vv  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D141V7, binary
                   cls
clus                 0  1
  PTPLAD2 MUTATED    3  3
  PTPLAD2 WILD-TYPE 48 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTPLAD2 MUTATED      3    3
  PTPLAD2 WILD-TYPE   48   72
        clus
vv       PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  FEMALE               3                48
  MALE                 3                72
[1] 2 2
[1] FALSE
D141V8, binary
                   cls
clus                 0  1
  PTPLAD2 MUTATED    4  1
  PTPLAD2 WILD-TYPE 84 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTPLAD2 MUTATED      4    1
  PTPLAD2 WILD-TYPE   84   29
     clus
vv    PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  NO                4                84
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPLAD2 MUTATED                                     5
  PTPLAD2 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPLAD2 MUTATED                                       1
  PTPLAD2 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPLAD2 MUTATED                                                  0
  PTPLAD2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PTPLAD2 MUTATED                                     0
  PTPLAD2 WILD-TYPE                                   1
D141V9, multiclass
                                                  clus
vv                                                 PTPLAD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PTPLAD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V10, continuous
D141V11, continuous
[1] "Remove cluster labels:" "PTPLAD2 MUTATED"       
clus
  PTPLAD2 MUTATED PTPLAD2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" "PTPLAD2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  PTPLAD2 MUTATED    4  2  0  0
  PTPLAD2 WILD-TYPE 76 33  4  2
D141V12, multiclass
    clus
vv   PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  R0               4                76
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPLAD2 MUTATED       1                         0     5
  PTPLAD2 WILD-TYPE     5                         5   109
D141V14, multiclass
                           clus
vv                          PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V15, binary
                   cls
clus                 0  1
  PTPLAD2 MUTATED    0  6
  PTPLAD2 WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTPLAD2 MUTATED      0    6
  PTPLAD2 WILD-TYPE    5   85
                        clus
vv                       PTPLAD2 MUTATED PTPLAD2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(142) Variable = HERC5 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2              0  1
  HERC5 MUTATED    5  1
  HERC5 WILD-TYPE 58 61
  HERC5 MUTATED HERC5 WILD-TYPE 
              6             119 
  HERC5 MUTATED HERC5 WILD-TYPE 
              1              61 
$`HERC5 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IX TCGA-HV-AA8V TCGA-IB-7651 TCGA-XD-AAUG TCGA-XD-AAUH 
        1.08        34.09        30.25        19.82        13.81        12.99 

$`HERC5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        32.15        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUI TCGA-XN-A8T3 
       39.98        16.80         0.39        18.67        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  HERC5 MUTATED HERC5 WILD-TYPE 
           1.08            0.23 
  HERC5 MUTATED HERC5 WILD-TYPE 
          34.09           90.12 
  HERC5 MUTATED HERC5 WILD-TYPE 
         16.815          15.220 
[1] "1.1 - 34.1 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.3"
D142V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HERC5 MUTATED         0        1        0         0         4         0
  HERC5 WILD-TYPE       1        2       12        19        78         4
                 vv
clus              STAGE IV
  HERC5 MUTATED          1
  HERC5 WILD-TYPE        2
D142V3, multiclass
           clus
vv          HERC5 MUTATED HERC5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HERC5 MUTATED    1  0     5
  HERC5 WILD-TYPE  4 17    97
D142V4, multiclass
       clus
vv      HERC5 MUTATED HERC5 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V5, binary
                 cls
clus               0  1
  HERC5 MUTATED    1  5
  HERC5 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      1    5
  HERC5 WILD-TYPE   34   84
   clus
vv  HERC5 MUTATED HERC5 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D142V6, binary
                 cls
clus               0  1
  HERC5 MUTATED    2  1
  HERC5 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      2    1
  HERC5 WILD-TYPE   55    2
   clus
vv  HERC5 MUTATED HERC5 WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D142V7, binary
                 cls
clus               0  1
  HERC5 MUTATED    4  2
  HERC5 WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      4    2
  HERC5 WILD-TYPE   47   73
        clus
vv       HERC5 MUTATED HERC5 WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D142V8, binary
                 cls
clus               0  1
  HERC5 MUTATED    3  2
  HERC5 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      3    2
  HERC5 WILD-TYPE   85   28
     clus
vv    HERC5 MUTATED HERC5 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HERC5 MUTATED                                     5
  HERC5 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HERC5 MUTATED                                       1
  HERC5 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HERC5 MUTATED                                                  0
  HERC5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HERC5 MUTATED                                     0
  HERC5 WILD-TYPE                                   1
D142V9, multiclass
                                                  clus
vv                                                 HERC5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HERC5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V10, continuous
D142V11, continuous
                 vv
clus              R0 R1 R2 RX
  HERC5 MUTATED    4  0  2  0
  HERC5 WILD-TYPE 76 35  2  2
D142V12, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             2               2
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HERC5 MUTATED       1                         0     5
  HERC5 WILD-TYPE     5                         5   109
D142V14, multiclass
                           clus
vv                          HERC5 MUTATED HERC5 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V15, binary
                 cls
clus               0  1
  HERC5 MUTATED    0  5
  HERC5 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      0    5
  HERC5 WILD-TYPE    5   86
                        clus
vv                       HERC5 MUTATED HERC5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(143) Variable = WDR67 MUTATION ANALYSIS
D143V1, survival
                 sevent
clus2              0  1
  WDR67 MUTATED    2  3
  WDR67 WILD-TYPE 61 59
  WDR67 MUTATED WDR67 WILD-TYPE 
              5             120 
  WDR67 MUTATED WDR67 WILD-TYPE 
              3              59 
$`WDR67 MUTATED`
TCGA-IB-A5SS TCGA-3A-A9IB TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A6UF 
       15.12         7.36        10.85        19.82        21.90 

$`WDR67 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  WDR67 MUTATED WDR67 WILD-TYPE 
           7.36            0.23 
  WDR67 MUTATED WDR67 WILD-TYPE 
          21.90           90.12 
  WDR67 MUTATED WDR67 WILD-TYPE 
          15.12           15.27 
[1] "7.4 - 21.9 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D143V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WDR67 MUTATED         0        0        0         0         5         0
  WDR67 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  WDR67 MUTATED          0
  WDR67 WILD-TYPE        3
D143V3, multiclass
           clus
vv          WDR67 MUTATED WDR67 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  WDR67 MUTATED    0  0     5
  WDR67 WILD-TYPE  5 17    97
D143V4, multiclass
       clus
vv      WDR67 MUTATED WDR67 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V5, binary
                 cls
clus               0  1
  WDR67 MUTATED    0  5
  WDR67 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR67 MUTATED      0    5
  WDR67 WILD-TYPE   35   84
   clus
vv  WDR67 MUTATED WDR67 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D143V6, binary
                 cls
clus               0  1
  WDR67 MUTATED    3  0
  WDR67 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR67 MUTATED      3    0
  WDR67 WILD-TYPE   54    3
   clus
vv  WDR67 MUTATED WDR67 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D143V7, binary
                 cls
clus               0  1
  WDR67 MUTATED    3  2
  WDR67 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR67 MUTATED      3    2
  WDR67 WILD-TYPE   48   73
        clus
vv       WDR67 MUTATED WDR67 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D143V8, binary
                 cls
clus               0  1
  WDR67 MUTATED    5  0
  WDR67 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR67 MUTATED      5    0
  WDR67 WILD-TYPE   83   30
     clus
vv    WDR67 MUTATED WDR67 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDR67 MUTATED                                     4
  WDR67 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDR67 MUTATED                                       1
  WDR67 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDR67 MUTATED                                                  0
  WDR67 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  WDR67 MUTATED                                     0
  WDR67 WILD-TYPE                                   1
D143V9, multiclass
                                                  clus
vv                                                 WDR67 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 WDR67 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V10, continuous
D143V11, continuous
                 vv
clus              R0 R1 R2 RX
  WDR67 MUTATED    4  1  0  0
  WDR67 WILD-TYPE 76 34  4  2
D143V12, multiclass
    clus
vv   WDR67 MUTATED WDR67 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR67 MUTATED       0                         0     5
  WDR67 WILD-TYPE     6                         5   109
D143V14, multiclass
                           clus
vv                          WDR67 MUTATED WDR67 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V15, binary
                 cls
clus               0  1
  WDR67 MUTATED    0  5
  WDR67 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR67 MUTATED      0    5
  WDR67 WILD-TYPE    5   86
                        clus
vv                       WDR67 MUTATED WDR67 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(144) Variable = TMEM40 MUTATION ANALYSIS
D144V1, survival
                  sevent
clus2               0  1
  TMEM40 MUTATED    6  0
  TMEM40 WILD-TYPE 57 62
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               6              119 
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               0               62 
$`TMEM40 MUTATED`
TCGA-2J-AABP TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HZ-A77P TCGA-IB-A6UF TCGA-RB-AA9M 
       15.22        22.06         8.28        10.85        21.90         9.40 

$`TMEM40 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TMEM40 MUTATED TMEM40 WILD-TYPE 
            8.28             0.23 
  TMEM40 MUTATED TMEM40 WILD-TYPE 
           22.06            90.12 
  TMEM40 MUTATED TMEM40 WILD-TYPE 
          13.035           15.320 
[1] "8.3 - 22.1 (13.0)" "0.2 - 90.1 (15.3)"
[1] "hr="     "2.6e+07"
D144V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM40 MUTATED         0        0        0         2         4         0
  TMEM40 WILD-TYPE       1        3       12        17        78         4
                  vv
clus               STAGE IV
  TMEM40 MUTATED          0
  TMEM40 WILD-TYPE        3
D144V3, multiclass
           clus
vv          TMEM40 MUTATED TMEM40 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TMEM40 MUTATED    1  0     5
  TMEM40 WILD-TYPE  4 17    97
D144V4, multiclass
       clus
vv      TMEM40 MUTATED TMEM40 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V5, binary
                  cls
clus                0  1
  TMEM40 MUTATED    2  4
  TMEM40 WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM40 MUTATED      2    4
  TMEM40 WILD-TYPE   33   85
   clus
vv  TMEM40 MUTATED TMEM40 WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D144V6, binary
                  cls
clus                0  1
  TMEM40 MUTATED    2  0
  TMEM40 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM40 MUTATED      2    0
  TMEM40 WILD-TYPE   55    3
   clus
vv  TMEM40 MUTATED TMEM40 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D144V7, binary
                  cls
clus                0  1
  TMEM40 MUTATED    1  5
  TMEM40 WILD-TYPE 50 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM40 MUTATED      1    5
  TMEM40 WILD-TYPE   50   70
        clus
vv       TMEM40 MUTATED TMEM40 WILD-TYPE
  FEMALE              1               50
  MALE                5               70
[1] 2 2
[1] FALSE
D144V8, binary
                  cls
clus                0  1
  TMEM40 MUTATED    5  1
  TMEM40 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM40 MUTATED      5    1
  TMEM40 WILD-TYPE   83   29
     clus
vv    TMEM40 MUTATED TMEM40 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM40 MUTATED                                     3
  TMEM40 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM40 MUTATED                                       2
  TMEM40 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM40 MUTATED                                                  0
  TMEM40 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM40 MUTATED                                     1
  TMEM40 WILD-TYPE                                   0
D144V9, multiclass
                                                  clus
vv                                                 TMEM40 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 TMEM40 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V10, continuous
[1] "Remove cluster labels:" "TMEM40 MUTATED"        
clus
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UG 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-YY-A8LH 
"TMEM40 WILD-TYPE" 
D144V11, continuous
[1] "Remove cluster labels:" "TMEM40 MUTATED"        
clus
  TMEM40 MUTATED TMEM40 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" "TMEM40 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TMEM40 MUTATED    4  1  1  0
  TMEM40 WILD-TYPE 76 34  3  2
D144V12, multiclass
    clus
vv   TMEM40 MUTATED TMEM40 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM40 MUTATED       1                         0     5
  TMEM40 WILD-TYPE     5                         5   109
D144V14, multiclass
                           clus
vv                          TMEM40 MUTATED TMEM40 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V15, binary
                  cls
clus                0  1
  TMEM40 MUTATED    0  4
  TMEM40 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM40 MUTATED      0    4
  TMEM40 WILD-TYPE    5   87
                        clus
vv                       TMEM40 MUTATED TMEM40 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(145) Variable = UNC5A MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2              0  1
  UNC5A MUTATED    2  6
  UNC5A WILD-TYPE 61 56
  UNC5A MUTATED UNC5A WILD-TYPE 
              8             117 
  UNC5A MUTATED UNC5A WILD-TYPE 
              6              56 
$`UNC5A MUTATED`
TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FZ-5924 TCGA-2L-AAQJ TCGA-F2-A7TX TCGA-IB-7651 
       60.95         7.66        15.78        12.95         3.12        19.82 
TCGA-IB-A5SQ TCGA-IB-A6UF 
        7.20        21.90 

$`UNC5A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-HZ-A77Q 
       14.40        10.49        58.98        90.12         8.02         1.08 
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.12        12.92        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49         3.39         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM 
       24.43        75.12        71.74        19.46        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG 
       41.33        15.19        12.00        15.85        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  UNC5A MUTATED UNC5A WILD-TYPE 
           3.12            0.23 
  UNC5A MUTATED UNC5A WILD-TYPE 
          60.95           90.12 
  UNC5A MUTATED UNC5A WILD-TYPE 
         14.365          15.220 
[1] "3.1 - 61.0 (14.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D145V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UNC5A MUTATED         0        0        2         1         4         1
  UNC5A WILD-TYPE       1        3       10        18        78         3
                 vv
clus              STAGE IV
  UNC5A MUTATED          0
  UNC5A WILD-TYPE        3
D145V3, multiclass
           clus
vv          UNC5A MUTATED UNC5A WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  UNC5A MUTATED    0  2     6
  UNC5A WILD-TYPE  5 15    96
D145V4, multiclass
       clus
vv      UNC5A MUTATED UNC5A WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V5, binary
                 cls
clus               0  1
  UNC5A MUTATED    3  5
  UNC5A WILD-TYPE 32 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      3    5
  UNC5A WILD-TYPE   32   84
   clus
vv  UNC5A MUTATED UNC5A WILD-TYPE
  0             3              32
  1             5              84
[1] 2 2
[1] FALSE
D145V6, binary
                 cls
clus               0  1
  UNC5A MUTATED    6  0
  UNC5A WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      6    0
  UNC5A WILD-TYPE   51    3
   clus
vv  UNC5A MUTATED UNC5A WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D145V7, binary
                 cls
clus               0  1
  UNC5A MUTATED    4  4
  UNC5A WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      4    4
  UNC5A WILD-TYPE   47   71
        clus
vv       UNC5A MUTATED UNC5A WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D145V8, binary
                 cls
clus               0  1
  UNC5A MUTATED    7  1
  UNC5A WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      7    1
  UNC5A WILD-TYPE   81   29
     clus
vv    UNC5A MUTATED UNC5A WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UNC5A MUTATED                                     7
  UNC5A WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UNC5A MUTATED                                       1
  UNC5A WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UNC5A MUTATED                                                  0
  UNC5A WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  UNC5A MUTATED                                     0
  UNC5A WILD-TYPE                                   1
D145V9, multiclass
                                                  clus
vv                                                 UNC5A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 UNC5A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V10, continuous
D145V11, continuous
                 vv
clus              R0 R1 R2 RX
  UNC5A MUTATED    4  4  0  0
  UNC5A WILD-TYPE 76 31  4  2
D145V12, multiclass
    clus
vv   UNC5A MUTATED UNC5A WILD-TYPE
  R0             4              76
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC5A MUTATED       0                         0     8
  UNC5A WILD-TYPE     6                         5   106
D145V14, multiclass
                           clus
vv                          UNC5A MUTATED UNC5A WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V15, binary
                 cls
clus               0  1
  UNC5A MUTATED    0  6
  UNC5A WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      0    6
  UNC5A WILD-TYPE    5   85
                        clus
vv                       UNC5A MUTATED UNC5A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(146) Variable = AARS2 MUTATION ANALYSIS
D146V1, survival
                 sevent
clus2              0  1
  AARS2 MUTATED    3  4
  AARS2 WILD-TYPE 60 58
  AARS2 MUTATED AARS2 WILD-TYPE 
              7             118 
  AARS2 MUTATED AARS2 WILD-TYPE 
              4              58 
$`AARS2 MUTATED`
TCGA-FB-AAQ1 TCGA-H8-A6C1 TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-AAUN 
        4.04        22.06        17.00        19.82        15.19         4.73 
TCGA-US-A776 
       39.98 

$`AARS2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         9.40         0.30        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  AARS2 MUTATED AARS2 WILD-TYPE 
           4.04            0.23 
  AARS2 MUTATED AARS2 WILD-TYPE 
          39.98           90.12 
  AARS2 MUTATED AARS2 WILD-TYPE 
          17.00           15.17 
[1] "4.0 - 40.0 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D146V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AARS2 MUTATED         0        0        1         2         3         1
  AARS2 WILD-TYPE       1        3       11        17        79         3
                 vv
clus              STAGE IV
  AARS2 MUTATED          0
  AARS2 WILD-TYPE        3
D146V3, multiclass
           clus
vv          AARS2 MUTATED AARS2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             3              79
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AARS2 MUTATED    0  1     6
  AARS2 WILD-TYPE  5 16    96
D146V4, multiclass
       clus
vv      AARS2 MUTATED AARS2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V5, binary
                 cls
clus               0  1
  AARS2 MUTATED    3  4
  AARS2 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      3    4
  AARS2 WILD-TYPE   32   85
   clus
vv  AARS2 MUTATED AARS2 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D146V6, binary
                 cls
clus               0  1
  AARS2 MUTATED    3  0
  AARS2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      3    0
  AARS2 WILD-TYPE   54    3
   clus
vv  AARS2 MUTATED AARS2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D146V7, binary
                 cls
clus               0  1
  AARS2 MUTATED    4  3
  AARS2 WILD-TYPE 47 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      4    3
  AARS2 WILD-TYPE   47   72
        clus
vv       AARS2 MUTATED AARS2 WILD-TYPE
  FEMALE             4              47
  MALE               3              72
[1] 2 2
[1] FALSE
D146V8, binary
                 cls
clus               0  1
  AARS2 MUTATED    6  1
  AARS2 WILD-TYPE 82 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      6    1
  AARS2 WILD-TYPE   82   29
     clus
vv    AARS2 MUTATED AARS2 WILD-TYPE
  NO              6              82
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AARS2 MUTATED                                     5
  AARS2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AARS2 MUTATED                                       1
  AARS2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AARS2 MUTATED                                                  1
  AARS2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AARS2 MUTATED                                     0
  AARS2 WILD-TYPE                                   1
D146V9, multiclass
                                                  clus
vv                                                 AARS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 AARS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V10, continuous
D146V11, continuous
                 vv
clus              R0 R1 R2 RX
  AARS2 MUTATED    4  3  0  0
  AARS2 WILD-TYPE 76 32  4  2
D146V12, multiclass
    clus
vv   AARS2 MUTATED AARS2 WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AARS2 MUTATED       0                         0     7
  AARS2 WILD-TYPE     6                         5   107
D146V14, multiclass
                           clus
vv                          AARS2 MUTATED AARS2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V15, binary
                 cls
clus               0  1
  AARS2 MUTATED    1  6
  AARS2 WILD-TYPE  4 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      1    6
  AARS2 WILD-TYPE    4   85
                        clus
vv                       AARS2 MUTATED AARS2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(147) Variable = PDILT MUTATION ANALYSIS
D147V1, survival
                 sevent
clus2              0  1
  PDILT MUTATED    5  4
  PDILT WILD-TYPE 58 58
  PDILT MUTATED PDILT WILD-TYPE 
              9             116 
  PDILT MUTATED PDILT WILD-TYPE 
              4              58 
$`PDILT MUTATED`
TCGA-LB-A7SX TCGA-2J-AABK TCGA-3A-A9IH TCGA-FB-AAQ3 TCGA-HZ-7925 TCGA-IB-7651 
       12.92        15.91        33.57         1.02        20.19        19.82 
TCGA-Q3-AA2A TCGA-XN-A8T3 TCGA-YH-A8SY 
        3.12        31.27        12.76 

$`PDILT WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         5.03        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 
        8.28        32.15        30.25        17.49        31.86        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PDILT MUTATED PDILT WILD-TYPE 
           1.02            0.23 
  PDILT MUTATED PDILT WILD-TYPE 
          33.57           90.12 
  PDILT MUTATED PDILT WILD-TYPE 
         15.910          15.205 
[1] "1.0 - 33.6 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D147V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PDILT MUTATED         0        1        2         0         5         1
  PDILT WILD-TYPE       1        2       10        19        77         3
                 vv
clus              STAGE IV
  PDILT MUTATED          0
  PDILT WILD-TYPE        3
D147V3, multiclass
           clus
vv          PDILT MUTATED PDILT WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PDILT MUTATED    1  1     7
  PDILT WILD-TYPE  4 16    95
D147V4, multiclass
       clus
vv      PDILT MUTATED PDILT WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V5, binary
                 cls
clus               0  1
  PDILT MUTATED    2  7
  PDILT WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      2    7
  PDILT WILD-TYPE   33   82
   clus
vv  PDILT MUTATED PDILT WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D147V6, binary
                 cls
clus               0  1
  PDILT MUTATED    3  0
  PDILT WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      3    0
  PDILT WILD-TYPE   54    3
   clus
vv  PDILT MUTATED PDILT WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D147V7, binary
                 cls
clus               0  1
  PDILT MUTATED    6  3
  PDILT WILD-TYPE 45 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      6    3
  PDILT WILD-TYPE   45   72
        clus
vv       PDILT MUTATED PDILT WILD-TYPE
  FEMALE             6              45
  MALE               3              72
[1] 2 2
[1] FALSE
D147V8, binary
                 cls
clus               0  1
  PDILT MUTATED    6  3
  PDILT WILD-TYPE 82 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      6    3
  PDILT WILD-TYPE   82   27
     clus
vv    PDILT MUTATED PDILT WILD-TYPE
  NO              6              82
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDILT MUTATED                                     8
  PDILT WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDILT MUTATED                                       0
  PDILT WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDILT MUTATED                                                  0
  PDILT WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PDILT MUTATED                                     0
  PDILT WILD-TYPE                                   1
D147V9, multiclass
                                                  clus
vv                                                 PDILT MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PDILT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V10, continuous
[1] "Remove cluster labels:" "PDILT MUTATED"         
clus
  PDILT MUTATED PDILT WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-YY-A8LH 
"PDILT WILD-TYPE" 
D147V11, continuous
[1] "Remove cluster labels:" "PDILT MUTATED"         
clus
  PDILT MUTATED PDILT WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PDILT MUTATED    4  3  0  1
  PDILT WILD-TYPE 76 32  4  1
D147V12, multiclass
    clus
vv   PDILT MUTATED PDILT WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDILT MUTATED       0                         1     8
  PDILT WILD-TYPE     6                         4   106
D147V14, multiclass
                           clus
vv                          PDILT MUTATED PDILT WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V15, binary
                 cls
clus               0  1
  PDILT MUTATED    1  7
  PDILT WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      1    7
  PDILT WILD-TYPE    4   84
                        clus
vv                       PDILT MUTATED PDILT WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(148) Variable = PTPN21 MUTATION ANALYSIS
D148V1, survival
                  sevent
clus2               0  1
  PTPN21 MUTATED    4  4
  PTPN21 WILD-TYPE 59 58
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               8              117 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               4               58 
$`PTPN21 MUTATED`
TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABP TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-A6UG 
        2.63        20.61        15.22        19.82        19.82         1.35 
TCGA-LB-A8F3 TCGA-US-A77J 
       12.46        18.67 

$`PTPN21 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABA 
       14.14        16.37         2.17        23.97         9.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PTPN21 MUTATED PTPN21 WILD-TYPE 
            1.35             0.23 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
           20.61            90.12 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
          16.945           15.190 
[1] "1.4 - 20.6 (16.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D148V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PTPN21 MUTATED         0        0        0         1         6         0
  PTPN21 WILD-TYPE       1        3       12        18        76         4
                  vv
clus               STAGE IV
  PTPN21 MUTATED          1
  PTPN21 WILD-TYPE        2
D148V3, multiclass
           clus
vv          PTPN21 MUTATED PTPN21 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PTPN21 MUTATED    0  0     8
  PTPN21 WILD-TYPE  5 17    94
D148V4, multiclass
       clus
vv      PTPN21 MUTATED PTPN21 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V5, binary
                  cls
clus                0  1
  PTPN21 MUTATED    2  6
  PTPN21 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      2    6
  PTPN21 WILD-TYPE   33   83
   clus
vv  PTPN21 MUTATED PTPN21 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D148V6, binary
                  cls
clus                0  1
  PTPN21 MUTATED    5  1
  PTPN21 WILD-TYPE 52  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      5    1
  PTPN21 WILD-TYPE   52    2
   clus
vv  PTPN21 MUTATED PTPN21 WILD-TYPE
  0              5               52
  1              1                2
[1] 2 2
[1] FALSE
D148V7, binary
                  cls
clus                0  1
  PTPN21 MUTATED    5  3
  PTPN21 WILD-TYPE 46 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      5    3
  PTPN21 WILD-TYPE   46   72
        clus
vv       PTPN21 MUTATED PTPN21 WILD-TYPE
  FEMALE              5               46
  MALE                3               72
[1] 2 2
[1] FALSE
D148V8, binary
                  cls
clus                0  1
  PTPN21 MUTATED    4  2
  PTPN21 WILD-TYPE 84 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      4    2
  PTPN21 WILD-TYPE   84   28
     clus
vv    PTPN21 MUTATED PTPN21 WILD-TYPE
  NO               4               84
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPN21 MUTATED                                     6
  PTPN21 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPN21 MUTATED                                       1
  PTPN21 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPN21 MUTATED                                                  0
  PTPN21 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PTPN21 MUTATED                                     1
  PTPN21 WILD-TYPE                                   0
D148V9, multiclass
                                                  clus
vv                                                 PTPN21 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 PTPN21 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V10, continuous
[1] "Remove cluster labels:" "PTPN21 MUTATED"        
clus
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-YY-A8LH 
"PTPN21 WILD-TYPE" 
D148V11, continuous
[1] "Remove cluster labels:" "PTPN21 MUTATED"        
clus
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PTPN21 MUTATED    6  2  0  0
  PTPN21 WILD-TYPE 74 33  4  2
D148V12, multiclass
    clus
vv   PTPN21 MUTATED PTPN21 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN21 MUTATED       0                         1     7
  PTPN21 WILD-TYPE     6                         4   107
D148V14, multiclass
                           clus
vv                          PTPN21 MUTATED PTPN21 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V15, binary
                  cls
clus                0  1
  PTPN21 MUTATED    0  5
  PTPN21 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      0    5
  PTPN21 WILD-TYPE    5   86
                        clus
vv                       PTPN21 MUTATED PTPN21 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(149) Variable = HIBCH MUTATION ANALYSIS
D149V1, survival
                 sevent
clus2              0  1
  HIBCH MUTATED    2  3
  HIBCH WILD-TYPE 61 59
  HIBCH MUTATED HIBCH WILD-TYPE 
              5             120 
  HIBCH MUTATED HIBCH WILD-TYPE 
              3              59 
$`HIBCH MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9IB TCGA-HZ-7918 TCGA-HZ-7925 TCGA-US-A77J 
       60.95         7.36        31.86        20.19        18.67 

$`HIBCH WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  HIBCH MUTATED HIBCH WILD-TYPE 
           7.36            0.23 
  HIBCH MUTATED HIBCH WILD-TYPE 
          60.95           90.12 
  HIBCH MUTATED HIBCH WILD-TYPE 
         20.190          15.155 
[1] "7.4 - 61.0 (20.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D149V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIBCH MUTATED         0        0        1         0         4         0
  HIBCH WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  HIBCH MUTATED          0
  HIBCH WILD-TYPE        3
D149V3, multiclass
           clus
vv          HIBCH MUTATED HIBCH WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HIBCH MUTATED    0  1     4
  HIBCH WILD-TYPE  5 16    98
D149V4, multiclass
       clus
vv      HIBCH MUTATED HIBCH WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V5, binary
                 cls
clus               0  1
  HIBCH MUTATED    1  4
  HIBCH WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      1    4
  HIBCH WILD-TYPE   34   85
   clus
vv  HIBCH MUTATED HIBCH WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D149V6, binary
                 cls
clus               0  1
  HIBCH MUTATED    1  0
  HIBCH WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      1    0
  HIBCH WILD-TYPE   56    3
   clus
vv  HIBCH MUTATED HIBCH WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D149V7, binary
                 cls
clus               0  1
  HIBCH MUTATED    2  3
  HIBCH WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      2    3
  HIBCH WILD-TYPE   49   72
        clus
vv       HIBCH MUTATED HIBCH WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D149V8, binary
                 cls
clus               0  1
  HIBCH MUTATED    3  1
  HIBCH WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      3    1
  HIBCH WILD-TYPE   85   29
     clus
vv    HIBCH MUTATED HIBCH WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIBCH MUTATED                                     4
  HIBCH WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIBCH MUTATED                                       1
  HIBCH WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIBCH MUTATED                                                  0
  HIBCH WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIBCH MUTATED                                     0
  HIBCH WILD-TYPE                                   1
D149V9, multiclass
                                                  clus
vv                                                 HIBCH MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HIBCH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V10, continuous
[1] "Remove cluster labels:" "HIBCH MUTATED"         
clus
  HIBCH MUTATED HIBCH WILD-TYPE 
              2              37 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IX      TCGA-F2-A8YN 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-YY-A8LH 
"HIBCH WILD-TYPE" 
D149V11, continuous
[1] "Remove cluster labels:" "HIBCH MUTATED"         
clus
  HIBCH MUTATED HIBCH WILD-TYPE 
              2              31 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IR      TCGA-3A-A9IX      TCGA-FB-A5VM 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"HIBCH WILD-TYPE" "HIBCH WILD-TYPE" "HIBCH WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HIBCH MUTATED    5  0  0  0
  HIBCH WILD-TYPE 75 35  4  2
D149V12, multiclass
    clus
vv   HIBCH MUTATED HIBCH WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIBCH MUTATED       0                         0     5
  HIBCH WILD-TYPE     6                         5   109
D149V14, multiclass
                           clus
vv                          HIBCH MUTATED HIBCH WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V15, binary
                 cls
clus               0  1
  HIBCH MUTATED    0  5
  HIBCH WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      0    5
  HIBCH WILD-TYPE    5   86
                        clus
vv                       HIBCH MUTATED HIBCH WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(150) Variable = C16ORF79 MUTATION ANALYSIS
D150V1, survival
                    sevent
clus2                 0  1
  C16ORF79 MUTATED    1  4
  C16ORF79 WILD-TYPE 62 58
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 5                120 
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 4                 58 
$`C16ORF79 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-FB-AAPU TCGA-HZ-A49I TCGA-IB-7651 
       20.61        22.22        12.53        10.13        19.82 

$`C16ORF79 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
             10.13               0.23 
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
             22.22              90.12 
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
            19.820             15.205 
[1] "10.1 - 22.2 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.5"
D150V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C16ORF79 MUTATED         0        0        0         2         3         0
  C16ORF79 WILD-TYPE       1        3       12        17        79         4
                    vv
clus                 STAGE IV
  C16ORF79 MUTATED          0
  C16ORF79 WILD-TYPE        3
D150V3, multiclass
           clus
vv          C16ORF79 MUTATED C16ORF79 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                2                 17
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C16ORF79 MUTATED    0  0     5
  C16ORF79 WILD-TYPE  5 17    97
D150V4, multiclass
       clus
vv      C16ORF79 MUTATED C16ORF79 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V5, binary
                    cls
clus                  0  1
  C16ORF79 MUTATED    2  3
  C16ORF79 WILD-TYPE 33 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF79 MUTATED      2    3
  C16ORF79 WILD-TYPE   33   86
   clus
vv  C16ORF79 MUTATED C16ORF79 WILD-TYPE
  0                2                 33
  1                3                 86
[1] 2 2
[1] FALSE
D150V6, binary
                    cls
clus                  0  1
  C16ORF79 MUTATED    3  0
  C16ORF79 WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF79 MUTATED      3    0
  C16ORF79 WILD-TYPE   54    3
   clus
vv  C16ORF79 MUTATED C16ORF79 WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D150V7, binary
                    cls
clus                  0  1
  C16ORF79 MUTATED    3  2
  C16ORF79 WILD-TYPE 48 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF79 MUTATED      3    2
  C16ORF79 WILD-TYPE   48   73
        clus
vv       C16ORF79 MUTATED C16ORF79 WILD-TYPE
  FEMALE                3                 48
  MALE                  2                 73
[1] 2 2
[1] FALSE
D150V8, binary
                    cls
clus                  0  1
  C16ORF79 MUTATED    2  3
  C16ORF79 WILD-TYPE 86 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF79 MUTATED      2    3
  C16ORF79 WILD-TYPE   86   27
     clus
vv    C16ORF79 MUTATED C16ORF79 WILD-TYPE
  NO                 2                 86
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C16ORF79 MUTATED                                     5
  C16ORF79 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C16ORF79 MUTATED                                       0
  C16ORF79 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C16ORF79 MUTATED                                                  0
  C16ORF79 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C16ORF79 MUTATED                                     0
  C16ORF79 WILD-TYPE                                   1
D150V9, multiclass
                                                  clus
vv                                                 C16ORF79 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C16ORF79 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V10, continuous
[1] "Remove cluster labels:" "C16ORF79 MUTATED"      
clus
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABF 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-YY-A8LH 
"C16ORF79 WILD-TYPE" 
D150V11, continuous
[1] "Remove cluster labels:" "C16ORF79 MUTATED"      
clus
  C16ORF79 MUTATED C16ORF79 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABF         TCGA-2J-AABO 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" "C16ORF79 WILD-TYPE" 
        TCGA-YY-A8LH 
"C16ORF79 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C16ORF79 MUTATED    3  2  0  0
  C16ORF79 WILD-TYPE 77 33  4  2
D150V12, multiclass
    clus
vv   C16ORF79 MUTATED C16ORF79 WILD-TYPE
  R0                3                 77
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C16ORF79 MUTATED       1                         0     4
  C16ORF79 WILD-TYPE     5                         5   110
D150V14, multiclass
                           clus
vv                          C16ORF79 MUTATED C16ORF79 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V15, binary
                    cls
clus                  0  1
  C16ORF79 MUTATED    0  3
  C16ORF79 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF79 MUTATED      0    3
  C16ORF79 WILD-TYPE    5   88
                        clus
vv                       C16ORF79 MUTATED C16ORF79 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(151) Variable = KIAA0430 MUTATION ANALYSIS
D151V1, survival
                    sevent
clus2                 0  1
  KIAA0430 MUTATED    7  2
  KIAA0430 WILD-TYPE 56 60
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 9                116 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
                 2                 60 
$`KIAA0430 MUTATED`
TCGA-2J-AABT TCGA-3A-A9IJ TCGA-LB-A7SX TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB8 
       10.49        60.95        12.92        16.37        23.97         2.63 
TCGA-IB-7651 TCGA-IB-A5SP TCGA-RB-AA9M 
       19.82        15.85         9.40 

$`KIAA0430 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        58.98        90.12         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB6 
        1.08        15.12        17.26        14.14         2.17         9.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
              2.63               0.23 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
             60.95              90.12 
  KIAA0430 MUTATED KIAA0430 WILD-TYPE 
            15.850             15.205 
[1] "2.6 - 61.0 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.2"
D151V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA0430 MUTATED         0        0        1         2         6         0
  KIAA0430 WILD-TYPE       1        3       11        17        76         4
                    vv
clus                 STAGE IV
  KIAA0430 MUTATED          0
  KIAA0430 WILD-TYPE        3
D151V3, multiclass
           clus
vv          KIAA0430 MUTATED KIAA0430 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                2                 17
  STAGE IIB                6                 76
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA0430 MUTATED    1  2     6
  KIAA0430 WILD-TYPE  4 15    96
D151V4, multiclass
       clus
vv      KIAA0430 MUTATED KIAA0430 WILD-TYPE
  T1                   1                  4
  T2                   2                 15
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V5, binary
                    cls
clus                  0  1
  KIAA0430 MUTATED    3  6
  KIAA0430 WILD-TYPE 32 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      3    6
  KIAA0430 WILD-TYPE   32   83
   clus
vv  KIAA0430 MUTATED KIAA0430 WILD-TYPE
  0                3                 32
  1                6                 83
[1] 2 2
[1] FALSE
D151V6, binary
                    cls
clus                  0  1
  KIAA0430 MUTATED    5  0
  KIAA0430 WILD-TYPE 52  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      5    0
  KIAA0430 WILD-TYPE   52    3
   clus
vv  KIAA0430 MUTATED KIAA0430 WILD-TYPE
  0                5                 52
  1                0                  3
[1] 2 2
[1] FALSE
D151V7, binary
                    cls
clus                  0  1
  KIAA0430 MUTATED    3  6
  KIAA0430 WILD-TYPE 48 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      3    6
  KIAA0430 WILD-TYPE   48   69
        clus
vv       KIAA0430 MUTATED KIAA0430 WILD-TYPE
  FEMALE                3                 48
  MALE                  6                 69
[1] 2 2
[1] FALSE
D151V8, binary
                    cls
clus                  0  1
  KIAA0430 MUTATED    6  1
  KIAA0430 WILD-TYPE 82 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      6    1
  KIAA0430 WILD-TYPE   82   29
     clus
vv    KIAA0430 MUTATED KIAA0430 WILD-TYPE
  NO                 6                 82
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0430 MUTATED                                     7
  KIAA0430 WILD-TYPE                                  98
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0430 MUTATED                                       2
  KIAA0430 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0430 MUTATED                                                  0
  KIAA0430 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA0430 MUTATED                                     0
  KIAA0430 WILD-TYPE                                   1
D151V9, multiclass
                                                  clus
vv                                                 KIAA0430 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA0430 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V10, continuous
D151V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA0430 MUTATED    6  3  0  0
  KIAA0430 WILD-TYPE 74 32  4  2
D151V12, multiclass
    clus
vv   KIAA0430 MUTATED KIAA0430 WILD-TYPE
  R0                6                 74
  R1                3                 32
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0430 MUTATED       0                         1     8
  KIAA0430 WILD-TYPE     6                         4   106
D151V14, multiclass
                           clus
vv                          KIAA0430 MUTATED KIAA0430 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    8                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V15, binary
                    cls
clus                  0  1
  KIAA0430 MUTATED    0  5
  KIAA0430 WILD-TYPE  5 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0430 MUTATED      0    5
  KIAA0430 WILD-TYPE    5   86
                        clus
vv                       KIAA0430 MUTATED KIAA0430 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                 86
[1] 2 2
[1] FALSE

Clustering(152) Variable = NOX5 MUTATION ANALYSIS
D152V1, survival
                sevent
clus2             0  1
  NOX5 MUTATED    2  4
  NOX5 WILD-TYPE 61 58
  NOX5 MUTATED NOX5 WILD-TYPE 
             6            119 
  NOX5 MUTATED NOX5 WILD-TYPE 
             4             58 
$`NOX5 MUTATED`
TCGA-LB-A7SX TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-LB-A9Q5 TCGA-US-A77J TCGA-YY-A8LH 
       12.92         0.23        19.82        10.29        18.67        66.28 

$`NOX5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  NOX5 MUTATED NOX5 WILD-TYPE 
          0.23           0.26 
  NOX5 MUTATED NOX5 WILD-TYPE 
         66.28          90.12 
  NOX5 MUTATED NOX5 WILD-TYPE 
        15.795         15.220 
[1] "0.2 - 66.3 (15.8)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.4"
D152V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NOX5 MUTATED         0        0        1         0         5         0
  NOX5 WILD-TYPE       1        3       11        19        77         4
                vv
clus             STAGE IV
  NOX5 MUTATED          0
  NOX5 WILD-TYPE        3
D152V3, multiclass
           clus
vv          NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NOX5 MUTATED    0  1     5
  NOX5 WILD-TYPE  5 16    97
D152V4, multiclass
       clus
vv      NOX5 MUTATED NOX5 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V5, binary
                cls
clus              0  1
  NOX5 MUTATED    1  5
  NOX5 WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    5
  NOX5 WILD-TYPE   34   84
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D152V6, binary
                cls
clus              0  1
  NOX5 MUTATED    1  0
  NOX5 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    0
  NOX5 WILD-TYPE   56    3
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D152V7, binary
                cls
clus              0  1
  NOX5 MUTATED    5  1
  NOX5 WILD-TYPE 46 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      5    1
  NOX5 WILD-TYPE   46   74
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE            5             46
  MALE              1             74
[1] 2 2
[1] FALSE
D152V8, binary
                cls
clus              0  1
  NOX5 MUTATED    2  2
  NOX5 WILD-TYPE 86 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      2    2
  NOX5 WILD-TYPE   86   28
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO             2             86
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NOX5 MUTATED                                     6
  NOX5 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NOX5 MUTATED                                       0
  NOX5 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NOX5 MUTATED                                                  0
  NOX5 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NOX5 MUTATED                                     0
  NOX5 WILD-TYPE                                   1
D152V9, multiclass
                                                  clus
vv                                                 NOX5 MUTATED NOX5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V10, continuous
D152V11, continuous
                vv
clus             R0 R1 R2 RX
  NOX5 MUTATED    5  1  0  0
  NOX5 WILD-TYPE 75 34  4  2
D152V12, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0            5             75
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOX5 MUTATED       0                         1     5
  NOX5 WILD-TYPE     6                         4   109
D152V14, multiclass
                           clus
vv                          NOX5 MUTATED NOX5 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V15, binary
                cls
clus              0  1
  NOX5 MUTATED    0  6
  NOX5 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      0    6
  NOX5 WILD-TYPE    5   85
                        clus
vv                       NOX5 MUTATED NOX5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(153) Variable = NF2 MUTATION ANALYSIS
D153V1, survival
               sevent
clus2            0  1
  NF2 MUTATED    3  2
  NF2 WILD-TYPE 60 60
  NF2 MUTATED NF2 WILD-TYPE 
            5           120 
  NF2 MUTATED NF2 WILD-TYPE 
            2            60 
$`NF2 MUTATED`
TCGA-3A-A9IB TCGA-3A-A9J0 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
        7.36        24.43        10.85        19.82        36.69 

$`NF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  NF2 MUTATED NF2 WILD-TYPE 
         7.36          0.23 
  NF2 MUTATED NF2 WILD-TYPE 
        36.69         90.12 
  NF2 MUTATED NF2 WILD-TYPE 
       19.820        15.205 
[1] "7.4 - 36.7 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D153V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NF2 MUTATED         0        0        0         0         5         0
  NF2 WILD-TYPE       1        3       12        19        77         4
               vv
clus            STAGE IV
  NF2 MUTATED          0
  NF2 WILD-TYPE        3
D153V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           0            19
  STAGE IIB           5            77
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  NF2 MUTATED    0  0     5
  NF2 WILD-TYPE  5 17    97
D153V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              0             5
  T2              0            17
  T3+T4           5            97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V5, binary
               cls
clus             0  1
  NF2 MUTATED    0  5
  NF2 WILD-TYPE 35 84
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      0    5
  NF2 WILD-TYPE   35   84
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           0            35
  1           5            84
[1] 2 2
[1] FALSE
D153V6, binary
               cls
clus             0  1
  NF2 MUTATED    2  0
  NF2 WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    0
  NF2 WILD-TYPE   55    3
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D153V7, binary
               cls
clus             0  1
  NF2 MUTATED    3  2
  NF2 WILD-TYPE 48 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      3    2
  NF2 WILD-TYPE   48   73
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           3            48
  MALE             2            73
[1] 2 2
[1] FALSE
D153V8, binary
               cls
clus             0  1
  NF2 MUTATED    5  0
  NF2 WILD-TYPE 83 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      5    0
  NF2 WILD-TYPE   83   30
     clus
vv    NF2 MUTATED NF2 WILD-TYPE
  NO            5            83
  YES           0            30
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NF2 MUTATED                                     4
  NF2 WILD-TYPE                                 101
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NF2 MUTATED                                       1
  NF2 WILD-TYPE                                    17
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NF2 MUTATED                                                  0
  NF2 WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  NF2 MUTATED                                     0
  NF2 WILD-TYPE                                   1
D153V9, multiclass
                                                  clus
vv                                                 NF2 MUTATED NF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      1            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V10, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            37 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1    TCGA-IB-7885 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
D153V11, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            31 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7885    TCGA-IB-8126 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI    TCGA-XN-A8T5 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-YY-A8LH 
"NF2 WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  NF2 MUTATED    4  1  0  0
  NF2 WILD-TYPE 76 34  4  2
D153V12, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  R0           4            76
  R1           1            34
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED       1                         0     4
  NF2 WILD-TYPE     5                         5   110
D153V14, multiclass
                           clus
vv                          NF2 MUTATED NF2 WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V15, binary
               cls
clus             0  1
  NF2 MUTATED    0  5
  NF2 WILD-TYPE  5 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      0    5
  NF2 WILD-TYPE    5   86
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           5            86
[1] 2 2
[1] FALSE

Clustering(154) Variable = EPHB6 MUTATION ANALYSIS
D154V1, survival
                 sevent
clus2              0  1
  EPHB6 MUTATED    3  4
  EPHB6 WILD-TYPE 60 58
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              7             118 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              4              58 
$`EPHB6 MUTATED`
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3E-AAAZ TCGA-HV-A7OP TCGA-HZ-A77P 
       15.06        36.26        10.13        71.74        32.15        10.85 
TCGA-IB-7651 
       19.82 

$`EPHB6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       34.09        24.43        75.12        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13         5.26         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  EPHB6 MUTATED EPHB6 WILD-TYPE 
          10.13            0.23 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
          71.74           90.12 
  EPHB6 MUTATED EPHB6 WILD-TYPE 
         19.820          15.205 
[1] "10.1 - 71.7 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D154V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EPHB6 MUTATED         0        0        1         1         5         0
  EPHB6 WILD-TYPE       1        3       11        18        77         4
                 vv
clus              STAGE IV
  EPHB6 MUTATED          0
  EPHB6 WILD-TYPE        3
D154V3, multiclass
           clus
vv          EPHB6 MUTATED EPHB6 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  EPHB6 MUTATED    0  1     6
  EPHB6 WILD-TYPE  5 16    96
D154V4, multiclass
       clus
vv      EPHB6 MUTATED EPHB6 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V5, binary
                 cls
clus               0  1
  EPHB6 MUTATED    2  5
  EPHB6 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      2    5
  EPHB6 WILD-TYPE   33   84
   clus
vv  EPHB6 MUTATED EPHB6 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D154V6, binary
                 cls
clus               0  1
  EPHB6 MUTATED    2  0
  EPHB6 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      2    0
  EPHB6 WILD-TYPE   55    3
   clus
vv  EPHB6 MUTATED EPHB6 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D154V7, binary
                 cls
clus               0  1
  EPHB6 MUTATED    2  5
  EPHB6 WILD-TYPE 49 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      2    5
  EPHB6 WILD-TYPE   49   70
        clus
vv       EPHB6 MUTATED EPHB6 WILD-TYPE
  FEMALE             2              49
  MALE               5              70
[1] 2 2
[1] FALSE
D154V8, binary
                 cls
clus               0  1
  EPHB6 MUTATED    5  1
  EPHB6 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      5    1
  EPHB6 WILD-TYPE   83   29
     clus
vv    EPHB6 MUTATED EPHB6 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EPHB6 MUTATED                                     4
  EPHB6 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EPHB6 MUTATED                                       3
  EPHB6 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EPHB6 MUTATED                                                  0
  EPHB6 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EPHB6 MUTATED                                     0
  EPHB6 WILD-TYPE                                   1
D154V9, multiclass
                                                  clus
vv                                                 EPHB6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 EPHB6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V10, continuous
[1] "Remove cluster labels:" "EPHB6 MUTATED"         
clus
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
D154V11, continuous
[1] "Remove cluster labels:" "EPHB6 MUTATED"         
clus
  EPHB6 MUTATED EPHB6 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" "EPHB6 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  EPHB6 MUTATED    5  1  0  0
  EPHB6 WILD-TYPE 75 34  4  2
D154V12, multiclass
    clus
vv   EPHB6 MUTATED EPHB6 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHB6 MUTATED       1                         0     6
  EPHB6 WILD-TYPE     5                         5   108
D154V14, multiclass
                           clus
vv                          EPHB6 MUTATED EPHB6 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V15, binary
                 cls
clus               0  1
  EPHB6 MUTATED    2  4
  EPHB6 WILD-TYPE  3 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB6 MUTATED      2    4
  EPHB6 WILD-TYPE    3   87
                        clus
vv                       EPHB6 MUTATED EPHB6 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(155) Variable = PRMT8 MUTATION ANALYSIS
D155V1, survival
                 sevent
clus2              0  1
  PRMT8 MUTATED    2  6
  PRMT8 WILD-TYPE 61 56
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              8             117 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              6              56 
$`PRMT8 MUTATED`
TCGA-2J-AAB6 TCGA-2L-AAQJ TCGA-3A-A9IU TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X 
        9.63        12.95        15.06         8.28        32.15        17.49 
TCGA-HZ-A77O TCGA-RB-A7B8 
        5.26        15.32 

$`PRMT8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       22.06        30.25        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PRMT8 MUTATED PRMT8 WILD-TYPE 
           5.26            0.23 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
          32.15           90.12 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
         14.005          15.350 
[1] "5.3 - 32.1 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D155V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRMT8 MUTATED         0        0        0         2         5         1
  PRMT8 WILD-TYPE       1        3       12        17        77         3
                 vv
clus              STAGE IV
  PRMT8 MUTATED          0
  PRMT8 WILD-TYPE        3
D155V3, multiclass
           clus
vv          PRMT8 MUTATED PRMT8 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PRMT8 MUTATED    0  2     6
  PRMT8 WILD-TYPE  5 15    96
D155V4, multiclass
       clus
vv      PRMT8 MUTATED PRMT8 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V5, binary
                 cls
clus               0  1
  PRMT8 MUTATED    3  5
  PRMT8 WILD-TYPE 32 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      3    5
  PRMT8 WILD-TYPE   32   84
   clus
vv  PRMT8 MUTATED PRMT8 WILD-TYPE
  0             3              32
  1             5              84
[1] 2 2
[1] FALSE
D155V6, binary
                 cls
clus               0  1
  PRMT8 MUTATED    2  0
  PRMT8 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      2    0
  PRMT8 WILD-TYPE   55    3
   clus
vv  PRMT8 MUTATED PRMT8 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D155V7, binary
                 cls
clus               0  1
  PRMT8 MUTATED    4  4
  PRMT8 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      4    4
  PRMT8 WILD-TYPE   47   71
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D155V8, binary
                 cls
clus               0  1
  PRMT8 MUTATED    7  1
  PRMT8 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      7    1
  PRMT8 WILD-TYPE   81   29
     clus
vv    PRMT8 MUTATED PRMT8 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRMT8 MUTATED                                     6
  PRMT8 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRMT8 MUTATED                                       2
  PRMT8 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRMT8 MUTATED                                                  0
  PRMT8 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRMT8 MUTATED                                     0
  PRMT8 WILD-TYPE                                   1
D155V9, multiclass
                                                  clus
vv                                                 PRMT8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRMT8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V10, continuous
D155V11, continuous
                 vv
clus              R0 R1 R2 RX
  PRMT8 MUTATED    5  1  2  0
  PRMT8 WILD-TYPE 75 34  2  2
D155V12, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             2               2
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRMT8 MUTATED       3                         0     5
  PRMT8 WILD-TYPE     3                         5   109
D155V14, multiclass
                           clus
vv                          PRMT8 MUTATED PRMT8 WILD-TYPE
  ASIAN                                 3               3
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V15, binary
                 cls
clus               0  1
  PRMT8 MUTATED    0  3
  PRMT8 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      0    3
  PRMT8 WILD-TYPE    5   88
                        clus
vv                       PRMT8 MUTATED PRMT8 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(156) Variable = TNRC6C MUTATION ANALYSIS
D156V1, survival
                  sevent
clus2               0  1
  TNRC6C MUTATED    2  7
  TNRC6C WILD-TYPE 61 55
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               9              116 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               7               55 
$`TNRC6C MUTATED`
TCGA-2J-AAB1 TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-FB-A78T TCGA-FB-AAPU TCGA-FZ-5923 
        2.17        12.95         9.60        12.33        12.53        20.35 
TCGA-HV-A7OL TCGA-IB-7651 TCGA-US-A776 
        8.28        19.82        39.98 

$`TNRC6C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ 
       17.00        16.37        15.95        37.15         7.50        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
        5.10        36.20        17.79        22.06        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
            2.17             0.23 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           39.98            90.12 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
          12.530           15.335 
[1] "2.2 - 40.0 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D156V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TNRC6C MUTATED         0        0        0         3         4         1
  TNRC6C WILD-TYPE       1        3       12        16        78         3
                  vv
clus               STAGE IV
  TNRC6C MUTATED          1
  TNRC6C WILD-TYPE        2
D156V3, multiclass
           clus
vv          TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              3               16
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TNRC6C MUTATED    0  0     9
  TNRC6C WILD-TYPE  5 17    93
D156V4, multiclass
       clus
vv      TNRC6C MUTATED TNRC6C WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              9               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V5, binary
                  cls
clus                0  1
  TNRC6C MUTATED    4  5
  TNRC6C WILD-TYPE 31 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      4    5
  TNRC6C WILD-TYPE   31   84
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              4               31
  1              5               84
[1] 2 2
[1] FALSE
D156V6, binary
                  cls
clus                0  1
  TNRC6C MUTATED    3  1
  TNRC6C WILD-TYPE 54  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      3    1
  TNRC6C WILD-TYPE   54    2
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              3               54
  1              1                2
[1] 2 2
[1] FALSE
D156V7, binary
                  cls
clus                0  1
  TNRC6C MUTATED    4  5
  TNRC6C WILD-TYPE 47 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      4    5
  TNRC6C WILD-TYPE   47   70
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE              4               47
  MALE                5               70
[1] 2 2
[1] FALSE
D156V8, binary
                  cls
clus                0  1
  TNRC6C MUTATED    9  0
  TNRC6C WILD-TYPE 79 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      9    0
  TNRC6C WILD-TYPE   79   30
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO               9               79
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNRC6C MUTATED                                     7
  TNRC6C WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNRC6C MUTATED                                       1
  TNRC6C WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNRC6C MUTATED                                                  1
  TNRC6C WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TNRC6C MUTATED                                     0
  TNRC6C WILD-TYPE                                   1
D156V9, multiclass
                                                  clus
vv                                                 TNRC6C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TNRC6C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V10, continuous
D156V11, continuous
                  vv
clus               R0 R1 R2 RX
  TNRC6C MUTATED    5  2  1  1
  TNRC6C WILD-TYPE 75 33  3  1
D156V12, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0              5               75
  R1              2               33
  R2              1                3
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNRC6C MUTATED       2                         0     7
  TNRC6C WILD-TYPE     4                         5   107
D156V14, multiclass
                           clus
vv                          TNRC6C MUTATED TNRC6C WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V15, binary
                  cls
clus                0  1
  TNRC6C MUTATED    0  5
  TNRC6C WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      0    5
  TNRC6C WILD-TYPE    5   86
                        clus
vv                       TNRC6C MUTATED TNRC6C WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(157) Variable = ZC3H4 MUTATION ANALYSIS
D157V1, survival
                 sevent
clus2              0  1
  ZC3H4 MUTATED    2  6
  ZC3H4 WILD-TYPE 61 56
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              8             117 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              6              56 
$`ZC3H4 MUTATED`
TCGA-2J-AAB6 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-H8-A6C1 TCGA-HZ-A77O TCGA-IB-7651 
        9.63         2.01         5.10        22.06         5.26        19.82 
TCGA-IB-A5SQ TCGA-IB-AAUU 
        7.20         8.05 

$`ZC3H4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        5.03         1.02        24.36        36.20        20.35        17.79 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         7.40        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
           2.01            0.23 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
          22.06           90.12 
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
          7.625          15.350 
[1] "2.0 - 22.1 (7.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "3"  
D157V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZC3H4 MUTATED         0        0        1         2         5         0
  ZC3H4 WILD-TYPE       1        3       11        17        77         4
                 vv
clus              STAGE IV
  ZC3H4 MUTATED          0
  ZC3H4 WILD-TYPE        3
D157V3, multiclass
           clus
vv          ZC3H4 MUTATED ZC3H4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZC3H4 MUTATED    0  2     6
  ZC3H4 WILD-TYPE  5 15    96
D157V4, multiclass
       clus
vv      ZC3H4 MUTATED ZC3H4 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V5, binary
                 cls
clus               0  1
  ZC3H4 MUTATED    3  5
  ZC3H4 WILD-TYPE 32 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      3    5
  ZC3H4 WILD-TYPE   32   84
   clus
vv  ZC3H4 MUTATED ZC3H4 WILD-TYPE
  0             3              32
  1             5              84
[1] 2 2
[1] FALSE
D157V6, binary
                 cls
clus               0  1
  ZC3H4 MUTATED    6  0
  ZC3H4 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      6    0
  ZC3H4 WILD-TYPE   51    3
   clus
vv  ZC3H4 MUTATED ZC3H4 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D157V7, binary
                 cls
clus               0  1
  ZC3H4 MUTATED    4  4
  ZC3H4 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      4    4
  ZC3H4 WILD-TYPE   47   71
        clus
vv       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D157V8, binary
                 cls
clus               0  1
  ZC3H4 MUTATED    7  1
  ZC3H4 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      7    1
  ZC3H4 WILD-TYPE   81   29
     clus
vv    ZC3H4 MUTATED ZC3H4 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZC3H4 MUTATED                                     7
  ZC3H4 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZC3H4 MUTATED                                       1
  ZC3H4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZC3H4 MUTATED                                                  0
  ZC3H4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZC3H4 MUTATED                                     0
  ZC3H4 WILD-TYPE                                   1
D157V9, multiclass
                                                  clus
vv                                                 ZC3H4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZC3H4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V10, continuous
D157V11, continuous
[1] "Remove cluster labels:" "ZC3H4 MUTATED"         
clus
  ZC3H4 MUTATED ZC3H4 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" "ZC3H4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZC3H4 MUTATED    7  0  0  0
  ZC3H4 WILD-TYPE 73 35  4  2
D157V12, multiclass
    clus
vv   ZC3H4 MUTATED ZC3H4 WILD-TYPE
  R0             7              73
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H4 MUTATED       0                         1     6
  ZC3H4 WILD-TYPE     6                         4   108
D157V14, multiclass
                           clus
vv                          ZC3H4 MUTATED ZC3H4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V15, binary
                 cls
clus               0  1
  ZC3H4 MUTATED    0  6
  ZC3H4 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H4 MUTATED      0    6
  ZC3H4 WILD-TYPE    5   85
                        clus
vv                       ZC3H4 MUTATED ZC3H4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(158) Variable = NRD1 MUTATION ANALYSIS
D158V1, survival
                sevent
clus2             0  1
  NRD1 MUTATED    3  6
  NRD1 WILD-TYPE 60 56
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            116 
  NRD1 MUTATED NRD1 WILD-TYPE 
             6             56 
$`NRD1 MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9IR TCGA-3A-A9IZ TCGA-IB-7651 TCGA-IB-A7LX TCGA-IB-AAUO 
       12.95        50.70        10.13        19.82         8.22         7.86 
TCGA-IB-AAUP TCGA-LB-A9Q5 TCGA-RB-AA9M 
       14.17        10.29         9.40 

$`NRD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        4.73         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NRD1 MUTATED NRD1 WILD-TYPE 
          7.86           0.23 
  NRD1 MUTATED NRD1 WILD-TYPE 
         50.70          90.12 
  NRD1 MUTATED NRD1 WILD-TYPE 
         10.29          15.45 
[1] "7.9 - 50.7 (10.3)" "0.2 - 90.1 (15.4)"
[1] "hr=" "1.8"
D158V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NRD1 MUTATED         0        0        1         0         7         1
  NRD1 WILD-TYPE       1        3       11        19        75         3
                vv
clus             STAGE IV
  NRD1 MUTATED          0
  NRD1 WILD-TYPE        3
D158V3, multiclass
           clus
vv          NRD1 MUTATED NRD1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            7             75
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NRD1 MUTATED    1  1     7
  NRD1 WILD-TYPE  4 16    95
D158V4, multiclass
       clus
vv      NRD1 MUTATED NRD1 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V5, binary
                cls
clus              0  1
  NRD1 MUTATED    2  7
  NRD1 WILD-TYPE 33 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      2    7
  NRD1 WILD-TYPE   33   82
   clus
vv  NRD1 MUTATED NRD1 WILD-TYPE
  0            2             33
  1            7             82
[1] 2 2
[1] FALSE
D158V6, binary
                cls
clus              0  1
  NRD1 MUTATED    3  0
  NRD1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      3    0
  NRD1 WILD-TYPE   54    3
   clus
vv  NRD1 MUTATED NRD1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D158V7, binary
                cls
clus              0  1
  NRD1 MUTATED    5  4
  NRD1 WILD-TYPE 46 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      5    4
  NRD1 WILD-TYPE   46   71
        clus
vv       NRD1 MUTATED NRD1 WILD-TYPE
  FEMALE            5             46
  MALE              4             71
[1] 2 2
[1] FALSE
D158V8, binary
                cls
clus              0  1
  NRD1 MUTATED    7  2
  NRD1 WILD-TYPE 81 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      7    2
  NRD1 WILD-TYPE   81   28
     clus
vv    NRD1 MUTATED NRD1 WILD-TYPE
  NO             7             81
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NRD1 MUTATED                                     8
  NRD1 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NRD1 MUTATED                                       1
  NRD1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NRD1 MUTATED                                                  0
  NRD1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NRD1 MUTATED                                     0
  NRD1 WILD-TYPE                                   1
D158V9, multiclass
                                                  clus
vv                                                 NRD1 MUTATED NRD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V10, continuous
[1] "Remove cluster labels:" "NRD1 MUTATED"          
clus
  NRD1 MUTATED NRD1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-OE-A75W     TCGA-XN-A8T5 
"NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" "NRD1 WILD-TYPE" 
    TCGA-YY-A8LH 
"NRD1 WILD-TYPE" 
D158V11, continuous
                vv
clus             R0 R1 R2 RX
  NRD1 MUTATED    5  4  0  0
  NRD1 WILD-TYPE 75 31  4  2
D158V12, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  R0            5             75
  R1            4             31
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRD1 MUTATED       0                         0     9
  NRD1 WILD-TYPE     6                         5   105
D158V14, multiclass
                           clus
vv                          NRD1 MUTATED NRD1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V15, binary
                cls
clus              0  1
  NRD1 MUTATED    1  7
  NRD1 WILD-TYPE  4 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      1    7
  NRD1 WILD-TYPE    4   84
                        clus
vv                       NRD1 MUTATED NRD1 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            7             84
[1] 2 2
[1] FALSE

Clustering(159) Variable = ZNF552 MUTATION ANALYSIS
D159V1, survival
                  sevent
clus2               0  1
  ZNF552 MUTATED    3  3
  ZNF552 WILD-TYPE 60 59
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               6              119 
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               3               59 
$`ZNF552 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABK TCGA-3A-A9IC TCGA-3A-A9IS TCGA-IB-7651 TCGA-XD-AAUG 
       12.92        15.91        24.26        32.81        19.82        13.81 

$`ZNF552 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  ZNF552 MUTATED ZNF552 WILD-TYPE 
           12.92             0.23 
  ZNF552 MUTATED ZNF552 WILD-TYPE 
           32.81            90.12 
  ZNF552 MUTATED ZNF552 WILD-TYPE 
          17.865           15.190 
[1] "12.9 - 32.8 (17.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D159V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF552 MUTATED         0        0        1         0         4         0
  ZNF552 WILD-TYPE       1        3       11        19        78         4
                  vv
clus               STAGE IV
  ZNF552 MUTATED          1
  ZNF552 WILD-TYPE        2
D159V3, multiclass
           clus
vv          ZNF552 MUTATED ZNF552 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF552 MUTATED    0  1     5
  ZNF552 WILD-TYPE  5 16    97
D159V4, multiclass
       clus
vv      ZNF552 MUTATED ZNF552 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V5, binary
                  cls
clus                0  1
  ZNF552 MUTATED    1  5
  ZNF552 WILD-TYPE 34 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF552 MUTATED      1    5
  ZNF552 WILD-TYPE   34   84
   clus
vv  ZNF552 MUTATED ZNF552 WILD-TYPE
  0              1               34
  1              5               84
[1] 2 2
[1] FALSE
D159V6, binary
                  cls
clus                0  1
  ZNF552 MUTATED    2  1
  ZNF552 WILD-TYPE 55  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF552 MUTATED      2    1
  ZNF552 WILD-TYPE   55    2
   clus
vv  ZNF552 MUTATED ZNF552 WILD-TYPE
  0              2               55
  1              1                2
[1] 2 2
[1] FALSE
D159V7, binary
                  cls
clus                0  1
  ZNF552 MUTATED    4  2
  ZNF552 WILD-TYPE 47 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF552 MUTATED      4    2
  ZNF552 WILD-TYPE   47   73
        clus
vv       ZNF552 MUTATED ZNF552 WILD-TYPE
  FEMALE              4               47
  MALE                2               73
[1] 2 2
[1] FALSE
D159V8, binary
                  cls
clus                0  1
  ZNF552 MUTATED    4  2
  ZNF552 WILD-TYPE 84 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF552 MUTATED      4    2
  ZNF552 WILD-TYPE   84   28
     clus
vv    ZNF552 MUTATED ZNF552 WILD-TYPE
  NO               4               84
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF552 MUTATED                                     5
  ZNF552 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF552 MUTATED                                       1
  ZNF552 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF552 MUTATED                                                  0
  ZNF552 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF552 MUTATED                                     0
  ZNF552 WILD-TYPE                                   1
D159V9, multiclass
                                                  clus
vv                                                 ZNF552 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF552 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V10, continuous
[1] "Remove cluster labels:" "ZNF552 MUTATED"        
clus
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-YY-A8LH 
"ZNF552 WILD-TYPE" 
D159V11, continuous
[1] "Remove cluster labels:" "ZNF552 MUTATED"        
clus
  ZNF552 MUTATED ZNF552 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" "ZNF552 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF552 MUTATED    4  2  0  0
  ZNF552 WILD-TYPE 76 33  4  2
D159V12, multiclass
    clus
vv   ZNF552 MUTATED ZNF552 WILD-TYPE
  R0              4               76
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF552 MUTATED       0                         1     5
  ZNF552 WILD-TYPE     6                         4   109
D159V14, multiclass
                           clus
vv                          ZNF552 MUTATED ZNF552 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V15, binary
                  cls
clus                0  1
  ZNF552 MUTATED    0  5
  ZNF552 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF552 MUTATED      0    5
  ZNF552 WILD-TYPE    5   86
                        clus
vv                       ZNF552 MUTATED ZNF552 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(160) Variable = BCAS1 MUTATION ANALYSIS
D160V1, survival
                 sevent
clus2              0  1
  BCAS1 MUTATED    3  1
  BCAS1 WILD-TYPE 60 61
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              4             121 
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              1              61 
$`BCAS1 MUTATED`
TCGA-3A-A9IH TCGA-3E-AAAZ TCGA-IB-A6UF TCGA-LB-A8F3 
       33.57        71.74        21.90        12.46 

$`BCAS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  BCAS1 MUTATED BCAS1 WILD-TYPE 
          12.46            0.23 
  BCAS1 MUTATED BCAS1 WILD-TYPE 
          71.74           90.12 
  BCAS1 MUTATED BCAS1 WILD-TYPE 
         27.735          15.190 
[1] "12.5 - 71.7 (27.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3.6"
D160V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BCAS1 MUTATED         0        1        0         2         2         0
  BCAS1 WILD-TYPE       1        2       12        17        80         4
                 vv
clus              STAGE IV
  BCAS1 MUTATED          0
  BCAS1 WILD-TYPE        3
D160V3, multiclass
           clus
vv          BCAS1 MUTATED BCAS1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  BCAS1 MUTATED    1  0     4
  BCAS1 WILD-TYPE  4 17    98
D160V4, multiclass
       clus
vv      BCAS1 MUTATED BCAS1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V5, binary
                 cls
clus               0  1
  BCAS1 MUTATED    3  2
  BCAS1 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAS1 MUTATED      3    2
  BCAS1 WILD-TYPE   32   87
   clus
vv  BCAS1 MUTATED BCAS1 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D160V6, binary
                 cls
clus               0  1
  BCAS1 MUTATED    1  0
  BCAS1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAS1 MUTATED      1    0
  BCAS1 WILD-TYPE   56    3
   clus
vv  BCAS1 MUTATED BCAS1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D160V7, binary
                 cls
clus               0  1
  BCAS1 MUTATED    2  3
  BCAS1 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAS1 MUTATED      2    3
  BCAS1 WILD-TYPE   49   72
        clus
vv       BCAS1 MUTATED BCAS1 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D160V8, binary
                 cls
clus               0  1
  BCAS1 MUTATED    2  1
  BCAS1 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAS1 MUTATED      2    1
  BCAS1 WILD-TYPE   86   29
     clus
vv    BCAS1 MUTATED BCAS1 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCAS1 MUTATED                                     5
  BCAS1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCAS1 MUTATED                                       0
  BCAS1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCAS1 MUTATED                                                  0
  BCAS1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  BCAS1 MUTATED                                     0
  BCAS1 WILD-TYPE                                   1
D160V9, multiclass
                                                  clus
vv                                                 BCAS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 BCAS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V10, continuous
[1] "Remove cluster labels:" "BCAS1 MUTATED"         
clus
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-YY-A8LH 
"BCAS1 WILD-TYPE" 
D160V11, continuous
[1] "Remove cluster labels:" "BCAS1 MUTATED"         
clus
  BCAS1 MUTATED BCAS1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" "BCAS1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  BCAS1 MUTATED    3  1  0  0
  BCAS1 WILD-TYPE 77 34  4  2
D160V12, multiclass
    clus
vv   BCAS1 MUTATED BCAS1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCAS1 MUTATED       0                         1     4
  BCAS1 WILD-TYPE     6                         4   110
D160V14, multiclass
                           clus
vv                          BCAS1 MUTATED BCAS1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V15, binary
                 cls
clus               0  1
  BCAS1 MUTATED    1  4
  BCAS1 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAS1 MUTATED      1    4
  BCAS1 WILD-TYPE    4   87
                        clus
vv                       BCAS1 MUTATED BCAS1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(161) Variable = SERTAD1 MUTATION ANALYSIS
D161V1, survival
                   sevent
clus2                0  1
  SERTAD1 MUTATED    1  5
  SERTAD1 WILD-TYPE 62 57
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
                6               119 
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
                5                57 
$`SERTAD1 MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQA TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-AAUQ 
       12.92         4.70        71.74        19.82        15.85         6.02 

$`SERTAD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       19.82        36.69        41.33        15.19        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86        14.17        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
             4.70              0.23 
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
            71.74             90.12 
  SERTAD1 MUTATED SERTAD1 WILD-TYPE 
           14.385            15.220 
[1] "4.7 - 71.7 (14.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D161V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SERTAD1 MUTATED         0        0        0         2         4         0
  SERTAD1 WILD-TYPE       1        3       12        17        78         4
                   vv
clus                STAGE IV
  SERTAD1 MUTATED          0
  SERTAD1 WILD-TYPE        3
D161V3, multiclass
           clus
vv          SERTAD1 MUTATED SERTAD1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               2                17
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SERTAD1 MUTATED    0  0     6
  SERTAD1 WILD-TYPE  5 17    96
D161V4, multiclass
       clus
vv      SERTAD1 MUTATED SERTAD1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V5, binary
                   cls
clus                 0  1
  SERTAD1 MUTATED    2  4
  SERTAD1 WILD-TYPE 33 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERTAD1 MUTATED      2    4
  SERTAD1 WILD-TYPE   33   85
   clus
vv  SERTAD1 MUTATED SERTAD1 WILD-TYPE
  0               2                33
  1               4                85
[1] 2 2
[1] FALSE
D161V6, binary
                   cls
clus                 0  1
  SERTAD1 MUTATED    3  0
  SERTAD1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERTAD1 MUTATED      3    0
  SERTAD1 WILD-TYPE   54    3
   clus
vv  SERTAD1 MUTATED SERTAD1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D161V7, binary
                   cls
clus                 0  1
  SERTAD1 MUTATED    2  4
  SERTAD1 WILD-TYPE 49 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERTAD1 MUTATED      2    4
  SERTAD1 WILD-TYPE   49   71
        clus
vv       SERTAD1 MUTATED SERTAD1 WILD-TYPE
  FEMALE               2                49
  MALE                 4                71
[1] 2 2
[1] FALSE
D161V8, binary
                   cls
clus                 0  1
  SERTAD1 MUTATED    5  0
  SERTAD1 WILD-TYPE 83 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERTAD1 MUTATED      5    0
  SERTAD1 WILD-TYPE   83   30
     clus
vv    SERTAD1 MUTATED SERTAD1 WILD-TYPE
  NO                5                83
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SERTAD1 MUTATED                                     6
  SERTAD1 WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SERTAD1 MUTATED                                       0
  SERTAD1 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SERTAD1 MUTATED                                                  0
  SERTAD1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SERTAD1 MUTATED                                     0
  SERTAD1 WILD-TYPE                                   1
D161V9, multiclass
                                                  clus
vv                                                 SERTAD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SERTAD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V10, continuous
D161V11, continuous
                   vv
clus                R0 R1 R2 RX
  SERTAD1 MUTATED    1  4  0  0
  SERTAD1 WILD-TYPE 79 31  4  2
D161V12, multiclass
    clus
vv   SERTAD1 MUTATED SERTAD1 WILD-TYPE
  R0               1                79
  R1               4                31
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SERTAD1 MUTATED       0                         1     5
  SERTAD1 WILD-TYPE     6                         4   109
D161V14, multiclass
                           clus
vv                          SERTAD1 MUTATED SERTAD1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V15, binary
                   cls
clus                 0  1
  SERTAD1 MUTATED    1  3
  SERTAD1 WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SERTAD1 MUTATED      1    3
  SERTAD1 WILD-TYPE    4   88
                        clus
vv                       SERTAD1 MUTATED SERTAD1 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(162) Variable = GLCCI1 MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2               0  1
  GLCCI1 MUTATED    3  3
  GLCCI1 WILD-TYPE 60 59
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
               6              119 
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
               3               59 
$`GLCCI1 MUTATED`
TCGA-2J-AABV TCGA-3A-A9IH TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A6UG TCGA-Q3-A5QY 
       21.44        33.57        19.82        41.33         1.35        13.68 

$`GLCCI1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
            1.35             0.23 
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
           41.33            90.12 
  GLCCI1 MUTATED GLCCI1 WILD-TYPE 
           20.63            15.19 
[1] "1.4 - 41.3 (20.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D162V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GLCCI1 MUTATED         0        1        0         0         5         0
  GLCCI1 WILD-TYPE       1        2       12        19        77         4
                  vv
clus               STAGE IV
  GLCCI1 MUTATED          0
  GLCCI1 WILD-TYPE        3
D162V3, multiclass
           clus
vv          GLCCI1 MUTATED GLCCI1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GLCCI1 MUTATED    1  0     5
  GLCCI1 WILD-TYPE  4 17    97
D162V4, multiclass
       clus
vv      GLCCI1 MUTATED GLCCI1 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V5, binary
                  cls
clus                0  1
  GLCCI1 MUTATED    1  5
  GLCCI1 WILD-TYPE 34 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLCCI1 MUTATED      1    5
  GLCCI1 WILD-TYPE   34   84
   clus
vv  GLCCI1 MUTATED GLCCI1 WILD-TYPE
  0              1               34
  1              5               84
[1] 2 2
[1] FALSE
D162V6, binary
                  cls
clus                0  1
  GLCCI1 MUTATED    4  0
  GLCCI1 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLCCI1 MUTATED      4    0
  GLCCI1 WILD-TYPE   53    3
   clus
vv  GLCCI1 MUTATED GLCCI1 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D162V7, binary
                  cls
clus                0  1
  GLCCI1 MUTATED    3  3
  GLCCI1 WILD-TYPE 48 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLCCI1 MUTATED      3    3
  GLCCI1 WILD-TYPE   48   72
        clus
vv       GLCCI1 MUTATED GLCCI1 WILD-TYPE
  FEMALE              3               48
  MALE                3               72
[1] 2 2
[1] FALSE
D162V8, binary
                  cls
clus                0  1
  GLCCI1 MUTATED    6  0
  GLCCI1 WILD-TYPE 82 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLCCI1 MUTATED      6    0
  GLCCI1 WILD-TYPE   82   30
     clus
vv    GLCCI1 MUTATED GLCCI1 WILD-TYPE
  NO               6               82
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GLCCI1 MUTATED                                     6
  GLCCI1 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GLCCI1 MUTATED                                       0
  GLCCI1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GLCCI1 MUTATED                                                  0
  GLCCI1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GLCCI1 MUTATED                                     0
  GLCCI1 WILD-TYPE                                   1
D162V9, multiclass
                                                  clus
vv                                                 GLCCI1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GLCCI1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V10, continuous
D162V11, continuous
                  vv
clus               R0 R1 R2 RX
  GLCCI1 MUTATED    4  2  0  0
  GLCCI1 WILD-TYPE 76 33  4  2
D162V12, multiclass
    clus
vv   GLCCI1 MUTATED GLCCI1 WILD-TYPE
  R0              4               76
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GLCCI1 MUTATED       0                         0     6
  GLCCI1 WILD-TYPE     6                         5   108
D162V14, multiclass
                           clus
vv                          GLCCI1 MUTATED GLCCI1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V15, binary
                  cls
clus                0  1
  GLCCI1 MUTATED    0  5
  GLCCI1 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLCCI1 MUTATED      0    5
  GLCCI1 WILD-TYPE    5   86
                        clus
vv                       GLCCI1 MUTATED GLCCI1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(163) Variable = WASF3 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2              0  1
  WASF3 MUTATED    4  4
  WASF3 WILD-TYPE 59 58
  WASF3 MUTATED WASF3 WILD-TYPE 
              8             117 
  WASF3 MUTATED WASF3 WILD-TYPE 
              4              58 
$`WASF3 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABF TCGA-2J-AABK TCGA-HZ-8637 TCGA-IB-A5SP TCGA-IB-A7M4 
       12.92        22.72        15.91        17.00        15.85        15.88 
TCGA-OE-A75W TCGA-Q3-A5QY 
        8.78        13.68 

$`WASF3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       19.96        22.22        42.31        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       19.82        36.69        41.33        15.19        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-AA2A TCGA-RB-A7B8 
       13.28         7.56        12.46        10.29         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  WASF3 MUTATED WASF3 WILD-TYPE 
           8.78            0.23 
  WASF3 MUTATED WASF3 WILD-TYPE 
          22.72           90.12 
  WASF3 MUTATED WASF3 WILD-TYPE 
         15.865          15.190 
[1] "8.8 - 22.7 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D163V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WASF3 MUTATED         0        0        0         2         6         0
  WASF3 WILD-TYPE       1        3       12        17        76         4
                 vv
clus              STAGE IV
  WASF3 MUTATED          0
  WASF3 WILD-TYPE        3
D163V3, multiclass
           clus
vv          WASF3 MUTATED WASF3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  WASF3 MUTATED    0  0     8
  WASF3 WILD-TYPE  5 17    94
D163V4, multiclass
       clus
vv      WASF3 MUTATED WASF3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V5, binary
                 cls
clus               0  1
  WASF3 MUTATED    2  6
  WASF3 WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      2    6
  WASF3 WILD-TYPE   33   83
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D163V6, binary
                 cls
clus               0  1
  WASF3 MUTATED    4  0
  WASF3 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      4    0
  WASF3 WILD-TYPE   53    3
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D163V7, binary
                 cls
clus               0  1
  WASF3 MUTATED    2  6
  WASF3 WILD-TYPE 49 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      2    6
  WASF3 WILD-TYPE   49   69
        clus
vv       WASF3 MUTATED WASF3 WILD-TYPE
  FEMALE             2              49
  MALE               6              69
[1] 2 2
[1] FALSE
D163V8, binary
                 cls
clus               0  1
  WASF3 MUTATED    4  4
  WASF3 WILD-TYPE 84 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      4    4
  WASF3 WILD-TYPE   84   26
     clus
vv    WASF3 MUTATED WASF3 WILD-TYPE
  NO              4              84
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WASF3 MUTATED                                     8
  WASF3 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WASF3 MUTATED                                       0
  WASF3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WASF3 MUTATED                                                  0
  WASF3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  WASF3 MUTATED                                     0
  WASF3 WILD-TYPE                                   1
D163V9, multiclass
                                                  clus
vv                                                 WASF3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 WASF3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V10, continuous
D163V11, continuous
                 vv
clus              R0 R1 R2 RX
  WASF3 MUTATED    4  4  0  0
  WASF3 WILD-TYPE 76 31  4  2
D163V12, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  R0             4              76
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WASF3 MUTATED       0                         1     7
  WASF3 WILD-TYPE     6                         4   107
D163V14, multiclass
                           clus
vv                          WASF3 MUTATED WASF3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V15, binary
                 cls
clus               0  1
  WASF3 MUTATED    1  4
  WASF3 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      1    4
  WASF3 WILD-TYPE    4   87
                        clus
vv                       WASF3 MUTATED WASF3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(164) Variable = WDR5 MUTATION ANALYSIS
D164V1, survival
                sevent
clus2             0  1
  WDR5 MUTATED    3  1
  WDR5 WILD-TYPE 60 61
  WDR5 MUTATED WDR5 WILD-TYPE 
             4            121 
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             61 
$`WDR5 MUTATED`
TCGA-3A-A9IS TCGA-HZ-A77O TCGA-RB-AA9M TCGA-RL-AAAS 
       32.81         5.26         9.40         0.30 

$`WDR5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  WDR5 MUTATED WDR5 WILD-TYPE 
          0.30           0.23 
  WDR5 MUTATED WDR5 WILD-TYPE 
         32.81          90.12 
  WDR5 MUTATED WDR5 WILD-TYPE 
          7.33          15.32 
[1] "0.3 - 32.8 (7.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D164V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WDR5 MUTATED         0        0        2         0         2         0
  WDR5 WILD-TYPE       1        3       10        19        80         4
                vv
clus             STAGE IV
  WDR5 MUTATED          0
  WDR5 WILD-TYPE        3
D164V3, multiclass
           clus
vv          WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  WDR5 MUTATED     1   3     0
  WDR5 WILD-TYPE   4  14   102
D164V4, multiclass
       clus
vv      WDR5 MUTATED WDR5 WILD-TYPE
  T1               1              4
  T2               3             14
  T3+T4            0            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V5, binary
                cls
clus              0  1
  WDR5 MUTATED    2  2
  WDR5 WILD-TYPE 33 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      2    2
  WDR5 WILD-TYPE   33   87
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            2             33
  1            2             87
[1] 2 2
[1] FALSE
D164V6, binary
                cls
clus              0  1
  WDR5 MUTATED    1  0
  WDR5 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      1    0
  WDR5 WILD-TYPE   56    3
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D164V7, binary
                cls
clus              0  1
  WDR5 MUTATED    2  2
  WDR5 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      2    2
  WDR5 WILD-TYPE   49   73
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D164V8, binary
                cls
clus              0  1
  WDR5 MUTATED    3  1
  WDR5 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      3    1
  WDR5 WILD-TYPE   85   29
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDR5 MUTATED                                     3
  WDR5 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDR5 MUTATED                                       1
  WDR5 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDR5 MUTATED                                                  0
  WDR5 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  WDR5 MUTATED                                     0
  WDR5 WILD-TYPE                                   1
D164V9, multiclass
                                                  clus
vv                                                 WDR5 MUTATED WDR5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V10, continuous
D164V11, continuous
                vv
clus             R0 R1 R2 RX
  WDR5 MUTATED    4  0  0  0
  WDR5 WILD-TYPE 76 35  4  2
D164V12, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            4             76
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR5 MUTATED       0                         0     4
  WDR5 WILD-TYPE     6                         5   110
D164V14, multiclass
                           clus
vv                          WDR5 MUTATED WDR5 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V15, binary
                cls
clus              0  1
  WDR5 MUTATED    0  4
  WDR5 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      0    4
  WDR5 WILD-TYPE    5   87
                        clus
vv                       WDR5 MUTATED WDR5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(165) Variable = FGF10 MUTATION ANALYSIS
D165V1, survival
                 sevent
clus2              0  1
  FGF10 MUTATED    2  4
  FGF10 WILD-TYPE 61 58
  FGF10 MUTATED FGF10 WILD-TYPE 
              6             119 
  FGF10 MUTATED FGF10 WILD-TYPE 
              4              58 
$`FGF10 MUTATED`
TCGA-LB-A7SX TCGA-FB-AAQ1 TCGA-HZ-A49I TCGA-IB-A6UF TCGA-XD-AAUI TCGA-YB-A89D 
       12.92         4.04        10.13        21.90        12.03        11.51 

$`FGF10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  FGF10 MUTATED FGF10 WILD-TYPE 
           4.04            0.23 
  FGF10 MUTATED FGF10 WILD-TYPE 
          21.90           90.12 
  FGF10 MUTATED FGF10 WILD-TYPE 
          11.77           15.35 
[1] "4.0 - 21.9 (11.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.1"
D165V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FGF10 MUTATED         0        0        0         0         6         0
  FGF10 WILD-TYPE       1        3       12        19        76         4
                 vv
clus              STAGE IV
  FGF10 MUTATED          0
  FGF10 WILD-TYPE        3
D165V3, multiclass
           clus
vv          FGF10 MUTATED FGF10 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FGF10 MUTATED    0  0     6
  FGF10 WILD-TYPE  5 17    96
D165V4, multiclass
       clus
vv      FGF10 MUTATED FGF10 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V5, binary
                 cls
clus               0  1
  FGF10 MUTATED    0  6
  FGF10 WILD-TYPE 35 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF10 MUTATED      0    6
  FGF10 WILD-TYPE   35   83
   clus
vv  FGF10 MUTATED FGF10 WILD-TYPE
  0             0              35
  1             6              83
[1] 2 2
[1] FALSE
D165V6, binary
                 cls
clus               0  1
  FGF10 MUTATED    1  0
  FGF10 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF10 MUTATED      1    0
  FGF10 WILD-TYPE   56    3
   clus
vv  FGF10 MUTATED FGF10 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D165V7, binary
                 cls
clus               0  1
  FGF10 MUTATED    2  4
  FGF10 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF10 MUTATED      2    4
  FGF10 WILD-TYPE   49   71
        clus
vv       FGF10 MUTATED FGF10 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D165V8, binary
                 cls
clus               0  1
  FGF10 MUTATED    4  2
  FGF10 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF10 MUTATED      4    2
  FGF10 WILD-TYPE   84   28
     clus
vv    FGF10 MUTATED FGF10 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FGF10 MUTATED                                     6
  FGF10 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FGF10 MUTATED                                       0
  FGF10 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FGF10 MUTATED                                                  0
  FGF10 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FGF10 MUTATED                                     0
  FGF10 WILD-TYPE                                   1
D165V9, multiclass
                                                  clus
vv                                                 FGF10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FGF10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V10, continuous
[1] "Remove cluster labels:" "FGF10 MUTATED"         
clus
  FGF10 MUTATED FGF10 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" "FGF10 WILD-TYPE" 
     TCGA-YY-A8LH 
"FGF10 WILD-TYPE" 
D165V11, continuous
                 vv
clus              R0 R1 R2 RX
  FGF10 MUTATED    1  5  0  0
  FGF10 WILD-TYPE 79 30  4  2
D165V12, multiclass
    clus
vv   FGF10 MUTATED FGF10 WILD-TYPE
  R0             1              79
  R1             5              30
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGF10 MUTATED       0                         1     5
  FGF10 WILD-TYPE     6                         4   109
D165V14, multiclass
                           clus
vv                          FGF10 MUTATED FGF10 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V15, binary
                 cls
clus               0  1
  FGF10 MUTATED    0  6
  FGF10 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF10 MUTATED      0    6
  FGF10 WILD-TYPE    5   85
                        clus
vv                       FGF10 MUTATED FGF10 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(166) Variable = FAM155B MUTATION ANALYSIS
D166V1, survival
                   sevent
clus2                0  1
  FAM155B MUTATED    2  2
  FAM155B WILD-TYPE 61 60
  FAM155B MUTATED FAM155B WILD-TYPE 
                4               121 
  FAM155B MUTATED FAM155B WILD-TYPE 
                2                60 
$`FAM155B MUTATED`
TCGA-3A-A9IJ TCGA-FZ-5926 TCGA-US-A779 TCGA-XN-A8T3 
       60.95        17.79        16.80        31.27 

$`FAM155B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        39.98         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FAM155B MUTATED FAM155B WILD-TYPE 
            16.80              0.23 
  FAM155B MUTATED FAM155B WILD-TYPE 
            60.95             90.12 
  FAM155B MUTATED FAM155B WILD-TYPE 
            24.53             15.12 
[1] "16.8 - 61.0 (24.5)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.5"
D166V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM155B MUTATED         0        0        2         0         1         1
  FAM155B WILD-TYPE       1        3       10        19        81         3
                   vv
clus                STAGE IV
  FAM155B MUTATED          0
  FAM155B WILD-TYPE        3
D166V3, multiclass
           clus
vv          FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               0                19
  STAGE IIB               1                81
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  FAM155B MUTATED     0   2     2
  FAM155B WILD-TYPE   5  15   100
D166V4, multiclass
       clus
vv      FAM155B MUTATED FAM155B WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V5, binary
                   cls
clus                 0  1
  FAM155B MUTATED    2  2
  FAM155B WILD-TYPE 33 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      2    2
  FAM155B WILD-TYPE   33   87
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0               2                33
  1               2                87
[1] 2 2
[1] FALSE
D166V6, binary
                   cls
clus                 0  1
  FAM155B MUTATED    2  0
  FAM155B WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      2    0
  FAM155B WILD-TYPE   55    3
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D166V7, binary
                   cls
clus                 0  1
  FAM155B MUTATED    2  2
  FAM155B WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      2    2
  FAM155B WILD-TYPE   49   73
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D166V8, binary
                   cls
clus                 0  1
  FAM155B MUTATED    2  1
  FAM155B WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      2    1
  FAM155B WILD-TYPE   86   29
     clus
vv    FAM155B MUTATED FAM155B WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM155B MUTATED                                     3
  FAM155B WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM155B MUTATED                                       1
  FAM155B WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM155B MUTATED                                                  0
  FAM155B WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM155B MUTATED                                     0
  FAM155B WILD-TYPE                                   1
D166V9, multiclass
                                                  clus
vv                                                 FAM155B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 FAM155B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V10, continuous
[1] "Remove cluster labels:" "FAM155B MUTATED"       
clus
  FAM155B MUTATED FAM155B WILD-TYPE 
                1                38 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
D166V11, continuous
[1] "Remove cluster labels:" "FAM155B MUTATED"       
clus
  FAM155B MUTATED FAM155B WILD-TYPE 
                1                32 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" "FAM155B WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  FAM155B MUTATED    3  1  0  0
  FAM155B WILD-TYPE 77 34  4  2
D166V12, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM155B MUTATED       0                         0     4
  FAM155B WILD-TYPE     6                         5   110
D166V14, multiclass
                           clus
vv                          FAM155B MUTATED FAM155B WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V15, binary
                   cls
clus                 0  1
  FAM155B MUTATED    1  3
  FAM155B WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      1    3
  FAM155B WILD-TYPE    4   88
                        clus
vv                       FAM155B MUTATED FAM155B WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(167) Variable = RBM12 MUTATION ANALYSIS
D167V1, survival
                 sevent
clus2              0  1
  RBM12 MUTATED    2  4
  RBM12 WILD-TYPE 61 58
  RBM12 MUTATED RBM12 WILD-TYPE 
              6             119 
  RBM12 MUTATED RBM12 WILD-TYPE 
              4              58 
$`RBM12 MUTATED`
TCGA-FB-AAQ6 TCGA-3A-A9IZ TCGA-F2-A8YN TCGA-FB-AAQ3 TCGA-IB-AAUP TCGA-RB-A7B8 
        8.02        10.13        17.00         1.02        14.17        15.32 

$`RBM12 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         5.03        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  RBM12 MUTATED RBM12 WILD-TYPE 
           1.02            0.23 
  RBM12 MUTATED RBM12 WILD-TYPE 
          17.00           90.12 
  RBM12 MUTATED RBM12 WILD-TYPE 
          12.15           15.35 
[1] "1.0 - 17.0 (12.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D167V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM12 MUTATED         0        1        0         1         4         0
  RBM12 WILD-TYPE       1        2       12        18        78         4
                 vv
clus              STAGE IV
  RBM12 MUTATED          0
  RBM12 WILD-TYPE        3
D167V3, multiclass
           clus
vv          RBM12 MUTATED RBM12 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM12 MUTATED    1  0     5
  RBM12 WILD-TYPE  4 17    97
D167V4, multiclass
       clus
vv      RBM12 MUTATED RBM12 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V5, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  4
  RBM12 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    4
  RBM12 WILD-TYPE   33   85
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D167V6, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  0
  RBM12 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    0
  RBM12 WILD-TYPE   55    3
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D167V7, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  4
  RBM12 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    4
  RBM12 WILD-TYPE   49   71
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D167V8, binary
                 cls
clus               0  1
  RBM12 MUTATED    6  0
  RBM12 WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      6    0
  RBM12 WILD-TYPE   82   30
     clus
vv    RBM12 MUTATED RBM12 WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM12 MUTATED                                     5
  RBM12 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM12 MUTATED                                       1
  RBM12 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM12 MUTATED                                                  0
  RBM12 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM12 MUTATED                                     0
  RBM12 WILD-TYPE                                   1
D167V9, multiclass
                                                  clus
vv                                                 RBM12 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RBM12 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V10, continuous
[1] "Remove cluster labels:" "RBM12 MUTATED"         
clus
  RBM12 MUTATED RBM12 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
D167V11, continuous
                 vv
clus              R0 R1 R2 RX
  RBM12 MUTATED    3  3  0  0
  RBM12 WILD-TYPE 77 32  4  2
D167V12, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0             3              77
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM12 MUTATED       0                         0     6
  RBM12 WILD-TYPE     6                         5   108
D167V14, multiclass
                           clus
vv                          RBM12 MUTATED RBM12 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V15, binary
                 cls
clus               0  1
  RBM12 MUTATED    1  5
  RBM12 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      1    5
  RBM12 WILD-TYPE    4   86
                        clus
vv                       RBM12 MUTATED RBM12 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(168) Variable = ZNF337 MUTATION ANALYSIS
D168V1, survival
                  sevent
clus2               0  1
  ZNF337 MUTATED    6  3
  ZNF337 WILD-TYPE 57 59
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               9              116 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               3               59 
$`ZNF337 MUTATED`
TCGA-3A-A9IJ TCGA-2L-AAQI TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-7652 
       60.95         3.39        22.06         8.28        19.82        36.69 
TCGA-IB-AAUU TCGA-US-A77G TCGA-XN-A8T5 
        8.05         0.39        23.67 

$`ZNF337 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J 
       15.32         9.40         0.30        39.98        16.80        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF337 MUTATED ZNF337 WILD-TYPE 
            0.39             0.23 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
           60.95            90.12 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
          19.820           15.205 
[1] "0.4 - 61.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D168V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF337 MUTATED         0        0        2         2         6         0
  ZNF337 WILD-TYPE       1        3       10        17        76         4
                  vv
clus               STAGE IV
  ZNF337 MUTATED          0
  ZNF337 WILD-TYPE        3
D168V3, multiclass
           clus
vv          ZNF337 MUTATED ZNF337 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              2               17
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF337 MUTATED    0  2     8
  ZNF337 WILD-TYPE  5 15    94
D168V4, multiclass
       clus
vv      ZNF337 MUTATED ZNF337 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V5, binary
                  cls
clus                0  1
  ZNF337 MUTATED    4  6
  ZNF337 WILD-TYPE 31 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      4    6
  ZNF337 WILD-TYPE   31   83
   clus
vv  ZNF337 MUTATED ZNF337 WILD-TYPE
  0              4               31
  1              6               83
[1] 2 2
[1] FALSE
D168V6, binary
                  cls
clus                0  1
  ZNF337 MUTATED    4  0
  ZNF337 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      4    0
  ZNF337 WILD-TYPE   53    3
   clus
vv  ZNF337 MUTATED ZNF337 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D168V7, binary
                  cls
clus                0  1
  ZNF337 MUTATED    3  7
  ZNF337 WILD-TYPE 48 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      3    7
  ZNF337 WILD-TYPE   48   68
        clus
vv       ZNF337 MUTATED ZNF337 WILD-TYPE
  FEMALE              3               48
  MALE                7               68
[1] 2 2
[1] FALSE
D168V8, binary
                  cls
clus                0  1
  ZNF337 MUTATED    8  1
  ZNF337 WILD-TYPE 80 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      8    1
  ZNF337 WILD-TYPE   80   29
     clus
vv    ZNF337 MUTATED ZNF337 WILD-TYPE
  NO               8               80
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF337 MUTATED                                     7
  ZNF337 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF337 MUTATED                                       3
  ZNF337 WILD-TYPE                                    15
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF337 MUTATED                                                  0
  ZNF337 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF337 MUTATED                                     0
  ZNF337 WILD-TYPE                                   1
D168V9, multiclass
                                                  clus
vv                                                 ZNF337 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF337 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V10, continuous
D168V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF337 MUTATED    6  3  1  0
  ZNF337 WILD-TYPE 74 32  3  2
D168V12, multiclass
    clus
vv   ZNF337 MUTATED ZNF337 WILD-TYPE
  R0              6               74
  R1              3               32
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF337 MUTATED       2                         0     8
  ZNF337 WILD-TYPE     4                         5   106
D168V14, multiclass
                           clus
vv                          ZNF337 MUTATED ZNF337 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V15, binary
                  cls
clus                0  1
  ZNF337 MUTATED    1  7
  ZNF337 WILD-TYPE  4 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      1    7
  ZNF337 WILD-TYPE    4   84
                        clus
vv                       ZNF337 MUTATED ZNF337 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(169) Variable = C16ORF46 MUTATION ANALYSIS
D169V1, survival
                    sevent
clus2                 0  1
  C16ORF46 MUTATED    2  2
  C16ORF46 WILD-TYPE 61 60
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 4                121 
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 2                 60 
$`C16ORF46 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-US-A77J TCGA-XD-AAUG 
       10.85        19.82        18.67        13.81 

$`C16ORF46 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUH 
        9.40         0.30        39.98        16.80         0.39        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
             10.85               0.23 
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
             19.82              90.12 
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
             16.24              15.22 
[1] "10.8 - 19.8 (16.2)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D169V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C16ORF46 MUTATED         0        0        0         0         3         0
  C16ORF46 WILD-TYPE       1        3       12        19        79         4
                    vv
clus                 STAGE IV
  C16ORF46 MUTATED          1
  C16ORF46 WILD-TYPE        2
D169V3, multiclass
           clus
vv          C16ORF46 MUTATED C16ORF46 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 1                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C16ORF46 MUTATED    0  0     4
  C16ORF46 WILD-TYPE  5 17    98
D169V4, multiclass
       clus
vv      C16ORF46 MUTATED C16ORF46 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V5, binary
                    cls
clus                  0  1
  C16ORF46 MUTATED    0  4
  C16ORF46 WILD-TYPE 35 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF46 MUTATED      0    4
  C16ORF46 WILD-TYPE   35   85
   clus
vv  C16ORF46 MUTATED C16ORF46 WILD-TYPE
  0                0                 35
  1                4                 85
[1] 2 2
[1] FALSE
D169V6, binary
                    cls
clus                  0  1
  C16ORF46 MUTATED    1  1
  C16ORF46 WILD-TYPE 56  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF46 MUTATED      1    1
  C16ORF46 WILD-TYPE   56    2
   clus
vv  C16ORF46 MUTATED C16ORF46 WILD-TYPE
  0                1                 56
  1                1                  2
[1] 2 2
[1] FALSE
D169V7, binary
                    cls
clus                  0  1
  C16ORF46 MUTATED    3  1
  C16ORF46 WILD-TYPE 48 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF46 MUTATED      3    1
  C16ORF46 WILD-TYPE   48   74
        clus
vv       C16ORF46 MUTATED C16ORF46 WILD-TYPE
  FEMALE                3                 48
  MALE                  1                 74
[1] 2 2
[1] FALSE
D169V8, binary
                    cls
clus                  0  1
  C16ORF46 MUTATED    3  0
  C16ORF46 WILD-TYPE 85 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF46 MUTATED      3    0
  C16ORF46 WILD-TYPE   85   30
     clus
vv    C16ORF46 MUTATED C16ORF46 WILD-TYPE
  NO                 3                 85
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C16ORF46 MUTATED                                     3
  C16ORF46 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C16ORF46 MUTATED                                       1
  C16ORF46 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C16ORF46 MUTATED                                                  0
  C16ORF46 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C16ORF46 MUTATED                                     0
  C16ORF46 WILD-TYPE                                   1
D169V9, multiclass
                                                  clus
vv                                                 C16ORF46 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C16ORF46 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V10, continuous
[1] "Remove cluster labels:" "C16ORF46 MUTATED"      
clus
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
D169V11, continuous
[1] "Remove cluster labels:" "C16ORF46 MUTATED"      
clus
  C16ORF46 MUTATED C16ORF46 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C16ORF46 WILD-TYPE" "C16ORF46 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C16ORF46 MUTATED    4  0  0  0
  C16ORF46 WILD-TYPE 76 35  4  2
D169V12, multiclass
    clus
vv   C16ORF46 MUTATED C16ORF46 WILD-TYPE
  R0                4                 76
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C16ORF46 MUTATED       0                         0     4
  C16ORF46 WILD-TYPE     6                         5   110
D169V14, multiclass
                           clus
vv                          C16ORF46 MUTATED C16ORF46 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V15, binary
                    cls
clus                  0  1
  C16ORF46 MUTATED    0  4
  C16ORF46 WILD-TYPE  5 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF46 MUTATED      0    4
  C16ORF46 WILD-TYPE    5   87
                        clus
vv                       C16ORF46 MUTATED C16ORF46 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(170) Variable = TAOK2 MUTATION ANALYSIS
D170V1, survival
                 sevent
clus2              0  1
  TAOK2 MUTATED    1  7
  TAOK2 WILD-TYPE 62 55
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              8             117 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              7              55 
$`TAOK2 MUTATED`
TCGA-2J-AABH TCGA-3A-A9IB TCGA-3A-A9IC TCGA-FB-A5VM TCGA-HZ-8637 TCGA-IB-7651 
       42.31         7.36        24.26        16.37        17.00        19.82 
TCGA-IB-A5SO TCGA-IB-A7LX 
       12.00         8.22 

$`TAOK2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IH 
       12.95         9.60        45.47        43.50        20.84        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TAOK2 MUTATED TAOK2 WILD-TYPE 
           7.36            0.23 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
          42.31           90.12 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
         16.685          15.190 
[1] "7.4 - 42.3 (16.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D170V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TAOK2 MUTATED         0        0        1         1         6         0
  TAOK2 WILD-TYPE       1        3       11        18        76         4
                 vv
clus              STAGE IV
  TAOK2 MUTATED          0
  TAOK2 WILD-TYPE        3
D170V3, multiclass
           clus
vv          TAOK2 MUTATED TAOK2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TAOK2 MUTATED    0  1     7
  TAOK2 WILD-TYPE  5 16    95
D170V4, multiclass
       clus
vv      TAOK2 MUTATED TAOK2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V5, binary
                 cls
clus               0  1
  TAOK2 MUTATED    2  6
  TAOK2 WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      2    6
  TAOK2 WILD-TYPE   33   83
   clus
vv  TAOK2 MUTATED TAOK2 WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D170V6, binary
                 cls
clus               0  1
  TAOK2 MUTATED    4  0
  TAOK2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      4    0
  TAOK2 WILD-TYPE   53    3
   clus
vv  TAOK2 MUTATED TAOK2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D170V7, binary
                 cls
clus               0  1
  TAOK2 MUTATED    4  4
  TAOK2 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      4    4
  TAOK2 WILD-TYPE   47   71
        clus
vv       TAOK2 MUTATED TAOK2 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D170V8, binary
                 cls
clus               0  1
  TAOK2 MUTATED    6  2
  TAOK2 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      6    2
  TAOK2 WILD-TYPE   82   28
     clus
vv    TAOK2 MUTATED TAOK2 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TAOK2 MUTATED                                     7
  TAOK2 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TAOK2 MUTATED                                       1
  TAOK2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TAOK2 MUTATED                                                  0
  TAOK2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TAOK2 MUTATED                                     0
  TAOK2 WILD-TYPE                                   1
D170V9, multiclass
                                                  clus
vv                                                 TAOK2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TAOK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V10, continuous
D170V11, continuous
                 vv
clus              R0 R1 R2 RX
  TAOK2 MUTATED    8  0  0  0
  TAOK2 WILD-TYPE 72 35  4  2
D170V12, multiclass
    clus
vv   TAOK2 MUTATED TAOK2 WILD-TYPE
  R0             8              72
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAOK2 MUTATED       0                         0     8
  TAOK2 WILD-TYPE     6                         5   106
D170V14, multiclass
                           clus
vv                          TAOK2 MUTATED TAOK2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V15, binary
                 cls
clus               0  1
  TAOK2 MUTATED    1  5
  TAOK2 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      1    5
  TAOK2 WILD-TYPE    4   86
                        clus
vv                       TAOK2 MUTATED TAOK2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(171) Variable = DHX9 MUTATION ANALYSIS
D171V1, survival
                sevent
clus2             0  1
  DHX9 MUTATED    5  2
  DHX9 WILD-TYPE 58 60
  DHX9 MUTATED DHX9 WILD-TYPE 
             7            118 
  DHX9 MUTATED DHX9 WILD-TYPE 
             2             60 
$`DHX9 MUTATED`
TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-FB-AAPS TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-A6UF 
        1.08        17.26         7.50        17.00        19.82        21.90 
TCGA-LB-A8F3 
       12.46 

$`DHX9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        15.12        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  DHX9 MUTATED DHX9 WILD-TYPE 
          1.08           0.23 
  DHX9 MUTATED DHX9 WILD-TYPE 
         21.90          90.12 
  DHX9 MUTATED DHX9 WILD-TYPE 
        17.000         15.205 
[1] "1.1 - 21.9 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D171V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DHX9 MUTATED         0        0        0         1         6         0
  DHX9 WILD-TYPE       1        3       12        18        76         4
                vv
clus             STAGE IV
  DHX9 MUTATED          0
  DHX9 WILD-TYPE        3
D171V3, multiclass
           clus
vv          DHX9 MUTATED DHX9 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  DHX9 MUTATED    0  1     6
  DHX9 WILD-TYPE  5 16    96
D171V4, multiclass
       clus
vv      DHX9 MUTATED DHX9 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V5, binary
                cls
clus              0  1
  DHX9 MUTATED    1  6
  DHX9 WILD-TYPE 34 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      1    6
  DHX9 WILD-TYPE   34   83
   clus
vv  DHX9 MUTATED DHX9 WILD-TYPE
  0            1             34
  1            6             83
[1] 2 2
[1] FALSE
D171V6, binary
                cls
clus              0  1
  DHX9 MUTATED    2  0
  DHX9 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      2    0
  DHX9 WILD-TYPE   55    3
   clus
vv  DHX9 MUTATED DHX9 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D171V7, binary
                cls
clus              0  1
  DHX9 MUTATED    6  1
  DHX9 WILD-TYPE 45 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      6    1
  DHX9 WILD-TYPE   45   74
        clus
vv       DHX9 MUTATED DHX9 WILD-TYPE
  FEMALE            6             45
  MALE              1             74
[1] 2 2
[1] FALSE
D171V8, binary
                cls
clus              0  1
  DHX9 MUTATED    2  4
  DHX9 WILD-TYPE 86 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      2    4
  DHX9 WILD-TYPE   86   26
     clus
vv    DHX9 MUTATED DHX9 WILD-TYPE
  NO             2             86
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DHX9 MUTATED                                     6
  DHX9 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DHX9 MUTATED                                       1
  DHX9 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DHX9 MUTATED                                                  0
  DHX9 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  DHX9 MUTATED                                     0
  DHX9 WILD-TYPE                                   1
D171V9, multiclass
                                                  clus
vv                                                 DHX9 MUTATED DHX9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V10, continuous
D171V11, continuous
                vv
clus             R0 R1 R2 RX
  DHX9 MUTATED    5  2  0  0
  DHX9 WILD-TYPE 75 33  4  2
D171V12, multiclass
    clus
vv   DHX9 MUTATED DHX9 WILD-TYPE
  R0            5             75
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHX9 MUTATED       0                         1     6
  DHX9 WILD-TYPE     6                         4   108
D171V14, multiclass
                           clus
vv                          DHX9 MUTATED DHX9 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V15, binary
                cls
clus              0  1
  DHX9 MUTATED    1  6
  DHX9 WILD-TYPE  4 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  DHX9 MUTATED      1    6
  DHX9 WILD-TYPE    4   85
                        clus
vv                       DHX9 MUTATED DHX9 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(172) Variable = ZNF608 MUTATION ANALYSIS
D172V1, survival
                  sevent
clus2               0  1
  ZNF608 MUTATED    5  3
  ZNF608 WILD-TYPE 58 59
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               8              117 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               3               59 
$`ZNF608 MUTATED`
TCGA-2J-AAB8 TCGA-FB-AAPU TCGA-FB-AAQ2 TCGA-HV-A7OL TCGA-HZ-A9TJ TCGA-IB-7651 
        2.63        12.53         5.03         8.28        19.82        19.82 
TCGA-IB-AAUS TCGA-Q3-A5QY 
        7.40        13.68 

$`ZNF608 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 
       37.15         7.50        23.54        15.55         4.04         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 
       17.00        10.13         5.26        10.85         0.23        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29         8.78         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZNF608 MUTATED ZNF608 WILD-TYPE 
            2.63             0.23 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           19.82            90.12 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
          10.405           15.350 
[1] "2.6 - 19.8 (10.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D172V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF608 MUTATED         0        0        0         2         5         0
  ZNF608 WILD-TYPE       1        3       12        17        77         4
                  vv
clus               STAGE IV
  ZNF608 MUTATED          1
  ZNF608 WILD-TYPE        2
D172V3, multiclass
           clus
vv          ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF608 MUTATED    0  0     8
  ZNF608 WILD-TYPE  5 17    94
D172V4, multiclass
       clus
vv      ZNF608 MUTATED ZNF608 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V5, binary
                  cls
clus                0  1
  ZNF608 MUTATED    3  5
  ZNF608 WILD-TYPE 32 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      3    5
  ZNF608 WILD-TYPE   32   84
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0              3               32
  1              5               84
[1] 2 2
[1] FALSE
D172V6, binary
                  cls
clus                0  1
  ZNF608 MUTATED    3  1
  ZNF608 WILD-TYPE 54  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      3    1
  ZNF608 WILD-TYPE   54    2
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0              3               54
  1              1                2
[1] 2 2
[1] FALSE
D172V7, binary
                  cls
clus                0  1
  ZNF608 MUTATED    4  4
  ZNF608 WILD-TYPE 47 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      4    4
  ZNF608 WILD-TYPE   47   71
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              4               47
  MALE                4               71
[1] 2 2
[1] FALSE
D172V8, binary
                  cls
clus                0  1
  ZNF608 MUTATED    7  0
  ZNF608 WILD-TYPE 81 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      7    0
  ZNF608 WILD-TYPE   81   30
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               7               81
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF608 MUTATED                                     7
  ZNF608 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF608 MUTATED                                       1
  ZNF608 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF608 MUTATED                                                  0
  ZNF608 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF608 MUTATED                                     0
  ZNF608 WILD-TYPE                                   1
D172V9, multiclass
                                                  clus
vv                                                 ZNF608 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF608 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V10, continuous
[1] "Remove cluster labels:" "ZNF608 MUTATED"        
clus
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUU 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-YY-A8LH 
"ZNF608 WILD-TYPE" 
D172V11, continuous
[1] "Remove cluster labels:" "ZNF608 MUTATED"        
clus
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF608 MUTATED    3  4  1  0
  ZNF608 WILD-TYPE 77 31  3  2
D172V12, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0              3               77
  R1              4               31
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF608 MUTATED       2                         0     6
  ZNF608 WILD-TYPE     4                         5   108
D172V14, multiclass
                           clus
vv                          ZNF608 MUTATED ZNF608 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V15, binary
                  cls
clus                0  1
  ZNF608 MUTATED    0  6
  ZNF608 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0    6
  ZNF608 WILD-TYPE    5   85
                        clus
vv                       ZNF608 MUTATED ZNF608 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(173) Variable = SLITRK5 MUTATION ANALYSIS
D173V1, survival
                   sevent
clus2                0  1
  SLITRK5 MUTATED   10  5
  SLITRK5 WILD-TYPE 53 57
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
               15               110 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                5                57 
$`SLITRK5 MUTATED`
TCGA-3A-A9IJ TCGA-F2-A44G TCGA-2J-AAB1 TCGA-2J-AABA TCGA-2J-AABH TCGA-2L-AAQI 
       60.95         7.66         2.17        19.96        42.31         3.39 
TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-HV-A7OP TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-AAUP 
       36.26        24.43        32.15        10.85        19.82        14.17 
TCGA-LB-A8F3 TCGA-XN-A8T3 TCGA-YB-A89D 
       12.46        31.27        11.51 

$`SLITRK5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        58.98        90.12         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        22.22        22.72 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        15.22         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
       22.49        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       15.06        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY 
       18.67        13.81        12.99        12.03        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
             2.17              0.23 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
            60.95             90.12 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
           19.820            15.205 
[1] "2.2 - 61.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D173V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLITRK5 MUTATED         0        0        3         2        10         0
  SLITRK5 WILD-TYPE       1        3        9        17        72         4
                   vv
clus                STAGE IV
  SLITRK5 MUTATED          0
  SLITRK5 WILD-TYPE        3
D173V3, multiclass
           clus
vv          SLITRK5 MUTATED SLITRK5 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                3                 9
  STAGE IIA               2                17
  STAGE IIB              10                72
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLITRK5 MUTATED    0  3    12
  SLITRK5 WILD-TYPE  5 14    90
D173V4, multiclass
       clus
vv      SLITRK5 MUTATED SLITRK5 WILD-TYPE
  T1                  0                 5
  T2                  3                14
  T3+T4              12                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V5, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    5 10
  SLITRK5 WILD-TYPE 30 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      5   10
  SLITRK5 WILD-TYPE   30   79
   clus
vv  SLITRK5 MUTATED SLITRK5 WILD-TYPE
  0               5                30
  1              10                79
[1] 2 2
[1] FALSE
D173V6, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    8  0
  SLITRK5 WILD-TYPE 49  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      8    0
  SLITRK5 WILD-TYPE   49    3
   clus
vv  SLITRK5 MUTATED SLITRK5 WILD-TYPE
  0               8                49
  1               0                 3
[1] 2 2
[1] FALSE
D173V7, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    4 11
  SLITRK5 WILD-TYPE 47 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      4   11
  SLITRK5 WILD-TYPE   47   64
        clus
vv       SLITRK5 MUTATED SLITRK5 WILD-TYPE
  FEMALE               4                47
  MALE                11                64
[1] 2 2
[1] FALSE
D173V8, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED   10  5
  SLITRK5 WILD-TYPE 78 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED     10    5
  SLITRK5 WILD-TYPE   78   25
     clus
vv    SLITRK5 MUTATED SLITRK5 WILD-TYPE
  NO               10                78
  YES               5                25
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLITRK5 MUTATED                                     9
  SLITRK5 WILD-TYPE                                  96
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLITRK5 MUTATED                                       6
  SLITRK5 WILD-TYPE                                    12
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLITRK5 MUTATED                                                  0
  SLITRK5 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLITRK5 MUTATED                                     0
  SLITRK5 WILD-TYPE                                   1
D173V9, multiclass
                                                  clus
vv                                                 SLITRK5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLITRK5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           12
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V10, continuous
D173V11, continuous
                   vv
clus                R0 R1 R2 RX
  SLITRK5 MUTATED   10  5  0  0
  SLITRK5 WILD-TYPE 70 30  4  2
D173V12, multiclass
    clus
vv   SLITRK5 MUTATED SLITRK5 WILD-TYPE
  R0              10                70
  R1               5                30
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLITRK5 MUTATED       1                         1    13
  SLITRK5 WILD-TYPE     5                         4   101
D173V14, multiclass
                           clus
vv                          SLITRK5 MUTATED SLITRK5 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                  13               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V15, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    1  9
  SLITRK5 WILD-TYPE  4 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      1    9
  SLITRK5 WILD-TYPE    4   82
                        clus
vv                       SLITRK5 MUTATED SLITRK5 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               9                82
[1] 2 2
[1] FALSE

Clustering(174) Variable = KIAA0802 MUTATION ANALYSIS
D174V1, survival
                    sevent
clus2                 0  1
  KIAA0802 MUTATED    1  4
  KIAA0802 WILD-TYPE 62 58
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
                 5                120 
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
                 4                 58 
$`KIAA0802 MUTATED`
TCGA-US-A77E TCGA-F2-7273 TCGA-FB-AAQ0 TCGA-HV-A7OP TCGA-IB-A5SQ 
       14.14        19.46        15.55        32.15         7.20 

$`KIAA0802 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
              7.20               0.23 
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
             32.15              90.12 
  KIAA0802 MUTATED KIAA0802 WILD-TYPE 
            15.550             15.205 
[1] "7.2 - 32.1 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D174V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA0802 MUTATED         0        0        1         1         3         0
  KIAA0802 WILD-TYPE       1        3       11        18        79         4
                    vv
clus                 STAGE IV
  KIAA0802 MUTATED          0
  KIAA0802 WILD-TYPE        3
D174V3, multiclass
           clus
vv          KIAA0802 MUTATED KIAA0802 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA0802 MUTATED    0  1     4
  KIAA0802 WILD-TYPE  5 16    98
D174V4, multiclass
       clus
vv      KIAA0802 MUTATED KIAA0802 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V5, binary
                    cls
clus                  0  1
  KIAA0802 MUTATED    2  3
  KIAA0802 WILD-TYPE 33 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0802 MUTATED      2    3
  KIAA0802 WILD-TYPE   33   86
   clus
vv  KIAA0802 MUTATED KIAA0802 WILD-TYPE
  0                2                 33
  1                3                 86
[1] 2 2
[1] FALSE
D174V6, binary
                    cls
clus                  0  1
  KIAA0802 MUTATED    3  0
  KIAA0802 WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0802 MUTATED      3    0
  KIAA0802 WILD-TYPE   54    3
   clus
vv  KIAA0802 MUTATED KIAA0802 WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D174V7, binary
                    cls
clus                  0  1
  KIAA0802 MUTATED    1  4
  KIAA0802 WILD-TYPE 50 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0802 MUTATED      1    4
  KIAA0802 WILD-TYPE   50   71
        clus
vv       KIAA0802 MUTATED KIAA0802 WILD-TYPE
  FEMALE                1                 50
  MALE                  4                 71
[1] 2 2
[1] FALSE
D174V8, binary
                    cls
clus                  0  1
  KIAA0802 MUTATED    3  2
  KIAA0802 WILD-TYPE 85 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0802 MUTATED      3    2
  KIAA0802 WILD-TYPE   85   28
     clus
vv    KIAA0802 MUTATED KIAA0802 WILD-TYPE
  NO                 3                 85
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0802 MUTATED                                     3
  KIAA0802 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0802 MUTATED                                       2
  KIAA0802 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0802 MUTATED                                                  0
  KIAA0802 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA0802 MUTATED                                     0
  KIAA0802 WILD-TYPE                                   1
D174V9, multiclass
                                                  clus
vv                                                 KIAA0802 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA0802 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V10, continuous
D174V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA0802 MUTATED    3  2  0  0
  KIAA0802 WILD-TYPE 77 33  4  2
D174V12, multiclass
    clus
vv   KIAA0802 MUTATED KIAA0802 WILD-TYPE
  R0                3                 77
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0802 MUTATED       1                         1     3
  KIAA0802 WILD-TYPE     5                         4   111
D174V14, multiclass
                           clus
vv                          KIAA0802 MUTATED KIAA0802 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V15, binary
                    cls
clus                  0  1
  KIAA0802 MUTATED    0  4
  KIAA0802 WILD-TYPE  5 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0802 MUTATED      0    4
  KIAA0802 WILD-TYPE    5   87
                        clus
vv                       KIAA0802 MUTATED KIAA0802 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(175) Variable = CTRL MUTATION ANALYSIS
D175V1, survival
                sevent
clus2             0  1
  CTRL MUTATED    2  3
  CTRL WILD-TYPE 61 59
  CTRL MUTATED CTRL WILD-TYPE 
             5            120 
  CTRL MUTATED CTRL WILD-TYPE 
             3             59 
$`CTRL MUTATED`
TCGA-2J-AAB1 TCGA-3A-A9I7 TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7651 
        2.17        43.50        20.19        10.85        19.82 

$`CTRL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CTRL MUTATED CTRL WILD-TYPE 
          2.17           0.23 
  CTRL MUTATED CTRL WILD-TYPE 
         43.50          90.12 
  CTRL MUTATED CTRL WILD-TYPE 
        19.820         15.205 
[1] "2.2 - 43.5 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D175V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CTRL MUTATED         0        0        0         0         5         0
  CTRL WILD-TYPE       1        3       12        19        77         4
                vv
clus             STAGE IV
  CTRL MUTATED          0
  CTRL WILD-TYPE        3
D175V3, multiclass
           clus
vv          CTRL MUTATED CTRL WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CTRL MUTATED    0  0     5
  CTRL WILD-TYPE  5 17    97
D175V4, multiclass
       clus
vv      CTRL MUTATED CTRL WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V5, binary
                cls
clus              0  1
  CTRL MUTATED    0  5
  CTRL WILD-TYPE 35 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTRL MUTATED      0    5
  CTRL WILD-TYPE   35   84
   clus
vv  CTRL MUTATED CTRL WILD-TYPE
  0            0             35
  1            5             84
[1] 2 2
[1] FALSE
D175V6, binary
                cls
clus              0  1
  CTRL MUTATED    2  0
  CTRL WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTRL MUTATED      2    0
  CTRL WILD-TYPE   55    3
   clus
vv  CTRL MUTATED CTRL WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D175V7, binary
                cls
clus              0  1
  CTRL MUTATED    1  4
  CTRL WILD-TYPE 50 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTRL MUTATED      1    4
  CTRL WILD-TYPE   50   71
        clus
vv       CTRL MUTATED CTRL WILD-TYPE
  FEMALE            1             50
  MALE              4             71
[1] 2 2
[1] FALSE
D175V8, binary
                cls
clus              0  1
  CTRL MUTATED    4  1
  CTRL WILD-TYPE 84 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTRL MUTATED      4    1
  CTRL WILD-TYPE   84   29
     clus
vv    CTRL MUTATED CTRL WILD-TYPE
  NO             4             84
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CTRL MUTATED                                     3
  CTRL WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CTRL MUTATED                                       2
  CTRL WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CTRL MUTATED                                                  0
  CTRL WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CTRL MUTATED                                     0
  CTRL WILD-TYPE                                   1
D175V9, multiclass
                                                  clus
vv                                                 CTRL MUTATED CTRL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V10, continuous
[1] "Remove cluster labels:" "CTRL MUTATED"          
clus
  CTRL MUTATED CTRL WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABA     TCGA-2J-AABE 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-YY-A8LH 
"CTRL WILD-TYPE" 
D175V11, continuous
[1] "Remove cluster labels:" "CTRL MUTATED"          
clus
  CTRL MUTATED CTRL WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CTRL WILD-TYPE" "CTRL WILD-TYPE" "CTRL WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CTRL MUTATED    5  0  0  0
  CTRL WILD-TYPE 75 35  4  2
D175V12, multiclass
    clus
vv   CTRL MUTATED CTRL WILD-TYPE
  R0            5             75
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTRL MUTATED       0                         1     4
  CTRL WILD-TYPE     6                         4   110
D175V14, multiclass
                           clus
vv                          CTRL MUTATED CTRL WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V15, binary
                cls
clus              0  1
  CTRL MUTATED    0  4
  CTRL WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTRL MUTATED      0    4
  CTRL WILD-TYPE    5   87
                        clus
vv                       CTRL MUTATED CTRL WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(176) Variable = DHX36 MUTATION ANALYSIS
D176V1, survival
                 sevent
clus2              0  1
  DHX36 MUTATED    1  9
  DHX36 WILD-TYPE 62 53
  DHX36 MUTATED DHX36 WILD-TYPE 
             10             115 
  DHX36 MUTATED DHX36 WILD-TYPE 
              9              53 
$`DHX36 MUTATED`
TCGA-2L-AAQI TCGA-3A-A9I9 TCGA-FB-A78T TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-IB-AAUQ 
        3.39        20.84        12.33        15.55        19.82         6.02 
TCGA-OE-A75W TCGA-RB-A7B8 TCGA-XD-AAUI TCGA-YH-A8SY 
        8.78        15.32        12.03        12.76 

$`DHX36 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86        14.17        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  DHX36 MUTATED DHX36 WILD-TYPE 
           3.39            0.23 
  DHX36 MUTATED DHX36 WILD-TYPE 
          20.84           90.12 
  DHX36 MUTATED DHX36 WILD-TYPE 
         12.545          15.350 
[1] "3.4 - 20.8 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.9"
D176V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DHX36 MUTATED         0        0        0         3         6         1
  DHX36 WILD-TYPE       1        3       12        16        76         3
                 vv
clus              STAGE IV
  DHX36 MUTATED          0
  DHX36 WILD-TYPE        3
D176V3, multiclass
           clus
vv          DHX36 MUTATED DHX36 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             6              76
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DHX36 MUTATED    0  0    10
  DHX36 WILD-TYPE  5 17    92
D176V4, multiclass
       clus
vv      DHX36 MUTATED DHX36 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V5, binary
                 cls
clus               0  1
  DHX36 MUTATED    3  7
  DHX36 WILD-TYPE 32 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      3    7
  DHX36 WILD-TYPE   32   82
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0             3              32
  1             7              82
[1] 2 2
[1] FALSE
D176V6, binary
                 cls
clus               0  1
  DHX36 MUTATED    4  0
  DHX36 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      4    0
  DHX36 WILD-TYPE   53    3
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D176V7, binary
                 cls
clus               0  1
  DHX36 MUTATED    5  5
  DHX36 WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      5    5
  DHX36 WILD-TYPE   46   70
        clus
vv       DHX36 MUTATED DHX36 WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D176V8, binary
                 cls
clus               0  1
  DHX36 MUTATED    7  3
  DHX36 WILD-TYPE 81 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      7    3
  DHX36 WILD-TYPE   81   27
     clus
vv    DHX36 MUTATED DHX36 WILD-TYPE
  NO              7              81
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DHX36 MUTATED                                     8
  DHX36 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DHX36 MUTATED                                       1
  DHX36 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DHX36 MUTATED                                                  0
  DHX36 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DHX36 MUTATED                                     0
  DHX36 WILD-TYPE                                   1
D176V9, multiclass
                                                  clus
vv                                                 DHX36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DHX36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V10, continuous
D176V11, continuous
                 vv
clus              R0 R1 R2 RX
  DHX36 MUTATED    6  3  0  0
  DHX36 WILD-TYPE 74 32  4  2
D176V12, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  R0             6              74
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHX36 MUTATED       0                         0    10
  DHX36 WILD-TYPE     6                         5   104
D176V14, multiclass
                           clus
vv                          DHX36 MUTATED DHX36 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V15, binary
                 cls
clus               0  1
  DHX36 MUTATED    0  9
  DHX36 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      0    9
  DHX36 WILD-TYPE    5   82
                        clus
vv                       DHX36 MUTATED DHX36 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(177) Variable = GTF3C3 MUTATION ANALYSIS
D177V1, survival
                  sevent
clus2               0  1
  GTF3C3 MUTATED    4  1
  GTF3C3 WILD-TYPE 59 61
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               5              120 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               1               61 
$`GTF3C3 MUTATED`
TCGA-2J-AABA TCGA-3A-A9IO TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       19.96        63.85         7.40         8.05        13.28 

$`GTF3C3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        6.02        11.11         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
            7.40             0.23 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           63.85            90.12 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           13.28            15.27 
[1] "7.4 - 63.9 (13.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D177V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GTF3C3 MUTATED         0        0        0         0         4         0
  GTF3C3 WILD-TYPE       1        3       12        19        78         4
                  vv
clus               STAGE IV
  GTF3C3 MUTATED          0
  GTF3C3 WILD-TYPE        3
D177V3, multiclass
           clus
vv          GTF3C3 MUTATED GTF3C3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GTF3C3 MUTATED    0  0     4
  GTF3C3 WILD-TYPE  5 17    98
D177V4, multiclass
       clus
vv      GTF3C3 MUTATED GTF3C3 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V5, binary
                  cls
clus                0  1
  GTF3C3 MUTATED    0  4
  GTF3C3 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      0    4
  GTF3C3 WILD-TYPE   35   85
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D177V6, binary
                  cls
clus                0  1
  GTF3C3 MUTATED    4  0
  GTF3C3 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      4    0
  GTF3C3 WILD-TYPE   53    3
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D177V7, binary
                  cls
clus                0  1
  GTF3C3 MUTATED    1  4
  GTF3C3 WILD-TYPE 50 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      1    4
  GTF3C3 WILD-TYPE   50   71
        clus
vv       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  FEMALE              1               50
  MALE                4               71
[1] 2 2
[1] FALSE
D177V8, binary
                  cls
clus                0  1
  GTF3C3 MUTATED    5  0
  GTF3C3 WILD-TYPE 83 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      5    0
  GTF3C3 WILD-TYPE   83   30
     clus
vv    GTF3C3 MUTATED GTF3C3 WILD-TYPE
  NO               5               83
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GTF3C3 MUTATED                                     4
  GTF3C3 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GTF3C3 MUTATED                                       1
  GTF3C3 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GTF3C3 MUTATED                                                  0
  GTF3C3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GTF3C3 MUTATED                                     0
  GTF3C3 WILD-TYPE                                   1
D177V9, multiclass
                                                  clus
vv                                                 GTF3C3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GTF3C3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V10, continuous
D177V11, continuous
[1] "Remove cluster labels:" "GTF3C3 MUTATED"        
clus
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-LB-A9Q5       TCGA-OE-A75W 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" "GTF3C3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GTF3C3 MUTATED    3  2  0  0
  GTF3C3 WILD-TYPE 77 33  4  2
D177V12, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  R0              3               77
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF3C3 MUTATED       0                         0     5
  GTF3C3 WILD-TYPE     6                         5   109
D177V14, multiclass
                           clus
vv                          GTF3C3 MUTATED GTF3C3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V15, binary
                  cls
clus                0  1
  GTF3C3 MUTATED    0  4
  GTF3C3 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      0    4
  GTF3C3 WILD-TYPE    5   87
                        clus
vv                       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(178) Variable = OTX1 MUTATION ANALYSIS
D178V1, survival
                sevent
clus2             0  1
  OTX1 MUTATED    2  5
  OTX1 WILD-TYPE 61 57
  OTX1 MUTATED OTX1 WILD-TYPE 
             7            118 
  OTX1 MUTATED OTX1 WILD-TYPE 
             5             57 
$`OTX1 MUTATED`
TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AABA TCGA-FB-A78T TCGA-IB-7651 
       12.92        14.14        16.37        19.96        12.33        19.82 
TCGA-RB-AA9M 
        9.40 

$`OTX1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-2J-AAB1 
        8.02        15.78         1.08        15.12        17.26         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       42.31        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  OTX1 MUTATED OTX1 WILD-TYPE 
          9.40           0.23 
  OTX1 MUTATED OTX1 WILD-TYPE 
         19.96          90.12 
  OTX1 MUTATED OTX1 WILD-TYPE 
         14.14          15.27 
[1] "9.4 - 20.0 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D178V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OTX1 MUTATED         0        0        0         1         6         0
  OTX1 WILD-TYPE       1        3       12        18        76         4
                vv
clus             STAGE IV
  OTX1 MUTATED          0
  OTX1 WILD-TYPE        3
D178V3, multiclass
           clus
vv          OTX1 MUTATED OTX1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  OTX1 MUTATED    1  0     6
  OTX1 WILD-TYPE  4 17    96
D178V4, multiclass
       clus
vv      OTX1 MUTATED OTX1 WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V5, binary
                cls
clus              0  1
  OTX1 MUTATED    1  6
  OTX1 WILD-TYPE 34 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      1    6
  OTX1 WILD-TYPE   34   83
   clus
vv  OTX1 MUTATED OTX1 WILD-TYPE
  0            1             34
  1            6             83
[1] 2 2
[1] FALSE
D178V6, binary
                cls
clus              0  1
  OTX1 MUTATED    3  0
  OTX1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      3    0
  OTX1 WILD-TYPE   54    3
   clus
vv  OTX1 MUTATED OTX1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D178V7, binary
                cls
clus              0  1
  OTX1 MUTATED    3  4
  OTX1 WILD-TYPE 48 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      3    4
  OTX1 WILD-TYPE   48   71
        clus
vv       OTX1 MUTATED OTX1 WILD-TYPE
  FEMALE            3             48
  MALE              4             71
[1] 2 2
[1] FALSE
D178V8, binary
                cls
clus              0  1
  OTX1 MUTATED    6  1
  OTX1 WILD-TYPE 82 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      6    1
  OTX1 WILD-TYPE   82   29
     clus
vv    OTX1 MUTATED OTX1 WILD-TYPE
  NO             6             82
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTX1 MUTATED                                     6
  OTX1 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTX1 MUTATED                                       1
  OTX1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTX1 MUTATED                                                  0
  OTX1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  OTX1 MUTATED                                     0
  OTX1 WILD-TYPE                                   1
D178V9, multiclass
                                                  clus
vv                                                 OTX1 MUTATED OTX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V10, continuous
D178V11, continuous
                vv
clus             R0 R1 R2 RX
  OTX1 MUTATED    4  3  0  0
  OTX1 WILD-TYPE 76 32  4  2
D178V12, multiclass
    clus
vv   OTX1 MUTATED OTX1 WILD-TYPE
  R0            4             76
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTX1 MUTATED       0                         1     6
  OTX1 WILD-TYPE     6                         4   108
D178V14, multiclass
                           clus
vv                          OTX1 MUTATED OTX1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V15, binary
                cls
clus              0  1
  OTX1 MUTATED    0  6
  OTX1 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      0    6
  OTX1 WILD-TYPE    5   85
                        clus
vv                       OTX1 MUTATED OTX1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(179) Variable = MTMR15 MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2               0  1
  MTMR15 MUTATED    3  4
  MTMR15 WILD-TYPE 60 58
  MTMR15 MUTATED MTMR15 WILD-TYPE 
               7              118 
  MTMR15 MUTATED MTMR15 WILD-TYPE 
               4               58 
$`MTMR15 MUTATED`
TCGA-XD-AAUL TCGA-2J-AABK TCGA-2L-AAQA TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-AAUU 
       16.37        15.91         4.70        10.13        19.82         8.05 
TCGA-LB-A9Q5 
       10.29 

$`MTMR15 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MTMR15 MUTATED MTMR15 WILD-TYPE 
            4.70             0.23 
  MTMR15 MUTATED MTMR15 WILD-TYPE 
           19.82            90.12 
  MTMR15 MUTATED MTMR15 WILD-TYPE 
           10.29            15.27 
[1] "4.7 - 19.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D179V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MTMR15 MUTATED         0        0        0         1         7         0
  MTMR15 WILD-TYPE       1        3       12        18        75         4
                  vv
clus               STAGE IV
  MTMR15 MUTATED          0
  MTMR15 WILD-TYPE        3
D179V3, multiclass
           clus
vv          MTMR15 MUTATED MTMR15 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MTMR15 MUTATED    0  0     8
  MTMR15 WILD-TYPE  5 17    94
D179V4, multiclass
       clus
vv      MTMR15 MUTATED MTMR15 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V5, binary
                  cls
clus                0  1
  MTMR15 MUTATED    1  7
  MTMR15 WILD-TYPE 34 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR15 MUTATED      1    7
  MTMR15 WILD-TYPE   34   82
   clus
vv  MTMR15 MUTATED MTMR15 WILD-TYPE
  0              1               34
  1              7               82
[1] 2 2
[1] FALSE
D179V6, binary
                  cls
clus                0  1
  MTMR15 MUTATED    3  0
  MTMR15 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR15 MUTATED      3    0
  MTMR15 WILD-TYPE   54    3
   clus
vv  MTMR15 MUTATED MTMR15 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D179V7, binary
                  cls
clus                0  1
  MTMR15 MUTATED    2  6
  MTMR15 WILD-TYPE 49 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR15 MUTATED      2    6
  MTMR15 WILD-TYPE   49   69
        clus
vv       MTMR15 MUTATED MTMR15 WILD-TYPE
  FEMALE              2               49
  MALE                6               69
[1] 2 2
[1] FALSE
D179V8, binary
                  cls
clus                0  1
  MTMR15 MUTATED    4  3
  MTMR15 WILD-TYPE 84 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR15 MUTATED      4    3
  MTMR15 WILD-TYPE   84   27
     clus
vv    MTMR15 MUTATED MTMR15 WILD-TYPE
  NO               4               84
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MTMR15 MUTATED                                     8
  MTMR15 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MTMR15 MUTATED                                       0
  MTMR15 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MTMR15 MUTATED                                                  0
  MTMR15 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MTMR15 MUTATED                                     0
  MTMR15 WILD-TYPE                                   1
D179V9, multiclass
                                                  clus
vv                                                 MTMR15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MTMR15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V10, continuous
D179V11, continuous
                  vv
clus               R0 R1 R2 RX
  MTMR15 MUTATED    5  3  0  0
  MTMR15 WILD-TYPE 75 32  4  2
D179V12, multiclass
    clus
vv   MTMR15 MUTATED MTMR15 WILD-TYPE
  R0              5               75
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTMR15 MUTATED       0                         0     8
  MTMR15 WILD-TYPE     6                         5   106
D179V14, multiclass
                           clus
vv                          MTMR15 MUTATED MTMR15 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V15, binary
                  cls
clus                0  1
  MTMR15 MUTATED    0  6
  MTMR15 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MTMR15 MUTATED      0    6
  MTMR15 WILD-TYPE    5   85
                        clus
vv                       MTMR15 MUTATED MTMR15 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(180) Variable = IYD MUTATION ANALYSIS
D180V1, survival
               sevent
clus2            0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 60 59
  IYD MUTATED IYD WILD-TYPE 
            6           119 
  IYD MUTATED IYD WILD-TYPE 
            3            59 
$`IYD MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FZ-5922 TCGA-LB-A8F3 TCGA-US-A779 TCGA-Z5-AAPL 
       23.54        15.55        36.20        12.46        16.80        15.35 

$`IYD WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       15.95        37.15         7.50        12.53         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        11.51        12.76        66.28 

  IYD MUTATED IYD WILD-TYPE 
        12.46          0.23 
  IYD MUTATED IYD WILD-TYPE 
        36.20         90.12 
  IYD MUTATED IYD WILD-TYPE 
       16.175        15.120 
[1] "12.5 - 36.2 (16.2)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.2"
D180V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IYD MUTATED         0        0        0         4         2         0
  IYD WILD-TYPE       1        3       12        15        80         4
               vv
clus            STAGE IV
  IYD MUTATED          0
  IYD WILD-TYPE        3
D180V3, multiclass
           clus
vv          IYD MUTATED IYD WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           4            15
  STAGE IIB           2            80
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  IYD MUTATED    0  1     5
  IYD WILD-TYPE  5 16    97
D180V4, multiclass
       clus
vv      IYD MUTATED IYD WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           5            97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V5, binary
               cls
clus             0  1
  IYD MUTATED    4  2
  IYD WILD-TYPE 31 87
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      4    2
  IYD WILD-TYPE   31   87
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           4            31
  1           2            87
[1] 2 2
[1] FALSE
D180V6, binary
               cls
clus             0  1
  IYD MUTATED    2  0
  IYD WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      2    0
  IYD WILD-TYPE   55    3
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D180V7, binary
               cls
clus             0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 48 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    3
  IYD WILD-TYPE   48   72
        clus
vv       IYD MUTATED IYD WILD-TYPE
  FEMALE           3            48
  MALE             3            72
[1] 2 2
[1] FALSE
D180V8, binary
               cls
clus             0  1
  IYD MUTATED    4  1
  IYD WILD-TYPE 84 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      4    1
  IYD WILD-TYPE   84   29
     clus
vv    IYD MUTATED IYD WILD-TYPE
  NO            4            84
  YES           1            29
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IYD MUTATED                                     6
  IYD WILD-TYPE                                  99
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IYD MUTATED                                       0
  IYD WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IYD MUTATED                                                  0
  IYD WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  IYD MUTATED                                     0
  IYD WILD-TYPE                                   1
D180V9, multiclass
                                                  clus
vv                                                 IYD MUTATED IYD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        6            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V10, continuous
D180V11, continuous
               vv
clus            R0 R1 R2 RX
  IYD MUTATED    6  0  0  0
  IYD WILD-TYPE 74 35  4  2
D180V12, multiclass
    clus
vv   IYD MUTATED IYD WILD-TYPE
  R0           6            74
  R1           0            35
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IYD MUTATED       0                         1     5
  IYD WILD-TYPE     6                         4   109
D180V14, multiclass
                           clus
vv                          IYD MUTATED IYD WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                               5           109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V15, binary
               cls
clus             0  1
  IYD MUTATED    0  6
  IYD WILD-TYPE  5 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      0    6
  IYD WILD-TYPE    5   85
                        clus
vv                       IYD MUTATED IYD WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           6            85
[1] 2 2
[1] FALSE

Clustering(181) Variable = GTF2F1 MUTATION ANALYSIS
D181V1, survival
                  sevent
clus2               0  1
  GTF2F1 MUTATED    0  5
  GTF2F1 WILD-TYPE 63 57
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               5              120 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               5               57 
$`GTF2F1 MUTATED`
TCGA-F2-A44G TCGA-US-A77E TCGA-2J-AABV TCGA-IB-7651 TCGA-IB-A5SQ 
        7.66        14.14        21.44        19.82         7.20 

$`GTF2F1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
            7.20             0.23 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
           21.44            90.12 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
           14.14            15.27 
[1] "7.2 - 21.4 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.6"
D181V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GTF2F1 MUTATED         0        0        1         0         4         0
  GTF2F1 WILD-TYPE       1        3       11        19        78         4
                  vv
clus               STAGE IV
  GTF2F1 MUTATED          0
  GTF2F1 WILD-TYPE        3
D181V3, multiclass
           clus
vv          GTF2F1 MUTATED GTF2F1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GTF2F1 MUTATED    0  1     4
  GTF2F1 WILD-TYPE  5 16    98
D181V4, multiclass
       clus
vv      GTF2F1 MUTATED GTF2F1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V5, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    1  4
  GTF2F1 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      1    4
  GTF2F1 WILD-TYPE   34   85
   clus
vv  GTF2F1 MUTATED GTF2F1 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D181V6, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    4  0
  GTF2F1 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      4    0
  GTF2F1 WILD-TYPE   53    3
   clus
vv  GTF2F1 MUTATED GTF2F1 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D181V7, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    3  2
  GTF2F1 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      3    2
  GTF2F1 WILD-TYPE   48   73
        clus
vv       GTF2F1 MUTATED GTF2F1 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D181V8, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    4  1
  GTF2F1 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      4    1
  GTF2F1 WILD-TYPE   84   29
     clus
vv    GTF2F1 MUTATED GTF2F1 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GTF2F1 MUTATED                                     4
  GTF2F1 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GTF2F1 MUTATED                                       1
  GTF2F1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GTF2F1 MUTATED                                                  0
  GTF2F1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GTF2F1 MUTATED                                     0
  GTF2F1 WILD-TYPE                                   1
D181V9, multiclass
                                                  clus
vv                                                 GTF2F1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GTF2F1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V10, continuous
[1] "Remove cluster labels:" "GTF2F1 MUTATED"        
clus
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2L-AAQA 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-YY-A8LH 
"GTF2F1 WILD-TYPE" 
D181V11, continuous
[1] "Remove cluster labels:" "GTF2F1 MUTATED"        
clus
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GTF2F1 MUTATED    2  3  0  0
  GTF2F1 WILD-TYPE 78 32  4  2
D181V12, multiclass
    clus
vv   GTF2F1 MUTATED GTF2F1 WILD-TYPE
  R0              2               78
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF2F1 MUTATED       0                         0     5
  GTF2F1 WILD-TYPE     6                         5   109
D181V14, multiclass
                           clus
vv                          GTF2F1 MUTATED GTF2F1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V15, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    0  4
  GTF2F1 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      0    4
  GTF2F1 WILD-TYPE    5   87
                        clus
vv                       GTF2F1 MUTATED GTF2F1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(182) Variable = DIDO1 MUTATION ANALYSIS
D182V1, survival
                 sevent
clus2              0  1
  DIDO1 MUTATED    7  7
  DIDO1 WILD-TYPE 56 55
  DIDO1 MUTATED DIDO1 WILD-TYPE 
             14             111 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
              7              55 
$`DIDO1 MUTATED`
TCGA-3A-A9IJ TCGA-IB-A5SS TCGA-US-A77E TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-F2-A7TX 
       60.95        15.12        14.14         4.70        12.95         3.12 
TCGA-FB-A5VM TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-8126 TCGA-RB-AA9M TCGA-RL-AAAS 
       16.37        32.15        19.82        15.19         9.40         0.30 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

$`DIDO1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        12.92        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 
       21.44        22.49         3.39         9.60        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       75.12        71.74        19.46        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-US-A776 TCGA-US-A779 
        8.78        13.68         3.12        15.32        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       23.67        11.51        12.76 

  DIDO1 MUTATED DIDO1 WILD-TYPE 
           0.30            0.23 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
          66.28           90.12 
  DIDO1 MUTATED DIDO1 WILD-TYPE 
         15.155          15.320 
[1] "0.3 - 66.3 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D182V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DIDO1 MUTATED         0        0        3         1         8         2
  DIDO1 WILD-TYPE       1        3        9        18        74         2
                 vv
clus              STAGE IV
  DIDO1 MUTATED          0
  DIDO1 WILD-TYPE        3
D182V3, multiclass
           clus
vv          DIDO1 MUTATED DIDO1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              3               9
  STAGE IIA             1              18
  STAGE IIB             8              74
  STAGE III             2               2
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DIDO1 MUTATED    1  3    10
  DIDO1 WILD-TYPE  4 14    92
D182V4, multiclass
       clus
vv      DIDO1 MUTATED DIDO1 WILD-TYPE
  T1                1               4
  T2                3              14
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V5, binary
                 cls
clus               0  1
  DIDO1 MUTATED    5  9
  DIDO1 WILD-TYPE 30 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      5    9
  DIDO1 WILD-TYPE   30   80
   clus
vv  DIDO1 MUTATED DIDO1 WILD-TYPE
  0             5              30
  1             9              80
[1] 2 2
[1] FALSE
D182V6, binary
                 cls
clus               0  1
  DIDO1 MUTATED    8  0
  DIDO1 WILD-TYPE 49  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      8    0
  DIDO1 WILD-TYPE   49    3
   clus
vv  DIDO1 MUTATED DIDO1 WILD-TYPE
  0             8              49
  1             0               3
[1] 2 2
[1] FALSE
D182V7, binary
                 cls
clus               0  1
  DIDO1 MUTATED    7  7
  DIDO1 WILD-TYPE 44 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      7    7
  DIDO1 WILD-TYPE   44   68
        clus
vv       DIDO1 MUTATED DIDO1 WILD-TYPE
  FEMALE             7              44
  MALE               7              68
[1] 2 2
[1] FALSE
D182V8, binary
                 cls
clus               0  1
  DIDO1 MUTATED   11  3
  DIDO1 WILD-TYPE 77 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED     11    3
  DIDO1 WILD-TYPE   77   27
     clus
vv    DIDO1 MUTATED DIDO1 WILD-TYPE
  NO             11              77
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DIDO1 MUTATED                                    11
  DIDO1 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DIDO1 MUTATED                                       3
  DIDO1 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DIDO1 MUTATED                                                  0
  DIDO1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DIDO1 MUTATED                                     0
  DIDO1 WILD-TYPE                                   1
D182V9, multiclass
                                                  clus
vv                                                 DIDO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DIDO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V10, continuous
D182V11, continuous
                 vv
clus              R0 R1 R2 RX
  DIDO1 MUTATED    9  5  0  0
  DIDO1 WILD-TYPE 71 30  4  2
D182V12, multiclass
    clus
vv   DIDO1 MUTATED DIDO1 WILD-TYPE
  R0             9              71
  R1             5              30
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIDO1 MUTATED       1                         0    13
  DIDO1 WILD-TYPE     5                         5   101
D182V14, multiclass
                           clus
vv                          DIDO1 MUTATED DIDO1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                13             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V15, binary
                 cls
clus               0  1
  DIDO1 MUTATED    0 10
  DIDO1 WILD-TYPE  5 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIDO1 MUTATED      0   10
  DIDO1 WILD-TYPE    5   81
                        clus
vv                       DIDO1 MUTATED DIDO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            10              81
[1] 2 2
[1] FALSE

Clustering(183) Variable = GNL3L MUTATION ANALYSIS
D183V1, survival
                 sevent
clus2              0  1
  GNL3L MUTATED    2  3
  GNL3L WILD-TYPE 61 59
  GNL3L MUTATED GNL3L WILD-TYPE 
              5             120 
  GNL3L MUTATED GNL3L WILD-TYPE 
              3              59 
$`GNL3L MUTATED`
TCGA-FB-AAPS TCGA-HV-AA8X TCGA-HZ-7925 TCGA-RB-A7B8 TCGA-XN-A8T5 
        7.50        17.49        20.19        15.32        23.67 

$`GNL3L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        11.51        12.76        66.28        15.35 

  GNL3L MUTATED GNL3L WILD-TYPE 
           7.50            0.23 
  GNL3L MUTATED GNL3L WILD-TYPE 
          23.67           90.12 
  GNL3L MUTATED GNL3L WILD-TYPE 
         17.490          15.155 
[1] "7.5 - 23.7 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D183V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GNL3L MUTATED         0        0        1         0         4         0
  GNL3L WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  GNL3L MUTATED          0
  GNL3L WILD-TYPE        3
D183V3, multiclass
           clus
vv          GNL3L MUTATED GNL3L WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  GNL3L MUTATED     0   3     2
  GNL3L WILD-TYPE   5  14   100
D183V4, multiclass
       clus
vv      GNL3L MUTATED GNL3L WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V5, binary
                 cls
clus               0  1
  GNL3L MUTATED    1  4
  GNL3L WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNL3L MUTATED      1    4
  GNL3L WILD-TYPE   34   85
   clus
vv  GNL3L MUTATED GNL3L WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D183V6, binary
                 cls
clus               0  1
  GNL3L MUTATED    1  0
  GNL3L WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNL3L MUTATED      1    0
  GNL3L WILD-TYPE   56    3
   clus
vv  GNL3L MUTATED GNL3L WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D183V7, binary
                 cls
clus               0  1
  GNL3L MUTATED    4  1
  GNL3L WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNL3L MUTATED      4    1
  GNL3L WILD-TYPE   47   74
        clus
vv       GNL3L MUTATED GNL3L WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D183V8, binary
                 cls
clus               0  1
  GNL3L MUTATED    3  2
  GNL3L WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNL3L MUTATED      3    2
  GNL3L WILD-TYPE   85   28
     clus
vv    GNL3L MUTATED GNL3L WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNL3L MUTATED                                     3
  GNL3L WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNL3L MUTATED                                       2
  GNL3L WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNL3L MUTATED                                                  0
  GNL3L WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  GNL3L MUTATED                                     0
  GNL3L WILD-TYPE                                   1
D183V9, multiclass
                                                  clus
vv                                                 GNL3L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 GNL3L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V10, continuous
[1] "Remove cluster labels:" "GNL3L MUTATED"         
clus
  GNL3L MUTATED GNL3L WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-YY-A8LH 
"GNL3L WILD-TYPE" 
D183V11, continuous
[1] "Remove cluster labels:" "GNL3L MUTATED"         
clus
  GNL3L MUTATED GNL3L WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-YY-A8LH 
"GNL3L WILD-TYPE" "GNL3L WILD-TYPE" "GNL3L WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  GNL3L MUTATED    3  1  1  0
  GNL3L WILD-TYPE 77 34  3  2
D183V12, multiclass
    clus
vv   GNL3L MUTATED GNL3L WILD-TYPE
  R0             3              77
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNL3L MUTATED       1                         0     4
  GNL3L WILD-TYPE     5                         5   110
D183V14, multiclass
                           clus
vv                          GNL3L MUTATED GNL3L WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V15, binary
                 cls
clus               0  1
  GNL3L MUTATED    1  3
  GNL3L WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNL3L MUTATED      1    3
  GNL3L WILD-TYPE    4   88
                        clus
vv                       GNL3L MUTATED GNL3L WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(184) Variable = ZC3H7B MUTATION ANALYSIS
D184V1, survival
                  sevent
clus2               0  1
  ZC3H7B MUTATED    4  3
  ZC3H7B WILD-TYPE 59 59
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
               7              118 
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
               3               59 
$`ZC3H7B MUTATED`
TCGA-S4-A8RO TCGA-2J-AABP TCGA-3A-A9IB TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SQ 
       17.26        15.22         7.36        19.82        41.33         7.20 
TCGA-IB-A5ST 
       20.88 

$`ZC3H7B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UF 
       19.82        36.69        15.19        12.00        15.85        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
            7.20             0.23 
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
           41.33            90.12 
  ZC3H7B MUTATED ZC3H7B WILD-TYPE 
          17.260           15.155 
[1] "7.2 - 41.3 (17.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D184V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZC3H7B MUTATED         0        0        1         0         6         0
  ZC3H7B WILD-TYPE       1        3       11        19        76         4
                  vv
clus               STAGE IV
  ZC3H7B MUTATED          0
  ZC3H7B WILD-TYPE        3
D184V3, multiclass
           clus
vv          ZC3H7B MUTATED ZC3H7B WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZC3H7B MUTATED    0  1     6
  ZC3H7B WILD-TYPE  5 16    96
D184V4, multiclass
       clus
vv      ZC3H7B MUTATED ZC3H7B WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V5, binary
                  cls
clus                0  1
  ZC3H7B MUTATED    1  6
  ZC3H7B WILD-TYPE 34 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7B MUTATED      1    6
  ZC3H7B WILD-TYPE   34   83
   clus
vv  ZC3H7B MUTATED ZC3H7B WILD-TYPE
  0              1               34
  1              6               83
[1] 2 2
[1] FALSE
D184V6, binary
                  cls
clus                0  1
  ZC3H7B MUTATED    5  0
  ZC3H7B WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7B MUTATED      5    0
  ZC3H7B WILD-TYPE   52    3
   clus
vv  ZC3H7B MUTATED ZC3H7B WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D184V7, binary
                  cls
clus                0  1
  ZC3H7B MUTATED    7  0
  ZC3H7B WILD-TYPE 44 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7B MUTATED      7    0
  ZC3H7B WILD-TYPE   44   75
        clus
vv       ZC3H7B MUTATED ZC3H7B WILD-TYPE
  FEMALE              7               44
  MALE                0               75
[1] 2 2
[1] FALSE
D184V8, binary
                  cls
clus                0  1
  ZC3H7B MUTATED    6  1
  ZC3H7B WILD-TYPE 82 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7B MUTATED      6    1
  ZC3H7B WILD-TYPE   82   29
     clus
vv    ZC3H7B MUTATED ZC3H7B WILD-TYPE
  NO               6               82
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZC3H7B MUTATED                                     6
  ZC3H7B WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZC3H7B MUTATED                                       0
  ZC3H7B WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZC3H7B MUTATED                                                  0
  ZC3H7B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZC3H7B MUTATED                                     1
  ZC3H7B WILD-TYPE                                   0
D184V9, multiclass
                                                  clus
vv                                                 ZC3H7B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 ZC3H7B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V10, continuous
D184V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZC3H7B MUTATED    6  1  0  0
  ZC3H7B WILD-TYPE 74 34  4  2
D184V12, multiclass
    clus
vv   ZC3H7B MUTATED ZC3H7B WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H7B MUTATED       0                         0     7
  ZC3H7B WILD-TYPE     6                         5   107
D184V14, multiclass
                           clus
vv                          ZC3H7B MUTATED ZC3H7B WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V15, binary
                  cls
clus                0  1
  ZC3H7B MUTATED    0  6
  ZC3H7B WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7B MUTATED      0    6
  ZC3H7B WILD-TYPE    5   85
                        clus
vv                       ZC3H7B MUTATED ZC3H7B WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(185) Variable = COL4A4 MUTATION ANALYSIS
D185V1, survival
                  sevent
clus2               0  1
  COL4A4 MUTATED    5  4
  COL4A4 WILD-TYPE 58 58
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               9              116 
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               4               58 
$`COL4A4 MUTATED`
TCGA-2J-AABP TCGA-3A-A9I9 TCGA-3A-A9J0 TCGA-F2-7273 TCGA-FB-AAPZ TCGA-HV-A7OP 
       15.22        20.84        24.43        19.46        23.54        32.15 
TCGA-IB-7651 TCGA-Q3-A5QY TCGA-RB-A7B8 
       19.82        13.68        15.32 

$`COL4A4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN 
       34.09        10.13        75.12        71.74         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-AA9M 
        7.56        12.46        10.29         8.78         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  COL4A4 MUTATED COL4A4 WILD-TYPE 
           13.68             0.23 
  COL4A4 MUTATED COL4A4 WILD-TYPE 
           32.15            90.12 
  COL4A4 MUTATED COL4A4 WILD-TYPE 
          19.820           14.765 
[1] "13.7 - 32.1 (19.8)" "0.2 - 90.1 (14.8)" 
[1] "hr=" "1.5"
D185V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  COL4A4 MUTATED         0        0        0         1         8         0
  COL4A4 WILD-TYPE       1        3       12        18        74         4
                  vv
clus               STAGE IV
  COL4A4 MUTATED          0
  COL4A4 WILD-TYPE        3
D185V3, multiclass
           clus
vv          COL4A4 MUTATED COL4A4 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              8               74
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  COL4A4 MUTATED    0  1     8
  COL4A4 WILD-TYPE  5 16    94
D185V4, multiclass
       clus
vv      COL4A4 MUTATED COL4A4 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V5, binary
                  cls
clus                0  1
  COL4A4 MUTATED    1  8
  COL4A4 WILD-TYPE 34 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A4 MUTATED      1    8
  COL4A4 WILD-TYPE   34   81
   clus
vv  COL4A4 MUTATED COL4A4 WILD-TYPE
  0              1               34
  1              8               81
[1] 2 2
[1] FALSE
D185V6, binary
                  cls
clus                0  1
  COL4A4 MUTATED    4  0
  COL4A4 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A4 MUTATED      4    0
  COL4A4 WILD-TYPE   53    3
   clus
vv  COL4A4 MUTATED COL4A4 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D185V7, binary
                  cls
clus                0  1
  COL4A4 MUTATED    3  6
  COL4A4 WILD-TYPE 48 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A4 MUTATED      3    6
  COL4A4 WILD-TYPE   48   69
        clus
vv       COL4A4 MUTATED COL4A4 WILD-TYPE
  FEMALE              3               48
  MALE                6               69
[1] 2 2
[1] FALSE
D185V8, binary
                  cls
clus                0  1
  COL4A4 MUTATED    6  3
  COL4A4 WILD-TYPE 82 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A4 MUTATED      6    3
  COL4A4 WILD-TYPE   82   27
     clus
vv    COL4A4 MUTATED COL4A4 WILD-TYPE
  NO               6               82
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COL4A4 MUTATED                                     6
  COL4A4 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COL4A4 MUTATED                                       2
  COL4A4 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COL4A4 MUTATED                                                  0
  COL4A4 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  COL4A4 MUTATED                                     1
  COL4A4 WILD-TYPE                                   0
D185V9, multiclass
                                                  clus
vv                                                 COL4A4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 COL4A4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V10, continuous
[1] "Remove cluster labels:" "COL4A4 MUTATED"        
clus
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9IB       TCGA-3A-A9IX 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-YY-A8LH 
"COL4A4 WILD-TYPE" 
D185V11, continuous
[1] "Remove cluster labels:" "COL4A4 MUTATED"        
clus
  COL4A4 MUTATED COL4A4 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" "COL4A4 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  COL4A4 MUTATED    8  1  0  0
  COL4A4 WILD-TYPE 72 34  4  2
D185V12, multiclass
    clus
vv   COL4A4 MUTATED COL4A4 WILD-TYPE
  R0              8               72
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL4A4 MUTATED       1                         1     7
  COL4A4 WILD-TYPE     5                         4   107
D185V14, multiclass
                           clus
vv                          COL4A4 MUTATED COL4A4 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V15, binary
                  cls
clus                0  1
  COL4A4 MUTATED    0  7
  COL4A4 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A4 MUTATED      0    7
  COL4A4 WILD-TYPE    5   84
                        clus
vv                       COL4A4 MUTATED COL4A4 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(186) Variable = SYCP2 MUTATION ANALYSIS
D186V1, survival
                 sevent
clus2              0  1
  SYCP2 MUTATED    5  3
  SYCP2 WILD-TYPE 58 59
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              8             117 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              3              59 
$`SYCP2 MUTATED`
TCGA-2L-AAQI TCGA-3A-A9IU TCGA-3A-A9IV TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-AAUR 
        3.39        15.06        36.26        10.85        19.82        11.11 
TCGA-Q3-AA2A TCGA-RB-AA9M 
        3.12         9.40 

$`SYCP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IX 
       24.26        33.57        63.85        50.70        32.81        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86        14.17         6.02         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SYCP2 MUTATED SYCP2 WILD-TYPE 
           3.12            0.23 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          36.26           90.12 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          10.98           15.35 
[1] "3.1 - 36.3 (11.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D186V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYCP2 MUTATED         0        0        2         0         6         0
  SYCP2 WILD-TYPE       1        3       10        19        76         4
                 vv
clus              STAGE IV
  SYCP2 MUTATED          0
  SYCP2 WILD-TYPE        3
D186V3, multiclass
           clus
vv          SYCP2 MUTATED SYCP2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SYCP2 MUTATED    1  1     6
  SYCP2 WILD-TYPE  4 16    96
D186V4, multiclass
       clus
vv      SYCP2 MUTATED SYCP2 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V5, binary
                 cls
clus               0  1
  SYCP2 MUTATED    1  7
  SYCP2 WILD-TYPE 34 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      1    7
  SYCP2 WILD-TYPE   34   82
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             1              34
  1             7              82
[1] 2 2
[1] FALSE
D186V6, binary
                 cls
clus               0  1
  SYCP2 MUTATED    2  0
  SYCP2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      2    0
  SYCP2 WILD-TYPE   55    3
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D186V7, binary
                 cls
clus               0  1
  SYCP2 MUTATED    3  5
  SYCP2 WILD-TYPE 48 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      3    5
  SYCP2 WILD-TYPE   48   70
        clus
vv       SYCP2 MUTATED SYCP2 WILD-TYPE
  FEMALE             3              48
  MALE               5              70
[1] 2 2
[1] FALSE
D186V8, binary
                 cls
clus               0  1
  SYCP2 MUTATED    7  1
  SYCP2 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      7    1
  SYCP2 WILD-TYPE   81   29
     clus
vv    SYCP2 MUTATED SYCP2 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYCP2 MUTATED                                     6
  SYCP2 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYCP2 MUTATED                                       2
  SYCP2 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYCP2 MUTATED                                                  0
  SYCP2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYCP2 MUTATED                                     0
  SYCP2 WILD-TYPE                                   1
D186V9, multiclass
                                                  clus
vv                                                 SYCP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SYCP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V10, continuous
[1] "Remove cluster labels:" "SYCP2 MUTATED"         
clus
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
D186V11, continuous
[1] "Remove cluster labels:" "SYCP2 MUTATED"         
clus
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" "SYCP2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SYCP2 MUTATED    5  2  0  1
  SYCP2 WILD-TYPE 75 33  4  1
D186V12, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYCP2 MUTATED       0                         0     8
  SYCP2 WILD-TYPE     6                         5   106
D186V14, multiclass
                           clus
vv                          SYCP2 MUTATED SYCP2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V15, binary
                 cls
clus               0  1
  SYCP2 MUTATED    0  7
  SYCP2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0    7
  SYCP2 WILD-TYPE    5   84
                        clus
vv                       SYCP2 MUTATED SYCP2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(187) Variable = CNKSR2 MUTATION ANALYSIS
D187V1, survival
                  sevent
clus2               0  1
  CNKSR2 MUTATED    6  5
  CNKSR2 WILD-TYPE 57 57
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
              11              114 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
               5               57 
$`CNKSR2 MUTATED`
TCGA-2J-AABR TCGA-3A-A9IL TCGA-F2-A44G TCGA-HZ-A77Q TCGA-XD-AAUL TCGA-2L-AAQJ 
       14.40        90.12         7.66         1.08        16.37        12.95 
TCGA-2L-AAQL TCGA-HV-AA8X TCGA-IB-7651 TCGA-LB-A8F3 TCGA-RL-AAAS 
        9.60        17.49        19.82        12.46         0.30 

$`CNKSR2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS 
       10.49        58.98        60.95         8.02        15.78        15.12 
TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 
       12.92        17.26        14.14         2.17        23.97         9.63 
TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH 
        2.63        20.61        19.96        22.22        22.72        42.31 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA 
       15.91        14.47        15.22         9.11        21.44         4.70 
TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       22.49         3.39        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
        8.78        13.68         3.12        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
            0.30             0.23 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
           90.12            75.12 
  CNKSR2 MUTATED CNKSR2 WILD-TYPE 
          12.950           15.335 
[1] "0.3 - 90.1 (12.9)" "0.2 - 75.1 (15.3)"
[1] "hr=" "1.1"
D187V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CNKSR2 MUTATED         1        0        1         3         5         1
  CNKSR2 WILD-TYPE       0        3       11        16        77         3
                  vv
clus               STAGE IV
  CNKSR2 MUTATED          0
  CNKSR2 WILD-TYPE        3
D187V3, multiclass
           clus
vv          CNKSR2 MUTATED CNKSR2 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              3               16
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CNKSR2 MUTATED    1  2     8
  CNKSR2 WILD-TYPE  4 15    94
D187V4, multiclass
       clus
vv      CNKSR2 MUTATED CNKSR2 WILD-TYPE
  T1                 1                4
  T2                 2               15
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V5, binary
                  cls
clus                0  1
  CNKSR2 MUTATED    5  5
  CNKSR2 WILD-TYPE 30 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      5    5
  CNKSR2 WILD-TYPE   30   84
   clus
vv  CNKSR2 MUTATED CNKSR2 WILD-TYPE
  0              5               30
  1              5               84
[1] 2 2
[1] FALSE
D187V6, binary
                  cls
clus                0  1
  CNKSR2 MUTATED    4  0
  CNKSR2 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      4    0
  CNKSR2 WILD-TYPE   53    3
   clus
vv  CNKSR2 MUTATED CNKSR2 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D187V7, binary
                  cls
clus                0  1
  CNKSR2 MUTATED    9  2
  CNKSR2 WILD-TYPE 42 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      9    2
  CNKSR2 WILD-TYPE   42   73
        clus
vv       CNKSR2 MUTATED CNKSR2 WILD-TYPE
  FEMALE              9               42
  MALE                2               73
[1] 2 2
[1] FALSE
D187V8, binary
                  cls
clus                0  1
  CNKSR2 MUTATED    8  2
  CNKSR2 WILD-TYPE 80 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      8    2
  CNKSR2 WILD-TYPE   80   28
     clus
vv    CNKSR2 MUTATED CNKSR2 WILD-TYPE
  NO               8               80
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CNKSR2 MUTATED                                     9
  CNKSR2 WILD-TYPE                                  96
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CNKSR2 MUTATED                                       2
  CNKSR2 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CNKSR2 MUTATED                                                  0
  CNKSR2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CNKSR2 MUTATED                                     0
  CNKSR2 WILD-TYPE                                   1
D187V9, multiclass
                                                  clus
vv                                                 CNKSR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CNKSR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V10, continuous
D187V11, continuous
                  vv
clus               R0 R1 R2 RX
  CNKSR2 MUTATED    7  2  1  1
  CNKSR2 WILD-TYPE 73 33  3  1
D187V12, multiclass
    clus
vv   CNKSR2 MUTATED CNKSR2 WILD-TYPE
  R0              7               73
  R1              2               33
  R2              1                3
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNKSR2 MUTATED       1                         1     9
  CNKSR2 WILD-TYPE     5                         4   105
D187V14, multiclass
                           clus
vv                          CNKSR2 MUTATED CNKSR2 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V15, binary
                  cls
clus                0  1
  CNKSR2 MUTATED    0  7
  CNKSR2 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNKSR2 MUTATED      0    7
  CNKSR2 WILD-TYPE    5   84
                        clus
vv                       CNKSR2 MUTATED CNKSR2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(188) Variable = OR5A1 MUTATION ANALYSIS
D188V1, survival
                 sevent
clus2              0  1
  OR5A1 MUTATED    2  2
  OR5A1 WILD-TYPE 61 60
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              4             121 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              2              60 
$`OR5A1 MUTATED`
TCGA-FB-AAPU TCGA-IB-7651 TCGA-IB-7652 TCGA-Q3-AA2A 
       12.53        19.82        36.69         3.12 

$`OR5A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85         0.23        19.82        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OR5A1 MUTATED OR5A1 WILD-TYPE 
           3.12            0.23 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
          36.69           90.12 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
         16.175          15.220 
[1] "3.1 - 36.7 (16.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D188V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR5A1 MUTATED         0        0        1         1         3         0
  OR5A1 WILD-TYPE       1        3       11        18        79         4
                 vv
clus              STAGE IV
  OR5A1 MUTATED          0
  OR5A1 WILD-TYPE        3
D188V3, multiclass
           clus
vv          OR5A1 MUTATED OR5A1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OR5A1 MUTATED    0  0     5
  OR5A1 WILD-TYPE  5 17    97
D188V4, multiclass
       clus
vv      OR5A1 MUTATED OR5A1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V5, binary
                 cls
clus               0  1
  OR5A1 MUTATED    1  4
  OR5A1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      1    4
  OR5A1 WILD-TYPE   34   85
   clus
vv  OR5A1 MUTATED OR5A1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D188V6, binary
                 cls
clus               0  1
  OR5A1 MUTATED    2  0
  OR5A1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      2    0
  OR5A1 WILD-TYPE   55    3
   clus
vv  OR5A1 MUTATED OR5A1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D188V7, binary
                 cls
clus               0  1
  OR5A1 MUTATED    4  1
  OR5A1 WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      4    1
  OR5A1 WILD-TYPE   47   74
        clus
vv       OR5A1 MUTATED OR5A1 WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D188V8, binary
                 cls
clus               0  1
  OR5A1 MUTATED    4  0
  OR5A1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      4    0
  OR5A1 WILD-TYPE   84   30
     clus
vv    OR5A1 MUTATED OR5A1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR5A1 MUTATED                                     5
  OR5A1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR5A1 MUTATED                                       0
  OR5A1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR5A1 MUTATED                                                  0
  OR5A1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR5A1 MUTATED                                     0
  OR5A1 WILD-TYPE                                   1
D188V9, multiclass
                                                  clus
vv                                                 OR5A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 OR5A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V10, continuous
[1] "Remove cluster labels:" "OR5A1 MUTATED"         
clus
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-YY-A8LH 
"OR5A1 WILD-TYPE" 
D188V11, continuous
[1] "Remove cluster labels:" "OR5A1 MUTATED"         
clus
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR5A1 MUTATED    2  2  0  1
  OR5A1 WILD-TYPE 78 33  4  1
D188V12, multiclass
    clus
vv   OR5A1 MUTATED OR5A1 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR5A1 MUTATED       2                         0     3
  OR5A1 WILD-TYPE     4                         5   111
D188V14, multiclass
                           clus
vv                          OR5A1 MUTATED OR5A1 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V15, binary
                 cls
clus               0  1
  OR5A1 MUTATED    0  5
  OR5A1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      0    5
  OR5A1 WILD-TYPE    5   86
                        clus
vv                       OR5A1 MUTATED OR5A1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(189) Variable = OSBPL3 MUTATION ANALYSIS
D189V1, survival
                  sevent
clus2               0  1
  OSBPL3 MUTATED    5  3
  OSBPL3 WILD-TYPE 58 59
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
               8              117 
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
               3               59 
$`OSBPL3 MUTATED`
TCGA-2J-AABT TCGA-HZ-A77Q TCGA-US-A77E TCGA-2J-AABP TCGA-3A-A9I9 TCGA-HZ-A8P1 
       10.49         1.08        14.14        15.22        20.84         0.23 
TCGA-IB-7651 TCGA-IB-AAUS 
       19.82         7.40 

$`OSBPL3 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78        15.12        12.92        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13         5.26        10.85        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17         6.02        11.11         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
            0.23             0.26 
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
           20.84            90.12 
  OSBPL3 MUTATED OSBPL3 WILD-TYPE 
          12.315           15.350 
[1] "0.2 - 20.8 (12.3)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.2"
D189V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OSBPL3 MUTATED         0        0        1         1         6         0
  OSBPL3 WILD-TYPE       1        3       11        18        76         4
                  vv
clus               STAGE IV
  OSBPL3 MUTATED          0
  OSBPL3 WILD-TYPE        3
D189V3, multiclass
           clus
vv          OSBPL3 MUTATED OSBPL3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  OSBPL3 MUTATED    0  1     7
  OSBPL3 WILD-TYPE  5 16    95
D189V4, multiclass
       clus
vv      OSBPL3 MUTATED OSBPL3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V5, binary
                  cls
clus                0  1
  OSBPL3 MUTATED    2  6
  OSBPL3 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL3 MUTATED      2    6
  OSBPL3 WILD-TYPE   33   83
   clus
vv  OSBPL3 MUTATED OSBPL3 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D189V6, binary
                  cls
clus                0  1
  OSBPL3 MUTATED    4  0
  OSBPL3 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL3 MUTATED      4    0
  OSBPL3 WILD-TYPE   53    3
   clus
vv  OSBPL3 MUTATED OSBPL3 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D189V7, binary
                  cls
clus                0  1
  OSBPL3 MUTATED    5  3
  OSBPL3 WILD-TYPE 46 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL3 MUTATED      5    3
  OSBPL3 WILD-TYPE   46   72
        clus
vv       OSBPL3 MUTATED OSBPL3 WILD-TYPE
  FEMALE              5               46
  MALE                3               72
[1] 2 2
[1] FALSE
D189V8, binary
                  cls
clus                0  1
  OSBPL3 MUTATED    4  1
  OSBPL3 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL3 MUTATED      4    1
  OSBPL3 WILD-TYPE   84   29
     clus
vv    OSBPL3 MUTATED OSBPL3 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OSBPL3 MUTATED                                     5
  OSBPL3 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OSBPL3 MUTATED                                       2
  OSBPL3 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OSBPL3 MUTATED                                                  0
  OSBPL3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OSBPL3 MUTATED                                     1
  OSBPL3 WILD-TYPE                                   0
D189V9, multiclass
                                                  clus
vv                                                 OSBPL3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 OSBPL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V10, continuous
D189V11, continuous
                  vv
clus               R0 R1 R2 RX
  OSBPL3 MUTATED    6  2  0  0
  OSBPL3 WILD-TYPE 74 33  4  2
D189V12, multiclass
    clus
vv   OSBPL3 MUTATED OSBPL3 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OSBPL3 MUTATED       0                         0     8
  OSBPL3 WILD-TYPE     6                         5   106
D189V14, multiclass
                           clus
vv                          OSBPL3 MUTATED OSBPL3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V15, binary
                  cls
clus                0  1
  OSBPL3 MUTATED    0  6
  OSBPL3 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL3 MUTATED      0    6
  OSBPL3 WILD-TYPE    5   85
                        clus
vv                       OSBPL3 MUTATED OSBPL3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(190) Variable = HSP90AB1 MUTATION ANALYSIS
D190V1, survival
                    sevent
clus2                 0  1
  HSP90AB1 MUTATED    2  3
  HSP90AB1 WILD-TYPE 61 59
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 5                120 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
                 3                 59 
$`HSP90AB1 MUTATED`
TCGA-F2-7273 TCGA-HV-A7OL TCGA-HZ-A77O TCGA-IB-A5SO TCGA-RB-AA9M 
       19.46         8.28         5.26        12.00         9.40 

$`HSP90AB1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
       19.82        19.82        36.69        41.33        15.19        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
              5.26               0.23 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
             19.46              90.12 
  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE 
             9.400             15.335 
[1] "5.3 - 19.5 (9.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.2"
D190V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HSP90AB1 MUTATED         0        0        0         1         4         0
  HSP90AB1 WILD-TYPE       1        3       12        18        78         4
                    vv
clus                 STAGE IV
  HSP90AB1 MUTATED          0
  HSP90AB1 WILD-TYPE        3
D190V3, multiclass
           clus
vv          HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  HSP90AB1 MUTATED    1  1     3
  HSP90AB1 WILD-TYPE  4 16    99
D190V4, multiclass
       clus
vv      HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  T1                   1                  4
  T2                   1                 16
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V5, binary
                    cls
clus                  0  1
  HSP90AB1 MUTATED    1  4
  HSP90AB1 WILD-TYPE 34 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      1    4
  HSP90AB1 WILD-TYPE   34   85
   clus
vv  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  0                1                 34
  1                4                 85
[1] 2 2
[1] FALSE
D190V6, binary
                    cls
clus                  0  1
  HSP90AB1 MUTATED    2  0
  HSP90AB1 WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      2    0
  HSP90AB1 WILD-TYPE   55    3
   clus
vv  HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D190V7, binary
                    cls
clus                  0  1
  HSP90AB1 MUTATED    1  4
  HSP90AB1 WILD-TYPE 50 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      1    4
  HSP90AB1 WILD-TYPE   50   71
        clus
vv       HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  FEMALE                1                 50
  MALE                  4                 71
[1] 2 2
[1] FALSE
D190V8, binary
                    cls
clus                  0  1
  HSP90AB1 MUTATED    3  2
  HSP90AB1 WILD-TYPE 85 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      3    2
  HSP90AB1 WILD-TYPE   85   28
     clus
vv    HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  NO                 3                 85
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HSP90AB1 MUTATED                                     5
  HSP90AB1 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HSP90AB1 MUTATED                                       0
  HSP90AB1 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HSP90AB1 MUTATED                                                  0
  HSP90AB1 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  HSP90AB1 MUTATED                                     0
  HSP90AB1 WILD-TYPE                                   1
D190V9, multiclass
                                                  clus
vv                                                 HSP90AB1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 HSP90AB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V10, continuous
D190V11, continuous
                    vv
clus                 R0 R1 R2 RX
  HSP90AB1 MUTATED    3  1  1  0
  HSP90AB1 WILD-TYPE 77 34  3  2
D190V12, multiclass
    clus
vv   HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  R0                3                 77
  R1                1                 34
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSP90AB1 MUTATED       1                         1     3
  HSP90AB1 WILD-TYPE     5                         4   111
D190V14, multiclass
                           clus
vv                          HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V15, binary
                    cls
clus                  0  1
  HSP90AB1 MUTATED    0  3
  HSP90AB1 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AB1 MUTATED      0    3
  HSP90AB1 WILD-TYPE    5   88
                        clus
vv                       HSP90AB1 MUTATED HSP90AB1 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(191) Variable = PLAUR MUTATION ANALYSIS
D191V1, survival
                 sevent
clus2              0  1
  PLAUR MUTATED    1  3
  PLAUR WILD-TYPE 62 59
  PLAUR MUTATED PLAUR WILD-TYPE 
              4             121 
  PLAUR MUTATED PLAUR WILD-TYPE 
              3              59 
$`PLAUR MUTATED`
TCGA-FZ-5926 TCGA-HZ-8637 TCGA-IB-A5SP TCGA-IB-A6UG 
       17.79        17.00        15.85         1.35 

$`PLAUR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        20.19        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       12.00         7.20        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PLAUR MUTATED PLAUR WILD-TYPE 
           1.35            0.23 
  PLAUR MUTATED PLAUR WILD-TYPE 
          17.79           90.12 
  PLAUR MUTATED PLAUR WILD-TYPE 
         16.425          15.190 
[1] "1.4 - 17.8 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D191V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PLAUR MUTATED         0        0        0         1         2         1
  PLAUR WILD-TYPE       1        3       12        18        80         3
                 vv
clus              STAGE IV
  PLAUR MUTATED          0
  PLAUR WILD-TYPE        3
D191V3, multiclass
           clus
vv          PLAUR MUTATED PLAUR WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PLAUR MUTATED    0  0     4
  PLAUR WILD-TYPE  5 17    98
D191V4, multiclass
       clus
vv      PLAUR MUTATED PLAUR WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V5, binary
                 cls
clus               0  1
  PLAUR MUTATED    1  3
  PLAUR WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAUR MUTATED      1    3
  PLAUR WILD-TYPE   34   86
   clus
vv  PLAUR MUTATED PLAUR WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D191V6, binary
                 cls
clus               0  1
  PLAUR MUTATED    3  0
  PLAUR WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAUR MUTATED      3    0
  PLAUR WILD-TYPE   54    3
   clus
vv  PLAUR MUTATED PLAUR WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D191V7, binary
                 cls
clus               0  1
  PLAUR MUTATED    2  2
  PLAUR WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAUR MUTATED      2    2
  PLAUR WILD-TYPE   49   73
        clus
vv       PLAUR MUTATED PLAUR WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D191V8, binary
                 cls
clus               0  1
  PLAUR MUTATED    3  1
  PLAUR WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAUR MUTATED      3    1
  PLAUR WILD-TYPE   85   29
     clus
vv    PLAUR MUTATED PLAUR WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLAUR MUTATED                                     4
  PLAUR WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLAUR MUTATED                                       0
  PLAUR WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLAUR MUTATED                                                  0
  PLAUR WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PLAUR MUTATED                                     0
  PLAUR WILD-TYPE                                   1
D191V9, multiclass
                                                  clus
vv                                                 PLAUR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PLAUR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V10, continuous
[1] "Remove cluster labels:" "PLAUR MUTATED"         
clus
  PLAUR MUTATED PLAUR WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
D191V11, continuous
[1] "Remove cluster labels:" "PLAUR MUTATED"         
clus
  PLAUR MUTATED PLAUR WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A7M4 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" "PLAUR WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PLAUR MUTATED    2  2  0  0
  PLAUR WILD-TYPE 78 33  4  2
D191V12, multiclass
    clus
vv   PLAUR MUTATED PLAUR WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLAUR MUTATED       0                         0     4
  PLAUR WILD-TYPE     6                         5   110
D191V14, multiclass
                           clus
vv                          PLAUR MUTATED PLAUR WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V15, binary
                 cls
clus               0  1
  PLAUR MUTATED    1  2
  PLAUR WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLAUR MUTATED      1    2
  PLAUR WILD-TYPE    4   89
                        clus
vv                       PLAUR MUTATED PLAUR WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(192) Variable = GPC2 MUTATION ANALYSIS
D192V1, survival
                sevent
clus2             0  1
  GPC2 MUTATED    3  2
  GPC2 WILD-TYPE 60 60
  GPC2 MUTATED GPC2 WILD-TYPE 
             5            120 
  GPC2 MUTATED GPC2 WILD-TYPE 
             2             60 
$`GPC2 MUTATED`
TCGA-2L-AAQI TCGA-3A-A9IV TCGA-F2-A7TX TCGA-Q3-AA2A TCGA-US-A776 
        3.39        36.26         3.12         3.12        39.98 

$`GPC2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  GPC2 MUTATED GPC2 WILD-TYPE 
          3.12           0.23 
  GPC2 MUTATED GPC2 WILD-TYPE 
         39.98          90.12 
  GPC2 MUTATED GPC2 WILD-TYPE 
          3.39          15.27 
[1] "3.1 - 40.0 (3.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D192V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GPC2 MUTATED         0        0        2         1         2         0
  GPC2 WILD-TYPE       1        3       10        18        80         4
                vv
clus             STAGE IV
  GPC2 MUTATED          0
  GPC2 WILD-TYPE        3
D192V3, multiclass
           clus
vv          GPC2 MUTATED GPC2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            1             18
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  GPC2 MUTATED    0  1     4
  GPC2 WILD-TYPE  5 16    98
D192V4, multiclass
       clus
vv      GPC2 MUTATED GPC2 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V5, binary
                cls
clus              0  1
  GPC2 MUTATED    2  3
  GPC2 WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      2    3
  GPC2 WILD-TYPE   33   86
   clus
vv  GPC2 MUTATED GPC2 WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D192V6, binary
                cls
clus              0  1
  GPC2 MUTATED    1  0
  GPC2 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      1    0
  GPC2 WILD-TYPE   56    3
   clus
vv  GPC2 MUTATED GPC2 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D192V7, binary
                cls
clus              0  1
  GPC2 MUTATED    2  3
  GPC2 WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      2    3
  GPC2 WILD-TYPE   49   72
        clus
vv       GPC2 MUTATED GPC2 WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D192V8, binary
                cls
clus              0  1
  GPC2 MUTATED    5  0
  GPC2 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      5    0
  GPC2 WILD-TYPE   83   30
     clus
vv    GPC2 MUTATED GPC2 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPC2 MUTATED                                     3
  GPC2 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPC2 MUTATED                                       1
  GPC2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPC2 MUTATED                                                  1
  GPC2 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  GPC2 MUTATED                                     0
  GPC2 WILD-TYPE                                   1
D192V9, multiclass
                                                  clus
vv                                                 GPC2 MUTATED GPC2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V10, continuous
D192V11, continuous
                vv
clus             R0 R1 R2 RX
  GPC2 MUTATED    2  2  0  1
  GPC2 WILD-TYPE 78 33  4  1
D192V12, multiclass
    clus
vv   GPC2 MUTATED GPC2 WILD-TYPE
  R0            2             78
  R1            2             33
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPC2 MUTATED       0                         0     5
  GPC2 WILD-TYPE     6                         5   109
D192V14, multiclass
                           clus
vv                          GPC2 MUTATED GPC2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V15, binary
                cls
clus              0  1
  GPC2 MUTATED    0  3
  GPC2 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPC2 MUTATED      0    3
  GPC2 WILD-TYPE    5   88
                        clus
vv                       GPC2 MUTATED GPC2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(193) Variable = ACBD3 MUTATION ANALYSIS
D193V1, survival
                 sevent
clus2              0  1
  ACBD3 MUTATED    2  2
  ACBD3 WILD-TYPE 61 60
  ACBD3 MUTATED ACBD3 WILD-TYPE 
              4             121 
  ACBD3 MUTATED ACBD3 WILD-TYPE 
              2              60 
$`ACBD3 MUTATED`
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-IB-7651 TCGA-IB-8126 
        1.08        15.12        19.82        15.19 

$`ACBD3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ACBD3 MUTATED ACBD3 WILD-TYPE 
           1.08            0.23 
  ACBD3 MUTATED ACBD3 WILD-TYPE 
          19.82           90.12 
  ACBD3 MUTATED ACBD3 WILD-TYPE 
         15.155          15.320 
[1] "1.1 - 19.8 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D193V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ACBD3 MUTATED         0        0        0         0         3         1
  ACBD3 WILD-TYPE       1        3       12        19        79         3
                 vv
clus              STAGE IV
  ACBD3 MUTATED          0
  ACBD3 WILD-TYPE        3
D193V3, multiclass
           clus
vv          ACBD3 MUTATED ACBD3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ACBD3 MUTATED    0  0     4
  ACBD3 WILD-TYPE  5 17    98
D193V4, multiclass
       clus
vv      ACBD3 MUTATED ACBD3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V5, binary
                 cls
clus               0  1
  ACBD3 MUTATED    0  4
  ACBD3 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD3 MUTATED      0    4
  ACBD3 WILD-TYPE   35   85
   clus
vv  ACBD3 MUTATED ACBD3 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D193V6, binary
                 cls
clus               0  1
  ACBD3 MUTATED    3  0
  ACBD3 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD3 MUTATED      3    0
  ACBD3 WILD-TYPE   54    3
   clus
vv  ACBD3 MUTATED ACBD3 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D193V7, binary
                 cls
clus               0  1
  ACBD3 MUTATED    4  0
  ACBD3 WILD-TYPE 47 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD3 MUTATED      4    0
  ACBD3 WILD-TYPE   47   75
        clus
vv       ACBD3 MUTATED ACBD3 WILD-TYPE
  FEMALE             4              47
  MALE               0              75
[1] 2 2
[1] FALSE
D193V8, binary
                 cls
clus               0  1
  ACBD3 MUTATED    3  0
  ACBD3 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD3 MUTATED      3    0
  ACBD3 WILD-TYPE   85   30
     clus
vv    ACBD3 MUTATED ACBD3 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACBD3 MUTATED                                     3
  ACBD3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACBD3 MUTATED                                       1
  ACBD3 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACBD3 MUTATED                                                  0
  ACBD3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ACBD3 MUTATED                                     0
  ACBD3 WILD-TYPE                                   1
D193V9, multiclass
                                                  clus
vv                                                 ACBD3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ACBD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V10, continuous
D193V11, continuous
                 vv
clus              R0 R1 R2 RX
  ACBD3 MUTATED    3  1  0  0
  ACBD3 WILD-TYPE 77 34  4  2
D193V12, multiclass
    clus
vv   ACBD3 MUTATED ACBD3 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACBD3 MUTATED       0                         0     4
  ACBD3 WILD-TYPE     6                         5   110
D193V14, multiclass
                           clus
vv                          ACBD3 MUTATED ACBD3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V15, binary
                 cls
clus               0  1
  ACBD3 MUTATED    0  4
  ACBD3 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACBD3 MUTATED      0    4
  ACBD3 WILD-TYPE    5   87
                        clus
vv                       ACBD3 MUTATED ACBD3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(194) Variable = PURB MUTATION ANALYSIS
D194V1, survival
                sevent
clus2             0  1
  PURB MUTATED    2  2
  PURB WILD-TYPE 61 60
  PURB MUTATED PURB WILD-TYPE 
             4            121 
  PURB MUTATED PURB WILD-TYPE 
             2             60 
$`PURB MUTATED`
TCGA-XD-AAUL TCGA-HV-A7OP TCGA-HZ-A77O TCGA-RB-A7B8 
       16.37        32.15         5.26        15.32 

$`PURB WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PURB MUTATED PURB WILD-TYPE 
          5.26           0.23 
  PURB MUTATED PURB WILD-TYPE 
         32.15          90.12 
  PURB MUTATED PURB WILD-TYPE 
        15.845         15.190 
[1] "5.3 - 32.1 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D194V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PURB MUTATED         0        0        0         1         3         0
  PURB WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  PURB MUTATED          0
  PURB WILD-TYPE        3
D194V3, multiclass
           clus
vv          PURB MUTATED PURB WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PURB MUTATED    0  1     3
  PURB WILD-TYPE  5 16    99
D194V4, multiclass
       clus
vv      PURB MUTATED PURB WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V5, binary
                cls
clus              0  1
  PURB MUTATED    1  3
  PURB WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  PURB MUTATED      1    3
  PURB WILD-TYPE   34   86
   clus
vv  PURB MUTATED PURB WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D194V6, binary
                cls
clus              0  1
  PURB MUTATED    1  0
  PURB WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PURB MUTATED      1    0
  PURB WILD-TYPE   56    3
   clus
vv  PURB MUTATED PURB WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D194V7, binary
                cls
clus              0  1
  PURB MUTATED    2  2
  PURB WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  PURB MUTATED      2    2
  PURB WILD-TYPE   49   73
        clus
vv       PURB MUTATED PURB WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D194V8, binary
                cls
clus              0  1
  PURB MUTATED    3  1
  PURB WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PURB MUTATED      3    1
  PURB WILD-TYPE   85   29
     clus
vv    PURB MUTATED PURB WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PURB MUTATED                                     2
  PURB WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PURB MUTATED                                       2
  PURB WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PURB MUTATED                                                  0
  PURB WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PURB MUTATED                                     0
  PURB WILD-TYPE                                   1
D194V9, multiclass
                                                  clus
vv                                                 PURB MUTATED PURB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V10, continuous
[1] "Remove cluster labels:" "PURB MUTATED"          
clus
  PURB MUTATED PURB WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"PURB WILD-TYPE" "PURB WILD-TYPE" 
D194V11, continuous
[1] "Remove cluster labels:" "PURB MUTATED"          
clus
  PURB MUTATED PURB WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" "PURB WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PURB MUTATED    4  0  0  0
  PURB WILD-TYPE 76 35  4  2
D194V12, multiclass
    clus
vv   PURB MUTATED PURB WILD-TYPE
  R0            4             76
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PURB MUTATED       1                         0     3
  PURB WILD-TYPE     5                         5   111
D194V14, multiclass
                           clus
vv                          PURB MUTATED PURB WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V15, binary
                cls
clus              0  1
  PURB MUTATED    0  3
  PURB WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  PURB MUTATED      0    3
  PURB WILD-TYPE    5   88
                        clus
vv                       PURB MUTATED PURB WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(195) Variable = ABCC2 MUTATION ANALYSIS
D195V1, survival
                 sevent
clus2              0  1
  ABCC2 MUTATED    4  2
  ABCC2 WILD-TYPE 59 60
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              6             119 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
              2              60 
$`ABCC2 MUTATED`
TCGA-2J-AABO TCGA-FZ-5920 TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-A5ST TCGA-XN-A8T5 
       14.47         2.01         8.28        19.82        20.88        23.67 

$`ABCC2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02        24.36         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        11.51        12.76        66.28        15.35 

  ABCC2 MUTATED ABCC2 WILD-TYPE 
           2.01            0.23 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
          23.67           90.12 
  ABCC2 MUTATED ABCC2 WILD-TYPE 
         17.145          15.220 
[1] "2.0 - 23.7 (17.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D195V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ABCC2 MUTATED         0        0        1         1         4         0
  ABCC2 WILD-TYPE       1        3       11        18        78         4
                 vv
clus              STAGE IV
  ABCC2 MUTATED          0
  ABCC2 WILD-TYPE        3
D195V3, multiclass
           clus
vv          ABCC2 MUTATED ABCC2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ABCC2 MUTATED    0  1     5
  ABCC2 WILD-TYPE  5 16    97
D195V4, multiclass
       clus
vv      ABCC2 MUTATED ABCC2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V5, binary
                 cls
clus               0  1
  ABCC2 MUTATED    2  4
  ABCC2 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      2    4
  ABCC2 WILD-TYPE   33   85
   clus
vv  ABCC2 MUTATED ABCC2 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D195V6, binary
                 cls
clus               0  1
  ABCC2 MUTATED    5  0
  ABCC2 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      5    0
  ABCC2 WILD-TYPE   52    3
   clus
vv  ABCC2 MUTATED ABCC2 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D195V7, binary
                 cls
clus               0  1
  ABCC2 MUTATED    3  3
  ABCC2 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      3    3
  ABCC2 WILD-TYPE   48   72
        clus
vv       ABCC2 MUTATED ABCC2 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D195V8, binary
                 cls
clus               0  1
  ABCC2 MUTATED    4  2
  ABCC2 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      4    2
  ABCC2 WILD-TYPE   84   28
     clus
vv    ABCC2 MUTATED ABCC2 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ABCC2 MUTATED                                     5
  ABCC2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ABCC2 MUTATED                                       1
  ABCC2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ABCC2 MUTATED                                                  0
  ABCC2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ABCC2 MUTATED                                     0
  ABCC2 WILD-TYPE                                   1
D195V9, multiclass
                                                  clus
vv                                                 ABCC2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ABCC2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V10, continuous
D195V11, continuous
                 vv
clus              R0 R1 R2 RX
  ABCC2 MUTATED    4  1  1  0
  ABCC2 WILD-TYPE 76 34  3  2
D195V12, multiclass
    clus
vv   ABCC2 MUTATED ABCC2 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCC2 MUTATED       1                         1     4
  ABCC2 WILD-TYPE     5                         4   110
D195V14, multiclass
                           clus
vv                          ABCC2 MUTATED ABCC2 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V15, binary
                 cls
clus               0  1
  ABCC2 MUTATED    1  3
  ABCC2 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC2 MUTATED      1    3
  ABCC2 WILD-TYPE    4   88
                        clus
vv                       ABCC2 MUTATED ABCC2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(196) Variable = KRT73 MUTATION ANALYSIS
D196V1, survival
                 sevent
clus2              0  1
  KRT73 MUTATED    2  3
  KRT73 WILD-TYPE 61 59
  KRT73 MUTATED KRT73 WILD-TYPE 
              5             120 
  KRT73 MUTATED KRT73 WILD-TYPE 
              3              59 
$`KRT73 MUTATED`
TCGA-2J-AAB9 TCGA-3A-A9IX TCGA-IB-7651 TCGA-IB-A5SQ TCGA-YB-A89D 
       20.61        34.09        19.82         7.20        11.51 

$`KRT73 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  KRT73 MUTATED KRT73 WILD-TYPE 
           7.20            0.23 
  KRT73 MUTATED KRT73 WILD-TYPE 
          34.09           90.12 
  KRT73 MUTATED KRT73 WILD-TYPE 
         19.820          15.205 
[1] "7.2 - 34.1 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D196V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KRT73 MUTATED         0        1        1         0         3         0
  KRT73 WILD-TYPE       1        2       11        19        79         4
                 vv
clus              STAGE IV
  KRT73 MUTATED          0
  KRT73 WILD-TYPE        3
D196V3, multiclass
           clus
vv          KRT73 MUTATED KRT73 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KRT73 MUTATED    1  1     3
  KRT73 WILD-TYPE  4 16    99
D196V4, multiclass
       clus
vv      KRT73 MUTATED KRT73 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V5, binary
                 cls
clus               0  1
  KRT73 MUTATED    2  3
  KRT73 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT73 MUTATED      2    3
  KRT73 WILD-TYPE   33   86
   clus
vv  KRT73 MUTATED KRT73 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D196V6, binary
                 cls
clus               0  1
  KRT73 MUTATED    3  0
  KRT73 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT73 MUTATED      3    0
  KRT73 WILD-TYPE   54    3
   clus
vv  KRT73 MUTATED KRT73 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D196V7, binary
                 cls
clus               0  1
  KRT73 MUTATED    3  2
  KRT73 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT73 MUTATED      3    2
  KRT73 WILD-TYPE   48   73
        clus
vv       KRT73 MUTATED KRT73 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D196V8, binary
                 cls
clus               0  1
  KRT73 MUTATED    2  3
  KRT73 WILD-TYPE 86 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT73 MUTATED      2    3
  KRT73 WILD-TYPE   86   27
     clus
vv    KRT73 MUTATED KRT73 WILD-TYPE
  NO              2              86
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRT73 MUTATED                                     5
  KRT73 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRT73 MUTATED                                       0
  KRT73 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRT73 MUTATED                                                  0
  KRT73 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KRT73 MUTATED                                     0
  KRT73 WILD-TYPE                                   1
D196V9, multiclass
                                                  clus
vv                                                 KRT73 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KRT73 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V10, continuous
[1] "Remove cluster labels:" "KRT73 MUTATED"         
clus
  KRT73 MUTATED KRT73 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-YY-A8LH 
"KRT73 WILD-TYPE" 
D196V11, continuous
[1] "Remove cluster labels:" "KRT73 MUTATED"         
clus
  KRT73 MUTATED KRT73 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KRT73 WILD-TYPE" "KRT73 WILD-TYPE" "KRT73 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KRT73 MUTATED    5  0  0  0
  KRT73 WILD-TYPE 75 35  4  2
D196V12, multiclass
    clus
vv   KRT73 MUTATED KRT73 WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT73 MUTATED       0                         0     5
  KRT73 WILD-TYPE     6                         5   109
D196V14, multiclass
                           clus
vv                          KRT73 MUTATED KRT73 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V15, binary
                 cls
clus               0  1
  KRT73 MUTATED    0  4
  KRT73 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT73 MUTATED      0    4
  KRT73 WILD-TYPE    5   87
                        clus
vv                       KRT73 MUTATED KRT73 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(197) Variable = SGOL2 MUTATION ANALYSIS
D197V1, survival
                 sevent
clus2              0  1
  SGOL2 MUTATED    3  4
  SGOL2 WILD-TYPE 60 58
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              7             118 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              4              58 
$`SGOL2 MUTATED`
TCGA-3A-A9IH TCGA-F2-A7TX TCGA-FB-AAPU TCGA-HV-A7OL TCGA-HZ-A77O TCGA-HZ-A8P1 
       33.57         3.12        12.53         8.28         5.26         0.23 
TCGA-IB-7651 
       19.82 

$`SGOL2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       17.00        10.13        10.85        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.23            0.26 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          33.57           90.12 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
          8.280          15.335 
[1] "0.2 - 33.6 (8.3)"  "0.3 - 90.1 (15.3)"
[1] "hr=" "1.9"
D197V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SGOL2 MUTATED         0        1        1         2         3         0
  SGOL2 WILD-TYPE       1        2       11        17        79         4
                 vv
clus              STAGE IV
  SGOL2 MUTATED          0
  SGOL2 WILD-TYPE        3
D197V3, multiclass
           clus
vv          SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SGOL2 MUTATED    1  2     4
  SGOL2 WILD-TYPE  4 15    98
D197V4, multiclass
       clus
vv      SGOL2 MUTATED SGOL2 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V5, binary
                 cls
clus               0  1
  SGOL2 MUTATED    4  3
  SGOL2 WILD-TYPE 31 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      4    3
  SGOL2 WILD-TYPE   31   86
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0             4              31
  1             3              86
[1] 2 2
[1] FALSE
D197V6, binary
                 cls
clus               0  1
  SGOL2 MUTATED    2  0
  SGOL2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      2    0
  SGOL2 WILD-TYPE   55    3
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D197V7, binary
                 cls
clus               0  1
  SGOL2 MUTATED    4  3
  SGOL2 WILD-TYPE 47 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      4    3
  SGOL2 WILD-TYPE   47   72
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             4              47
  MALE               3              72
[1] 2 2
[1] FALSE
D197V8, binary
                 cls
clus               0  1
  SGOL2 MUTATED    6  0
  SGOL2 WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      6    0
  SGOL2 WILD-TYPE   82   30
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SGOL2 MUTATED                                     7
  SGOL2 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SGOL2 MUTATED                                       0
  SGOL2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SGOL2 MUTATED                                                  0
  SGOL2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SGOL2 MUTATED                                     0
  SGOL2 WILD-TYPE                                   1
D197V9, multiclass
                                                  clus
vv                                                 SGOL2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SGOL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V10, continuous
[1] "Remove cluster labels:" "SGOL2 MUTATED"         
clus
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-YY-A8LH 
"SGOL2 WILD-TYPE" 
D197V11, continuous
[1] "Remove cluster labels:" "SGOL2 MUTATED"         
clus
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-IB-7885      TCGA-IB-8126 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" "SGOL2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SGOL2 MUTATED    4  2  1  0
  SGOL2 WILD-TYPE 76 33  3  2
D197V12, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SGOL2 MUTATED       2                         0     5
  SGOL2 WILD-TYPE     4                         5   109
D197V14, multiclass
                           clus
vv                          SGOL2 MUTATED SGOL2 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V15, binary
                 cls
clus               0  1
  SGOL2 MUTATED    0  5
  SGOL2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      0    5
  SGOL2 WILD-TYPE    5   86
                        clus
vv                       SGOL2 MUTATED SGOL2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(198) Variable = MAGEC1 MUTATION ANALYSIS
D198V1, survival
                  sevent
clus2               0  1
  MAGEC1 MUTATED   10 11
  MAGEC1 WILD-TYPE 53 51
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              21              104 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              11               51 
$`MAGEC1 MUTATED`
TCGA-2J-AABR TCGA-3A-A9IJ TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-3A-A9IX 
       14.40        60.95         3.39        12.95         7.36        34.09 
TCGA-F2-A8YN TCGA-FB-AAPP TCGA-FB-AAPU TCGA-HV-AA8X TCGA-HZ-A77P TCGA-IB-7651 
       17.00        15.95        12.53        17.49        10.85        19.82 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A7LX TCGA-LB-A9Q5 TCGA-RL-AAAS 
       12.00        15.85        20.88         8.22        10.29         0.30 
TCGA-US-A776 TCGA-US-A77J TCGA-XD-AAUG 
       39.98        18.67        13.81 

$`MAGEC1 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       10.49        58.98        90.12         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM 
        9.11        21.44         4.70        22.49         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50        20.84        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       32.81        15.06        36.26        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       71.74        19.46         3.12        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13         5.26         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
       41.33        15.19         7.20        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A779 TCGA-US-A77G 
       13.68         3.12        15.32         9.40        16.80         0.39 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
            0.30             0.23 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           60.95            90.12 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           14.40            15.27 
[1] "0.3 - 61.0 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D198V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAGEC1 MUTATED         0        1        2         5        11         1
  MAGEC1 WILD-TYPE       1        2       10        14        71         3
                  vv
clus               STAGE IV
  MAGEC1 MUTATED          1
  MAGEC1 WILD-TYPE        2
D198V3, multiclass
           clus
vv          MAGEC1 MUTATED MAGEC1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               2               10
  STAGE IIA              5               14
  STAGE IIB             11               71
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MAGEC1 MUTATED    1  3    17
  MAGEC1 WILD-TYPE  4 14    85
D198V4, multiclass
       clus
vv      MAGEC1 MUTATED MAGEC1 WILD-TYPE
  T1                 1                4
  T2                 3               14
  T3+T4             17               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V5, binary
                  cls
clus                0  1
  MAGEC1 MUTATED    9 12
  MAGEC1 WILD-TYPE 26 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED      9   12
  MAGEC1 WILD-TYPE   26   77
   clus
vv  MAGEC1 MUTATED MAGEC1 WILD-TYPE
  0              9               26
  1             12               77
[1] 2 2
[1] FALSE
D198V6, binary
                  cls
clus                0  1
  MAGEC1 MUTATED    7  1
  MAGEC1 WILD-TYPE 50  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED      7    1
  MAGEC1 WILD-TYPE   50    2
   clus
vv  MAGEC1 MUTATED MAGEC1 WILD-TYPE
  0              7               50
  1              1                2
[1] 2 2
[1] FALSE
D198V7, binary
                  cls
clus                0  1
  MAGEC1 MUTATED   11 10
  MAGEC1 WILD-TYPE 40 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     11   10
  MAGEC1 WILD-TYPE   40   65
        clus
vv       MAGEC1 MUTATED MAGEC1 WILD-TYPE
  FEMALE             11               40
  MALE               10               65
[1] 2 2
[1] FALSE
D198V8, binary
                  cls
clus                0  1
  MAGEC1 MUTATED   17  3
  MAGEC1 WILD-TYPE 71 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     17    3
  MAGEC1 WILD-TYPE   71   27
     clus
vv    MAGEC1 MUTATED MAGEC1 WILD-TYPE
  NO              17               71
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAGEC1 MUTATED                                    18
  MAGEC1 WILD-TYPE                                  87
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAGEC1 MUTATED                                       2
  MAGEC1 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAGEC1 MUTATED                                                  1
  MAGEC1 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAGEC1 MUTATED                                     0
  MAGEC1 WILD-TYPE                                   1
D198V9, multiclass
                                                  clus
vv                                                 MAGEC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MAGEC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            87
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V10, continuous
D198V11, continuous
                  vv
clus               R0 R1 R2 RX
  MAGEC1 MUTATED   15  5  1  0
  MAGEC1 WILD-TYPE 65 30  3  2
D198V12, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  R0             15               65
  R1              5               30
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAGEC1 MUTATED       2                         0    19
  MAGEC1 WILD-TYPE     4                         5    95
D198V14, multiclass
                           clus
vv                          MAGEC1 MUTATED MAGEC1 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 19               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V15, binary
                  cls
clus                0  1
  MAGEC1 MUTATED    0 15
  MAGEC1 WILD-TYPE  5 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED      0   15
  MAGEC1 WILD-TYPE    5   76
                        clus
vv                       MAGEC1 MUTATED MAGEC1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             15               76
[1] 2 2
[1] FALSE

Clustering(199) Variable = ZNF609 MUTATION ANALYSIS
D199V1, survival
                  sevent
clus2               0  1
  ZNF609 MUTATED    3  1
  ZNF609 WILD-TYPE 60 61
  ZNF609 MUTATED ZNF609 WILD-TYPE 
               4              121 
  ZNF609 MUTATED ZNF609 WILD-TYPE 
               1               61 
$`ZNF609 MUTATED`
TCGA-3A-A9IJ TCGA-2J-AABO TCGA-3A-A9IV TCGA-IB-7651 
       60.95        14.47        36.26        19.82 

$`ZNF609 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF609 MUTATED ZNF609 WILD-TYPE 
           14.47             0.23 
  ZNF609 MUTATED ZNF609 WILD-TYPE 
           60.95            90.12 
  ZNF609 MUTATED ZNF609 WILD-TYPE 
           28.04            15.19 
[1] "14.5 - 61.0 (28.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3.1"
D199V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF609 MUTATED         0        0        2         0         2         0
  ZNF609 WILD-TYPE       1        3       10        19        80         4
                  vv
clus               STAGE IV
  ZNF609 MUTATED          0
  ZNF609 WILD-TYPE        3
D199V3, multiclass
           clus
vv          ZNF609 MUTATED ZNF609 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF609 MUTATED     0   2     2
  ZNF609 WILD-TYPE   5  15   100
D199V4, multiclass
       clus
vv      ZNF609 MUTATED ZNF609 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V5, binary
                  cls
clus                0  1
  ZNF609 MUTATED    2  2
  ZNF609 WILD-TYPE 33 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF609 MUTATED      2    2
  ZNF609 WILD-TYPE   33   87
   clus
vv  ZNF609 MUTATED ZNF609 WILD-TYPE
  0              2               33
  1              2               87
[1] 2 2
[1] FALSE
D199V6, binary
                  cls
clus                0  1
  ZNF609 MUTATED    2  0
  ZNF609 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF609 MUTATED      2    0
  ZNF609 WILD-TYPE   55    3
   clus
vv  ZNF609 MUTATED ZNF609 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D199V7, binary
                  cls
clus                0  1
  ZNF609 MUTATED    2  2
  ZNF609 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF609 MUTATED      2    2
  ZNF609 WILD-TYPE   49   73
        clus
vv       ZNF609 MUTATED ZNF609 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D199V8, binary
                  cls
clus                0  1
  ZNF609 MUTATED    3  1
  ZNF609 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF609 MUTATED      3    1
  ZNF609 WILD-TYPE   85   29
     clus
vv    ZNF609 MUTATED ZNF609 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF609 MUTATED                                     2
  ZNF609 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF609 MUTATED                                       2
  ZNF609 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF609 MUTATED                                                  0
  ZNF609 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF609 MUTATED                                     0
  ZNF609 WILD-TYPE                                   1
D199V9, multiclass
                                                  clus
vv                                                 ZNF609 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF609 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V10, continuous
D199V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF609 MUTATED    4  0  0  0
  ZNF609 WILD-TYPE 76 35  4  2
D199V12, multiclass
    clus
vv   ZNF609 MUTATED ZNF609 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF609 MUTATED       0                         0     4
  ZNF609 WILD-TYPE     6                         5   110
D199V14, multiclass
                           clus
vv                          ZNF609 MUTATED ZNF609 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V15, binary
                  cls
clus                0  1
  ZNF609 MUTATED    0  3
  ZNF609 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF609 MUTATED      0    3
  ZNF609 WILD-TYPE    5   88
                        clus
vv                       ZNF609 MUTATED ZNF609 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(200) Variable = ATP4A MUTATION ANALYSIS
D200V1, survival
                 sevent
clus2              0  1
  ATP4A MUTATED    5  5
  ATP4A WILD-TYPE 58 57
  ATP4A MUTATED ATP4A WILD-TYPE 
             10             115 
  ATP4A MUTATED ATP4A WILD-TYPE 
              5              57 
$`ATP4A MUTATED`
TCGA-2J-AABR TCGA-LB-A7SX TCGA-2J-AAB6 TCGA-2L-AAQI TCGA-3A-A9IV TCGA-FB-AAPZ 
       14.40        12.92         9.63         3.39        36.26        23.54 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-AAUW 
       10.85        19.82        19.82         7.56 

$`ATP4A WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 
       12.33        15.95        37.15         7.50        12.53        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        5.26         0.23        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ATP4A MUTATED ATP4A WILD-TYPE 
           3.39            0.23 
  ATP4A MUTATED ATP4A WILD-TYPE 
          36.26           90.12 
  ATP4A MUTATED ATP4A WILD-TYPE 
          13.66           15.32 
[1] "3.4 - 36.3 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D200V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP4A MUTATED         0        0        1         2         6         0
  ATP4A WILD-TYPE       1        3       11        17        76         4
                 vv
clus              STAGE IV
  ATP4A MUTATED          1
  ATP4A WILD-TYPE        2
D200V3, multiclass
           clus
vv          ATP4A MUTATED ATP4A WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ATP4A MUTATED    0  2     8
  ATP4A WILD-TYPE  5 15    94
D200V4, multiclass
       clus
vv      ATP4A MUTATED ATP4A WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V5, binary
                 cls
clus               0  1
  ATP4A MUTATED    4  6
  ATP4A WILD-TYPE 31 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATP4A MUTATED      4    6
  ATP4A WILD-TYPE   31   83
   clus
vv  ATP4A MUTATED ATP4A WILD-TYPE
  0             4              31
  1             6              83
[1] 2 2
[1] FALSE
D200V6, binary
                 cls
clus               0  1
  ATP4A MUTATED    4  1
  ATP4A WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATP4A MUTATED      4    1
  ATP4A WILD-TYPE   53    2
   clus
vv  ATP4A MUTATED ATP4A WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D200V7, binary
                 cls
clus               0  1
  ATP4A MUTATED    5  5
  ATP4A WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATP4A MUTATED      5    5
  ATP4A WILD-TYPE   46   70
        clus
vv       ATP4A MUTATED ATP4A WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D200V8, binary
                 cls
clus               0  1
  ATP4A MUTATED   10  0
  ATP4A WILD-TYPE 78 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATP4A MUTATED     10    0
  ATP4A WILD-TYPE   78   30
     clus
vv    ATP4A MUTATED ATP4A WILD-TYPE
  NO             10              78
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP4A MUTATED                                     7
  ATP4A WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP4A MUTATED                                       3
  ATP4A WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP4A MUTATED                                                  0
  ATP4A WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP4A MUTATED                                     0
  ATP4A WILD-TYPE                                   1
D200V9, multiclass
                                                  clus
vv                                                 ATP4A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ATP4A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V10, continuous
[1] "Remove cluster labels:" "ATP4A MUTATED"         
clus
  ATP4A MUTATED ATP4A WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-YY-A8LH 
"ATP4A WILD-TYPE" 
D200V11, continuous
[1] "Remove cluster labels:" "ATP4A MUTATED"         
clus
  ATP4A MUTATED ATP4A WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ATP4A WILD-TYPE" "ATP4A WILD-TYPE" "ATP4A WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ATP4A MUTATED    8  2  0  0
  ATP4A WILD-TYPE 72 33  4  2
D200V12, multiclass
    clus
vv   ATP4A MUTATED ATP4A WILD-TYPE
  R0             8              72
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP4A MUTATED       0                         1     9
  ATP4A WILD-TYPE     6                         4   105
D200V14, multiclass
                           clus
vv                          ATP4A MUTATED ATP4A WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V15, binary
                 cls
clus               0  1
  ATP4A MUTATED    0  7
  ATP4A WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATP4A MUTATED      0    7
  ATP4A WILD-TYPE    5   84
                        clus
vv                       ATP4A MUTATED ATP4A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(201) Variable = TRPV2 MUTATION ANALYSIS
D201V1, survival
                 sevent
clus2              0  1
  TRPV2 MUTATED    4  3
  TRPV2 WILD-TYPE 59 59
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              7             118 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              3              59 
$`TRPV2 MUTATED`
TCGA-F2-A8YN TCGA-FB-AAPP TCGA-FB-AAPU TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-AAUP 
       17.00        15.95        12.53        19.82        19.82        14.17 
TCGA-YH-A8SY 
       12.76 

$`TRPV2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       71.74        19.46         3.12        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  TRPV2 MUTATED TRPV2 WILD-TYPE 
          12.53            0.23 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
          19.82           90.12 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
         15.950          15.205 
[1] "12.5 - 19.8 (15.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D201V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TRPV2 MUTATED         0        0        0         2         3         1
  TRPV2 WILD-TYPE       1        3       12        17        79         3
                 vv
clus              STAGE IV
  TRPV2 MUTATED          1
  TRPV2 WILD-TYPE        2
D201V3, multiclass
           clus
vv          TRPV2 MUTATED TRPV2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             3              79
  STAGE III             1               3
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TRPV2 MUTATED    0  0     7
  TRPV2 WILD-TYPE  5 17    95
D201V4, multiclass
       clus
vv      TRPV2 MUTATED TRPV2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V5, binary
                 cls
clus               0  1
  TRPV2 MUTATED    3  4
  TRPV2 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      3    4
  TRPV2 WILD-TYPE   32   85
   clus
vv  TRPV2 MUTATED TRPV2 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D201V6, binary
                 cls
clus               0  1
  TRPV2 MUTATED    3  1
  TRPV2 WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      3    1
  TRPV2 WILD-TYPE   54    2
   clus
vv  TRPV2 MUTATED TRPV2 WILD-TYPE
  0             3              54
  1             1               2
[1] 2 2
[1] FALSE
D201V7, binary
                 cls
clus               0  1
  TRPV2 MUTATED    3  4
  TRPV2 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      3    4
  TRPV2 WILD-TYPE   48   71
        clus
vv       TRPV2 MUTATED TRPV2 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D201V8, binary
                 cls
clus               0  1
  TRPV2 MUTATED    5  2
  TRPV2 WILD-TYPE 83 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      5    2
  TRPV2 WILD-TYPE   83   28
     clus
vv    TRPV2 MUTATED TRPV2 WILD-TYPE
  NO              5              83
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TRPV2 MUTATED                                     5
  TRPV2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TRPV2 MUTATED                                       1
  TRPV2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TRPV2 MUTATED                                                  0
  TRPV2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TRPV2 MUTATED                                     0
  TRPV2 WILD-TYPE                                   1
D201V9, multiclass
                                                  clus
vv                                                 TRPV2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TRPV2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V10, continuous
[1] "Remove cluster labels:" "TRPV2 MUTATED"         
clus
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-YY-A8LH 
"TRPV2 WILD-TYPE" 
D201V11, continuous
[1] "Remove cluster labels:" "TRPV2 MUTATED"         
clus
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" "TRPV2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TRPV2 MUTATED    3  3  0  0
  TRPV2 WILD-TYPE 77 32  4  2
D201V12, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  R0             3              77
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRPV2 MUTATED       1                         0     6
  TRPV2 WILD-TYPE     5                         5   108
D201V14, multiclass
                           clus
vv                          TRPV2 MUTATED TRPV2 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V15, binary
                 cls
clus               0  1
  TRPV2 MUTATED    0  7
  TRPV2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      0    7
  TRPV2 WILD-TYPE    5   84
                        clus
vv                       TRPV2 MUTATED TRPV2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(202) Variable = N4BP2 MUTATION ANALYSIS
D202V1, survival
                 sevent
clus2              0  1
  N4BP2 MUTATED    2  4
  N4BP2 WILD-TYPE 61 58
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              6             119 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              4              58 
$`N4BP2 MUTATED`
TCGA-2L-AAQI TCGA-FB-AAPQ TCGA-HZ-8637 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-A5SP 
        3.39        37.15        17.00        19.82        19.82        15.85 

$`N4BP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        15.19        12.00         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  N4BP2 MUTATED N4BP2 WILD-TYPE 
           3.39            0.23 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          37.15           90.12 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          18.41           15.12 
[1] "3.4 - 37.1 (18.4)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.2"
D202V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  N4BP2 MUTATED         0        0        0         1         4         0
  N4BP2 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  N4BP2 MUTATED          1
  N4BP2 WILD-TYPE        2
D202V3, multiclass
           clus
vv          N4BP2 MUTATED N4BP2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  N4BP2 MUTATED    0  0     6
  N4BP2 WILD-TYPE  5 17    96
D202V4, multiclass
       clus
vv      N4BP2 MUTATED N4BP2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V5, binary
                 cls
clus               0  1
  N4BP2 MUTATED    2  4
  N4BP2 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      2    4
  N4BP2 WILD-TYPE   33   85
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D202V6, binary
                 cls
clus               0  1
  N4BP2 MUTATED    2  1
  N4BP2 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      2    1
  N4BP2 WILD-TYPE   55    2
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D202V7, binary
                 cls
clus               0  1
  N4BP2 MUTATED    2  4
  N4BP2 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      2    4
  N4BP2 WILD-TYPE   49   71
        clus
vv       N4BP2 MUTATED N4BP2 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D202V8, binary
                 cls
clus               0  1
  N4BP2 MUTATED    5  1
  N4BP2 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      5    1
  N4BP2 WILD-TYPE   83   29
     clus
vv    N4BP2 MUTATED N4BP2 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  N4BP2 MUTATED                                     5
  N4BP2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  N4BP2 MUTATED                                       1
  N4BP2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  N4BP2 MUTATED                                                  0
  N4BP2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  N4BP2 MUTATED                                     0
  N4BP2 WILD-TYPE                                   1
D202V9, multiclass
                                                  clus
vv                                                 N4BP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 N4BP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V10, continuous
[1] "Remove cluster labels:" "N4BP2 MUTATED"         
clus
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-YY-A8LH 
"N4BP2 WILD-TYPE" 
D202V11, continuous
[1] "Remove cluster labels:" "N4BP2 MUTATED"         
clus
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" "N4BP2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  N4BP2 MUTATED    4  2  0  0
  N4BP2 WILD-TYPE 76 33  4  2
D202V12, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  N4BP2 MUTATED       0                         0     6
  N4BP2 WILD-TYPE     6                         5   108
D202V14, multiclass
                           clus
vv                          N4BP2 MUTATED N4BP2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V15, binary
                 cls
clus               0  1
  N4BP2 MUTATED    1  3
  N4BP2 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED      1    3
  N4BP2 WILD-TYPE    4   88
                        clus
vv                       N4BP2 MUTATED N4BP2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(203) Variable = HMMR MUTATION ANALYSIS
D203V1, survival
                sevent
clus2             0  1
  HMMR MUTATED    2  4
  HMMR WILD-TYPE 61 58
  HMMR MUTATED HMMR WILD-TYPE 
             6            119 
  HMMR MUTATED HMMR WILD-TYPE 
             4             58 
$`HMMR MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9IZ TCGA-FB-AAPP TCGA-HV-A7OL TCGA-HZ-A77P TCGA-IB-7651 
       12.95        10.13        15.95         8.28        10.85        19.82 

$`HMMR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13         5.26         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  HMMR MUTATED HMMR WILD-TYPE 
          8.28           0.23 
  HMMR MUTATED HMMR WILD-TYPE 
         19.82          90.12 
  HMMR MUTATED HMMR WILD-TYPE 
         11.90          15.32 
[1] "8.3 - 19.8 (11.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D203V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HMMR MUTATED         0        0        0         1         4         1
  HMMR WILD-TYPE       1        3       12        18        78         3
                vv
clus             STAGE IV
  HMMR MUTATED          0
  HMMR WILD-TYPE        3
D203V3, multiclass
           clus
vv          HMMR MUTATED HMMR WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            4             78
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  HMMR MUTATED    0  0     6
  HMMR WILD-TYPE  5 17    96
D203V4, multiclass
       clus
vv      HMMR MUTATED HMMR WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V5, binary
                cls
clus              0  1
  HMMR MUTATED    2  4
  HMMR WILD-TYPE 33 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      2    4
  HMMR WILD-TYPE   33   85
   clus
vv  HMMR MUTATED HMMR WILD-TYPE
  0            2             33
  1            4             85
[1] 2 2
[1] FALSE
D203V6, binary
                cls
clus              0  1
  HMMR MUTATED    1  0
  HMMR WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      1    0
  HMMR WILD-TYPE   56    3
   clus
vv  HMMR MUTATED HMMR WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D203V7, binary
                cls
clus              0  1
  HMMR MUTATED    2  4
  HMMR WILD-TYPE 49 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      2    4
  HMMR WILD-TYPE   49   71
        clus
vv       HMMR MUTATED HMMR WILD-TYPE
  FEMALE            2             49
  MALE              4             71
[1] 2 2
[1] FALSE
D203V8, binary
                cls
clus              0  1
  HMMR MUTATED    5  1
  HMMR WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      5    1
  HMMR WILD-TYPE   83   29
     clus
vv    HMMR MUTATED HMMR WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HMMR MUTATED                                     5
  HMMR WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HMMR MUTATED                                       1
  HMMR WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HMMR MUTATED                                                  0
  HMMR WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  HMMR MUTATED                                     0
  HMMR WILD-TYPE                                   1
D203V9, multiclass
                                                  clus
vv                                                 HMMR MUTATED HMMR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V10, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" 
D203V11, continuous
[1] "Remove cluster labels:" "HMMR MUTATED"          
clus
  HMMR MUTATED HMMR WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" "HMMR WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  HMMR MUTATED    3  2  1  0
  HMMR WILD-TYPE 77 33  3  2
D203V12, multiclass
    clus
vv   HMMR MUTATED HMMR WILD-TYPE
  R0            3             77
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMMR MUTATED       1                         0     5
  HMMR WILD-TYPE     5                         5   109
D203V14, multiclass
                           clus
vv                          HMMR MUTATED HMMR WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V15, binary
                cls
clus              0  1
  HMMR MUTATED    1  3
  HMMR WILD-TYPE  4 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMMR MUTATED      1    3
  HMMR WILD-TYPE    4   88
                        clus
vv                       HMMR MUTATED HMMR WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(204) Variable = CSNK1G3 MUTATION ANALYSIS
D204V1, survival
                   sevent
clus2                0  1
  CSNK1G3 MUTATED    4  1
  CSNK1G3 WILD-TYPE 59 61
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                5               120 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
                1                61 
$`CSNK1G3 MUTATED`
TCGA-3A-A9IL TCGA-2J-AABO TCGA-FZ-5921 TCGA-IB-8126 TCGA-YY-A8LH 
       90.12        14.47         5.10        15.19        66.28 

$`CSNK1G3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        12.76        15.35 

  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
             5.10              0.23 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
            90.12             75.12 
  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE 
            15.19             15.27 
[1] "5.1 - 90.1 (15.2)" "0.2 - 75.1 (15.3)"
[1] "hr=" "3.5"
D204V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CSNK1G3 MUTATED         1        0        0         0         3         1
  CSNK1G3 WILD-TYPE       0        3       12        19        79         3
                   vv
clus                STAGE IV
  CSNK1G3 MUTATED          0
  CSNK1G3 WILD-TYPE        3
D204V3, multiclass
           clus
vv          CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CSNK1G3 MUTATED    1  0     4
  CSNK1G3 WILD-TYPE  4 17    98
D204V4, multiclass
       clus
vv      CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  T1                  1                 4
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V5, binary
                   cls
clus                 0  1
  CSNK1G3 MUTATED    0  4
  CSNK1G3 WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      0    4
  CSNK1G3 WILD-TYPE   35   85
   clus
vv  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D204V6, binary
                   cls
clus                 0  1
  CSNK1G3 MUTATED    3  0
  CSNK1G3 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      3    0
  CSNK1G3 WILD-TYPE   54    3
   clus
vv  CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D204V7, binary
                   cls
clus                 0  1
  CSNK1G3 MUTATED    4  1
  CSNK1G3 WILD-TYPE 47 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      4    1
  CSNK1G3 WILD-TYPE   47   74
        clus
vv       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  FEMALE               4                47
  MALE                 1                74
[1] 2 2
[1] FALSE
D204V8, binary
                   cls
clus                 0  1
  CSNK1G3 MUTATED    2  3
  CSNK1G3 WILD-TYPE 86 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      2    3
  CSNK1G3 WILD-TYPE   86   27
     clus
vv    CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  NO                2                86
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CSNK1G3 MUTATED                                     4
  CSNK1G3 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CSNK1G3 MUTATED                                       1
  CSNK1G3 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CSNK1G3 MUTATED                                                  0
  CSNK1G3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CSNK1G3 MUTATED                                     0
  CSNK1G3 WILD-TYPE                                   1
D204V9, multiclass
                                                  clus
vv                                                 CSNK1G3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CSNK1G3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V10, continuous
D204V11, continuous
                   vv
clus                R0 R1 R2 RX
  CSNK1G3 MUTATED    3  1  0  0
  CSNK1G3 WILD-TYPE 77 34  4  2
D204V12, multiclass
    clus
vv   CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSNK1G3 MUTATED       0                         0     4
  CSNK1G3 WILD-TYPE     6                         5   110
D204V14, multiclass
                           clus
vv                          CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V15, binary
                   cls
clus                 0  1
  CSNK1G3 MUTATED    0  3
  CSNK1G3 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK1G3 MUTATED      0    3
  CSNK1G3 WILD-TYPE    5   88
                        clus
vv                       CSNK1G3 MUTATED CSNK1G3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(205) Variable = ATP13A3 MUTATION ANALYSIS
D205V1, survival
                   sevent
clus2                0  1
  ATP13A3 MUTATED    5  0
  ATP13A3 WILD-TYPE 58 62
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                5               120 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                0                62 
$`ATP13A3 MUTATED`
TCGA-2J-AABR TCGA-IB-A7M4 TCGA-IB-AAUP TCGA-XN-A8T5 TCGA-YB-A89D 
       14.40        15.88        14.17        23.67        11.51 

$`ATP13A3 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ 
        1.35         8.22         0.26         4.73         7.86         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        31.27        12.76        66.28        15.35 

  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
            11.51              0.23 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
            23.67             90.12 
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
            14.40             15.27 
[1] "11.5 - 23.7 (14.4)" "0.2 - 90.1 (15.3)" 
[1] "hr="     "2.6e+07"
D205V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP13A3 MUTATED         0        0        1         1         3         0
  ATP13A3 WILD-TYPE       1        3       11        18        79         4
                   vv
clus                STAGE IV
  ATP13A3 MUTATED          0
  ATP13A3 WILD-TYPE        3
D205V3, multiclass
           clus
vv          ATP13A3 MUTATED ATP13A3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ATP13A3 MUTATED    0  1     4
  ATP13A3 WILD-TYPE  5 16    98
D205V4, multiclass
       clus
vv      ATP13A3 MUTATED ATP13A3 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V5, binary
                   cls
clus                 0  1
  ATP13A3 MUTATED    2  3
  ATP13A3 WILD-TYPE 33 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      2    3
  ATP13A3 WILD-TYPE   33   86
   clus
vv  ATP13A3 MUTATED ATP13A3 WILD-TYPE
  0               2                33
  1               3                86
[1] 2 2
[1] FALSE
D205V6, binary
                   cls
clus                 0  1
  ATP13A3 MUTATED    3  0
  ATP13A3 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      3    0
  ATP13A3 WILD-TYPE   54    3
   clus
vv  ATP13A3 MUTATED ATP13A3 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D205V7, binary
                   cls
clus                 0  1
  ATP13A3 MUTATED    2  3
  ATP13A3 WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      2    3
  ATP13A3 WILD-TYPE   49   72
        clus
vv       ATP13A3 MUTATED ATP13A3 WILD-TYPE
  FEMALE               2                49
  MALE                 3                72
[1] 2 2
[1] FALSE
D205V8, binary
                   cls
clus                 0  1
  ATP13A3 MUTATED    3  2
  ATP13A3 WILD-TYPE 85 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      3    2
  ATP13A3 WILD-TYPE   85   28
     clus
vv    ATP13A3 MUTATED ATP13A3 WILD-TYPE
  NO                3                85
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP13A3 MUTATED                                     4
  ATP13A3 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP13A3 MUTATED                                       1
  ATP13A3 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP13A3 MUTATED                                                  0
  ATP13A3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP13A3 MUTATED                                     0
  ATP13A3 WILD-TYPE                                   1
D205V9, multiclass
                                                  clus
vv                                                 ATP13A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ATP13A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V10, continuous
[1] "Remove cluster labels:" "ATP13A3 MUTATED"       
clus
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-YY-A8LH 
"ATP13A3 WILD-TYPE" 
D205V11, continuous
[1] "Remove cluster labels:" "ATP13A3 MUTATED"       
clus
  ATP13A3 MUTATED ATP13A3 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-YY-A8LH 
"ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" "ATP13A3 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ATP13A3 MUTATED    3  2  0  0
  ATP13A3 WILD-TYPE 77 33  4  2
D205V12, multiclass
    clus
vv   ATP13A3 MUTATED ATP13A3 WILD-TYPE
  R0               3                77
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP13A3 MUTATED       0                         0     5
  ATP13A3 WILD-TYPE     6                         5   109
D205V14, multiclass
                           clus
vv                          ATP13A3 MUTATED ATP13A3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V15, binary
                   cls
clus                 0  1
  ATP13A3 MUTATED    1  3
  ATP13A3 WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A3 MUTATED      1    3
  ATP13A3 WILD-TYPE    4   88
                        clus
vv                       ATP13A3 MUTATED ATP13A3 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(206) Variable = ZNF626 MUTATION ANALYSIS
D206V1, survival
                  sevent
clus2               0  1
  ZNF626 MUTATED    5  5
  ZNF626 WILD-TYPE 58 57
  ZNF626 MUTATED ZNF626 WILD-TYPE 
              10              115 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
               5               57 
$`ZNF626 MUTATED`
TCGA-2J-AAB8 TCGA-3A-A9IH TCGA-3A-A9IV TCGA-3A-A9IX TCGA-FB-A78T TCGA-FB-AAQ2 
        2.63        33.57        36.26        34.09        12.33         5.03 
TCGA-HV-AA8V TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-AAUW 
       30.25         5.26        19.82         7.56 

$`ZNF626 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IZ 
       24.26        63.85        50.70        32.81        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         4.04         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF626 MUTATED ZNF626 WILD-TYPE 
            2.63             0.23 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
           36.26            90.12 
  ZNF626 MUTATED ZNF626 WILD-TYPE 
          16.075           15.220 
[1] "2.6 - 36.3 (16.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D206V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF626 MUTATED         0        2        1         0         7         0
  ZNF626 WILD-TYPE       1        1       11        19        75         4
                  vv
clus               STAGE IV
  ZNF626 MUTATED          0
  ZNF626 WILD-TYPE        3
D206V3, multiclass
           clus
vv          ZNF626 MUTATED ZNF626 WILD-TYPE
  STAGE I                0                1
  STAGE IA               2                1
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF626 MUTATED    2  2     6
  ZNF626 WILD-TYPE  3 15    96
D206V4, multiclass
       clus
vv      ZNF626 MUTATED ZNF626 WILD-TYPE
  T1                 2                3
  T2                 2               15
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V5, binary
                  cls
clus                0  1
  ZNF626 MUTATED    3  7
  ZNF626 WILD-TYPE 32 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      3    7
  ZNF626 WILD-TYPE   32   82
   clus
vv  ZNF626 MUTATED ZNF626 WILD-TYPE
  0              3               32
  1              7               82
[1] 2 2
[1] FALSE
D206V6, binary
                  cls
clus                0  1
  ZNF626 MUTATED    4  0
  ZNF626 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      4    0
  ZNF626 WILD-TYPE   53    3
   clus
vv  ZNF626 MUTATED ZNF626 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D206V7, binary
                  cls
clus                0  1
  ZNF626 MUTATED    7  3
  ZNF626 WILD-TYPE 44 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      7    3
  ZNF626 WILD-TYPE   44   72
        clus
vv       ZNF626 MUTATED ZNF626 WILD-TYPE
  FEMALE              7               44
  MALE                3               72
[1] 2 2
[1] FALSE
D206V8, binary
                  cls
clus                0  1
  ZNF626 MUTATED    8  1
  ZNF626 WILD-TYPE 80 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      8    1
  ZNF626 WILD-TYPE   80   29
     clus
vv    ZNF626 MUTATED ZNF626 WILD-TYPE
  NO               8               80
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF626 MUTATED                                     9
  ZNF626 WILD-TYPE                                  96
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF626 MUTATED                                       1
  ZNF626 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF626 MUTATED                                                  0
  ZNF626 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF626 MUTATED                                     0
  ZNF626 WILD-TYPE                                   1
D206V9, multiclass
                                                  clus
vv                                                 ZNF626 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF626 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V10, continuous
D206V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF626 MUTATED    7  2  1  0
  ZNF626 WILD-TYPE 73 33  3  2
D206V12, multiclass
    clus
vv   ZNF626 MUTATED ZNF626 WILD-TYPE
  R0              7               73
  R1              2               33
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF626 MUTATED       1                         0     9
  ZNF626 WILD-TYPE     5                         5   105
D206V14, multiclass
                           clus
vv                          ZNF626 MUTATED ZNF626 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V15, binary
                  cls
clus                0  1
  ZNF626 MUTATED    0  8
  ZNF626 WILD-TYPE  5 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF626 MUTATED      0    8
  ZNF626 WILD-TYPE    5   83
                        clus
vv                       ZNF626 MUTATED ZNF626 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              8               83
[1] 2 2
[1] FALSE

Clustering(207) Variable = LIMD1 MUTATION ANALYSIS
D207V1, survival
                 sevent
clus2              0  1
  LIMD1 MUTATED    2  6
  LIMD1 WILD-TYPE 61 56
  LIMD1 MUTATED LIMD1 WILD-TYPE 
              8             117 
  LIMD1 MUTATED LIMD1 WILD-TYPE 
              6              56 
$`LIMD1 MUTATED`
TCGA-US-A77E TCGA-2J-AABU TCGA-FB-AAQ1 TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-A6UF 
       14.14         9.11         4.04        22.06        19.82        21.90 
TCGA-IB-A7LX TCGA-OE-A75W 
        8.22         8.78 

$`LIMD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88         1.35        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  LIMD1 MUTATED LIMD1 WILD-TYPE 
           4.04            0.23 
  LIMD1 MUTATED LIMD1 WILD-TYPE 
          22.06           90.12 
  LIMD1 MUTATED LIMD1 WILD-TYPE 
         11.625          15.320 
[1] "4.0 - 22.1 (11.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D207V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LIMD1 MUTATED         0        0        0         2         6         0
  LIMD1 WILD-TYPE       1        3       12        17        76         4
                 vv
clus              STAGE IV
  LIMD1 MUTATED          0
  LIMD1 WILD-TYPE        3
D207V3, multiclass
           clus
vv          LIMD1 MUTATED LIMD1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LIMD1 MUTATED    0  0     8
  LIMD1 WILD-TYPE  5 17    94
D207V4, multiclass
       clus
vv      LIMD1 MUTATED LIMD1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V5, binary
                 cls
clus               0  1
  LIMD1 MUTATED    2  6
  LIMD1 WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMD1 MUTATED      2    6
  LIMD1 WILD-TYPE   33   83
   clus
vv  LIMD1 MUTATED LIMD1 WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D207V6, binary
                 cls
clus               0  1
  LIMD1 MUTATED    4  0
  LIMD1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMD1 MUTATED      4    0
  LIMD1 WILD-TYPE   53    3
   clus
vv  LIMD1 MUTATED LIMD1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D207V7, binary
                 cls
clus               0  1
  LIMD1 MUTATED    1  7
  LIMD1 WILD-TYPE 50 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMD1 MUTATED      1    7
  LIMD1 WILD-TYPE   50   68
        clus
vv       LIMD1 MUTATED LIMD1 WILD-TYPE
  FEMALE             1              50
  MALE               7              68
[1] 2 2
[1] FALSE
D207V8, binary
                 cls
clus               0  1
  LIMD1 MUTATED    7  1
  LIMD1 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMD1 MUTATED      7    1
  LIMD1 WILD-TYPE   81   29
     clus
vv    LIMD1 MUTATED LIMD1 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LIMD1 MUTATED                                     6
  LIMD1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LIMD1 MUTATED                                       2
  LIMD1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LIMD1 MUTATED                                                  0
  LIMD1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LIMD1 MUTATED                                     0
  LIMD1 WILD-TYPE                                   1
D207V9, multiclass
                                                  clus
vv                                                 LIMD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LIMD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V10, continuous
D207V11, continuous
                 vv
clus              R0 R1 R2 RX
  LIMD1 MUTATED    5  3  0  0
  LIMD1 WILD-TYPE 75 32  4  2
D207V12, multiclass
    clus
vv   LIMD1 MUTATED LIMD1 WILD-TYPE
  R0             5              75
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LIMD1 MUTATED       0                         0     8
  LIMD1 WILD-TYPE     6                         5   106
D207V14, multiclass
                           clus
vv                          LIMD1 MUTATED LIMD1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V15, binary
                 cls
clus               0  1
  LIMD1 MUTATED    0  7
  LIMD1 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LIMD1 MUTATED      0    7
  LIMD1 WILD-TYPE    5   84
                        clus
vv                       LIMD1 MUTATED LIMD1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(208) Variable = ESCO2 MUTATION ANALYSIS
D208V1, survival
                 sevent
clus2              0  1
  ESCO2 MUTATED    3  1
  ESCO2 WILD-TYPE 60 61
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              4             121 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              1              61 
$`ESCO2 MUTATED`
TCGA-IB-A5ST TCGA-IB-AAUQ TCGA-RB-AA9M TCGA-Z5-AAPL 
       20.88         6.02         9.40        15.35 

$`ESCO2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85         7.20        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  ESCO2 MUTATED ESCO2 WILD-TYPE 
           6.02            0.23 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          20.88           90.12 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
         12.375          15.220 
[1] "6.0 - 20.9 (12.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D208V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ESCO2 MUTATED         0        0        0         1         3         0
  ESCO2 WILD-TYPE       1        3       12        18        79         4
                 vv
clus              STAGE IV
  ESCO2 MUTATED          0
  ESCO2 WILD-TYPE        3
D208V3, multiclass
           clus
vv          ESCO2 MUTATED ESCO2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ESCO2 MUTATED    1  0     3
  ESCO2 WILD-TYPE  4 17    99
D208V4, multiclass
       clus
vv      ESCO2 MUTATED ESCO2 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V5, binary
                 cls
clus               0  1
  ESCO2 MUTATED    1  3
  ESCO2 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      1    3
  ESCO2 WILD-TYPE   34   86
   clus
vv  ESCO2 MUTATED ESCO2 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D208V6, binary
                 cls
clus               0  1
  ESCO2 MUTATED    3  0
  ESCO2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      3    0
  ESCO2 WILD-TYPE   54    3
   clus
vv  ESCO2 MUTATED ESCO2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D208V7, binary
                 cls
clus               0  1
  ESCO2 MUTATED    2  2
  ESCO2 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      2    2
  ESCO2 WILD-TYPE   49   73
        clus
vv       ESCO2 MUTATED ESCO2 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D208V8, binary
                 cls
clus               0  1
  ESCO2 MUTATED    3  1
  ESCO2 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      3    1
  ESCO2 WILD-TYPE   85   29
     clus
vv    ESCO2 MUTATED ESCO2 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ESCO2 MUTATED                                     4
  ESCO2 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ESCO2 MUTATED                                       0
  ESCO2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ESCO2 MUTATED                                                  0
  ESCO2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ESCO2 MUTATED                                     0
  ESCO2 WILD-TYPE                                   1
D208V9, multiclass
                                                  clus
vv                                                 ESCO2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ESCO2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V10, continuous
[1] "Remove cluster labels:" "ESCO2 MUTATED"         
clus
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUS 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
D208V11, continuous
[1] "Remove cluster labels:" "ESCO2 MUTATED"         
clus
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" "ESCO2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ESCO2 MUTATED    3  1  0  0
  ESCO2 WILD-TYPE 77 34  4  2
D208V12, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESCO2 MUTATED       0                         0     4
  ESCO2 WILD-TYPE     6                         5   110
D208V14, multiclass
                           clus
vv                          ESCO2 MUTATED ESCO2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V15, binary
                 cls
clus               0  1
  ESCO2 MUTATED    0  4
  ESCO2 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      0    4
  ESCO2 WILD-TYPE    5   87
                        clus
vv                       ESCO2 MUTATED ESCO2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(209) Variable = MRPS5 MUTATION ANALYSIS
D209V1, survival
                 sevent
clus2              0  1
  MRPS5 MUTATED    1  3
  MRPS5 WILD-TYPE 62 59
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4             121 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              3              59 
$`MRPS5 MUTATED`
TCGA-2J-AABU TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-A7M4 
        9.11        19.82         7.20        15.88 

$`MRPS5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
           7.20            0.23 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          19.82           90.12 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
         12.495          15.220 
[1] "7.2 - 19.8 (12.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.2"
D209V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MRPS5 MUTATED         0        0        1         0         3         0
  MRPS5 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  MRPS5 MUTATED          0
  MRPS5 WILD-TYPE        3
D209V3, multiclass
           clus
vv          MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MRPS5 MUTATED    0  1     3
  MRPS5 WILD-TYPE  5 16    99
D209V4, multiclass
       clus
vv      MRPS5 MUTATED MRPS5 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V5, binary
                 cls
clus               0  1
  MRPS5 MUTATED    1  3
  MRPS5 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      1    3
  MRPS5 WILD-TYPE   34   86
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D209V6, binary
                 cls
clus               0  1
  MRPS5 MUTATED    3  0
  MRPS5 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      3    0
  MRPS5 WILD-TYPE   54    3
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D209V7, binary
                 cls
clus               0  1
  MRPS5 MUTATED    2  2
  MRPS5 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      2    2
  MRPS5 WILD-TYPE   49   73
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D209V8, binary
                 cls
clus               0  1
  MRPS5 MUTATED    4  0
  MRPS5 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      4    0
  MRPS5 WILD-TYPE   84   30
     clus
vv    MRPS5 MUTATED MRPS5 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MRPS5 MUTATED                                     4
  MRPS5 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MRPS5 MUTATED                                       0
  MRPS5 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MRPS5 MUTATED                                                  0
  MRPS5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MRPS5 MUTATED                                     0
  MRPS5 WILD-TYPE                                   1
D209V9, multiclass
                                                  clus
vv                                                 MRPS5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MRPS5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V10, continuous
[1] "Remove cluster labels:" "MRPS5 MUTATED"         
clus
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-YY-A8LH 
"MRPS5 WILD-TYPE" 
D209V11, continuous
[1] "Remove cluster labels:" "MRPS5 MUTATED"         
clus
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-AAUQ 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" "MRPS5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MRPS5 MUTATED    4  0  0  0
  MRPS5 WILD-TYPE 76 35  4  2
D209V12, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MRPS5 MUTATED       0                         0     4
  MRPS5 WILD-TYPE     6                         5   110
D209V14, multiclass
                           clus
vv                          MRPS5 MUTATED MRPS5 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V15, binary
                 cls
clus               0  1
  MRPS5 MUTATED    0  3
  MRPS5 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      0    3
  MRPS5 WILD-TYPE    5   88
                        clus
vv                       MRPS5 MUTATED MRPS5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(210) Variable = TFIP11 MUTATION ANALYSIS
D210V1, survival
                  sevent
clus2               0  1
  TFIP11 MUTATED    3  3
  TFIP11 WILD-TYPE 60 59
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               6              119 
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               3               59 
$`TFIP11 MUTATED`
TCGA-2J-AABR TCGA-2J-AABO TCGA-FZ-5922 TCGA-IB-7651 TCGA-IB-AAUP TCGA-US-A77G 
       14.40        14.47        36.20        19.82        14.17         0.39 

$`TFIP11 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TFIP11 MUTATED TFIP11 WILD-TYPE 
            0.39             0.23 
  TFIP11 MUTATED TFIP11 WILD-TYPE 
           36.20            90.12 
  TFIP11 MUTATED TFIP11 WILD-TYPE 
          14.435           15.320 
[1] "0.4 - 36.2 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D210V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TFIP11 MUTATED         0        0        0         2         4         0
  TFIP11 WILD-TYPE       1        3       12        17        78         4
                  vv
clus               STAGE IV
  TFIP11 MUTATED          0
  TFIP11 WILD-TYPE        3
D210V3, multiclass
           clus
vv          TFIP11 MUTATED TFIP11 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TFIP11 MUTATED    0  0     6
  TFIP11 WILD-TYPE  5 17    96
D210V4, multiclass
       clus
vv      TFIP11 MUTATED TFIP11 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V5, binary
                  cls
clus                0  1
  TFIP11 MUTATED    2  4
  TFIP11 WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFIP11 MUTATED      2    4
  TFIP11 WILD-TYPE   33   85
   clus
vv  TFIP11 MUTATED TFIP11 WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D210V6, binary
                  cls
clus                0  1
  TFIP11 MUTATED    5  0
  TFIP11 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFIP11 MUTATED      5    0
  TFIP11 WILD-TYPE   52    3
   clus
vv  TFIP11 MUTATED TFIP11 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D210V7, binary
                  cls
clus                0  1
  TFIP11 MUTATED    2  4
  TFIP11 WILD-TYPE 49 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFIP11 MUTATED      2    4
  TFIP11 WILD-TYPE   49   71
        clus
vv       TFIP11 MUTATED TFIP11 WILD-TYPE
  FEMALE              2               49
  MALE                4               71
[1] 2 2
[1] FALSE
D210V8, binary
                  cls
clus                0  1
  TFIP11 MUTATED    5  1
  TFIP11 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFIP11 MUTATED      5    1
  TFIP11 WILD-TYPE   83   29
     clus
vv    TFIP11 MUTATED TFIP11 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TFIP11 MUTATED                                     6
  TFIP11 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TFIP11 MUTATED                                       0
  TFIP11 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TFIP11 MUTATED                                                  0
  TFIP11 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TFIP11 MUTATED                                     0
  TFIP11 WILD-TYPE                                   1
D210V9, multiclass
                                                  clus
vv                                                 TFIP11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TFIP11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V10, continuous
[1] "Remove cluster labels:" "TFIP11 MUTATED"        
clus
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABV       TCGA-2L-AAQA 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-YY-A8LH 
"TFIP11 WILD-TYPE" 
D210V11, continuous
[1] "Remove cluster labels:" "TFIP11 MUTATED"        
clus
  TFIP11 MUTATED TFIP11 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" "TFIP11 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TFIP11 MUTATED    5  1  0  0
  TFIP11 WILD-TYPE 75 34  4  2
D210V12, multiclass
    clus
vv   TFIP11 MUTATED TFIP11 WILD-TYPE
  R0              5               75
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TFIP11 MUTATED       0                         0     6
  TFIP11 WILD-TYPE     6                         5   108
D210V14, multiclass
                           clus
vv                          TFIP11 MUTATED TFIP11 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V15, binary
                  cls
clus                0  1
  TFIP11 MUTATED    0  4
  TFIP11 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFIP11 MUTATED      0    4
  TFIP11 WILD-TYPE    5   87
                        clus
vv                       TFIP11 MUTATED TFIP11 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(211) Variable = PVRL1 MUTATION ANALYSIS
D211V1, survival
                 sevent
clus2              0  1
  PVRL1 MUTATED    4  4
  PVRL1 WILD-TYPE 59 58
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              8             117 
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              4              58 
$`PVRL1 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2L-AAQM TCGA-HV-A7OL 
        9.63         2.63        20.61        42.31        45.47         8.28 
TCGA-HZ-7925 TCGA-IB-7651 
       20.19        19.82 

$`PVRL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AABA TCGA-2J-AABE 
       14.14        16.37         2.17        23.97        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 
        4.70        22.49         3.39        12.95         9.60        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP 
        5.10        36.20        20.35        17.79        22.06        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        17.49        31.86        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PVRL1 MUTATED PVRL1 WILD-TYPE 
           2.63            0.23 
  PVRL1 MUTATED PVRL1 WILD-TYPE 
          45.47           90.12 
  PVRL1 MUTATED PVRL1 WILD-TYPE 
         20.005          15.190 
[1] "2.6 - 45.5 (20.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D211V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PVRL1 MUTATED         0        0        0         3         5         0
  PVRL1 WILD-TYPE       1        3       12        16        77         4
                 vv
clus              STAGE IV
  PVRL1 MUTATED          0
  PVRL1 WILD-TYPE        3
D211V3, multiclass
           clus
vv          PVRL1 MUTATED PVRL1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PVRL1 MUTATED    0  0     8
  PVRL1 WILD-TYPE  5 17    94
D211V4, multiclass
       clus
vv      PVRL1 MUTATED PVRL1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V5, binary
                 cls
clus               0  1
  PVRL1 MUTATED    3  5
  PVRL1 WILD-TYPE 32 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL1 MUTATED      3    5
  PVRL1 WILD-TYPE   32   84
   clus
vv  PVRL1 MUTATED PVRL1 WILD-TYPE
  0             3              32
  1             5              84
[1] 2 2
[1] FALSE
D211V6, binary
                 cls
clus               0  1
  PVRL1 MUTATED    5  0
  PVRL1 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL1 MUTATED      5    0
  PVRL1 WILD-TYPE   52    3
   clus
vv  PVRL1 MUTATED PVRL1 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D211V7, binary
                 cls
clus               0  1
  PVRL1 MUTATED    2  6
  PVRL1 WILD-TYPE 49 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL1 MUTATED      2    6
  PVRL1 WILD-TYPE   49   69
        clus
vv       PVRL1 MUTATED PVRL1 WILD-TYPE
  FEMALE             2              49
  MALE               6              69
[1] 2 2
[1] FALSE
D211V8, binary
                 cls
clus               0  1
  PVRL1 MUTATED    6  1
  PVRL1 WILD-TYPE 82 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL1 MUTATED      6    1
  PVRL1 WILD-TYPE   82   29
     clus
vv    PVRL1 MUTATED PVRL1 WILD-TYPE
  NO              6              82
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PVRL1 MUTATED                                     6
  PVRL1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PVRL1 MUTATED                                       2
  PVRL1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PVRL1 MUTATED                                                  0
  PVRL1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PVRL1 MUTATED                                     0
  PVRL1 WILD-TYPE                                   1
D211V9, multiclass
                                                  clus
vv                                                 PVRL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PVRL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V10, continuous
[1] "Remove cluster labels:" "PVRL1 MUTATED"         
clus
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
D211V11, continuous
[1] "Remove cluster labels:" "PVRL1 MUTATED"         
clus
  PVRL1 MUTATED PVRL1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" "PVRL1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PVRL1 MUTATED    5  2  1  0
  PVRL1 WILD-TYPE 75 33  3  2
D211V12, multiclass
    clus
vv   PVRL1 MUTATED PVRL1 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PVRL1 MUTATED       1                         0     7
  PVRL1 WILD-TYPE     5                         5   107
D211V14, multiclass
                           clus
vv                          PVRL1 MUTATED PVRL1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V15, binary
                 cls
clus               0  1
  PVRL1 MUTATED    0  2
  PVRL1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL1 MUTATED      0    2
  PVRL1 WILD-TYPE    5   89
                        clus
vv                       PVRL1 MUTATED PVRL1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(212) Variable = DIAPH3 MUTATION ANALYSIS
D212V1, survival
                  sevent
clus2               0  1
  DIAPH3 MUTATED    3  4
  DIAPH3 WILD-TYPE 60 58
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               7              118 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               4               58 
$`DIAPH3 MUTATED`
TCGA-US-A77E TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A5SO 
       14.14         8.28        32.15         5.26        19.82        12.00 
TCGA-Q3-A5QY 
       13.68 

$`DIAPH3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79        22.06        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        15.19        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
            5.26             0.23 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
           32.15            90.12 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          13.680           15.335 
[1] "5.3 - 32.1 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D212V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DIAPH3 MUTATED         0        0        0         1         6         0
  DIAPH3 WILD-TYPE       1        3       12        18        76         4
                  vv
clus               STAGE IV
  DIAPH3 MUTATED          0
  DIAPH3 WILD-TYPE        3
D212V3, multiclass
           clus
vv          DIAPH3 MUTATED DIAPH3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  DIAPH3 MUTATED    0  1     6
  DIAPH3 WILD-TYPE  5 16    96
D212V4, multiclass
       clus
vv      DIAPH3 MUTATED DIAPH3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V5, binary
                  cls
clus                0  1
  DIAPH3 MUTATED    1  6
  DIAPH3 WILD-TYPE 34 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      1    6
  DIAPH3 WILD-TYPE   34   83
   clus
vv  DIAPH3 MUTATED DIAPH3 WILD-TYPE
  0              1               34
  1              6               83
[1] 2 2
[1] FALSE
D212V6, binary
                  cls
clus                0  1
  DIAPH3 MUTATED    3  0
  DIAPH3 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      3    0
  DIAPH3 WILD-TYPE   54    3
   clus
vv  DIAPH3 MUTATED DIAPH3 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D212V7, binary
                  cls
clus                0  1
  DIAPH3 MUTATED    2  5
  DIAPH3 WILD-TYPE 49 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      2    5
  DIAPH3 WILD-TYPE   49   70
        clus
vv       DIAPH3 MUTATED DIAPH3 WILD-TYPE
  FEMALE              2               49
  MALE                5               70
[1] 2 2
[1] FALSE
D212V8, binary
                  cls
clus                0  1
  DIAPH3 MUTATED    6  1
  DIAPH3 WILD-TYPE 82 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      6    1
  DIAPH3 WILD-TYPE   82   29
     clus
vv    DIAPH3 MUTATED DIAPH3 WILD-TYPE
  NO               6               82
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DIAPH3 MUTATED                                     5
  DIAPH3 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DIAPH3 MUTATED                                       2
  DIAPH3 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DIAPH3 MUTATED                                                  0
  DIAPH3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  DIAPH3 MUTATED                                     0
  DIAPH3 WILD-TYPE                                   1
D212V9, multiclass
                                                  clus
vv                                                 DIAPH3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 DIAPH3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V10, continuous
[1] "Remove cluster labels:" "DIAPH3 MUTATED"        
clus
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
D212V11, continuous
[1] "Remove cluster labels:" "DIAPH3 MUTATED"        
clus
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" "DIAPH3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  DIAPH3 MUTATED    5  1  1  0
  DIAPH3 WILD-TYPE 75 34  3  2
D212V12, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  R0              5               75
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIAPH3 MUTATED       2                         0     5
  DIAPH3 WILD-TYPE     4                         5   109
D212V14, multiclass
                           clus
vv                          DIAPH3 MUTATED DIAPH3 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V15, binary
                  cls
clus                0  1
  DIAPH3 MUTATED    0  4
  DIAPH3 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      0    4
  DIAPH3 WILD-TYPE    5   87
                        clus
vv                       DIAPH3 MUTATED DIAPH3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(213) Variable = IRS4 MUTATION ANALYSIS
D213V1, survival
                sevent
clus2             0  1
  IRS4 MUTATED    2  6
  IRS4 WILD-TYPE 61 56
  IRS4 MUTATED IRS4 WILD-TYPE 
             8            117 
  IRS4 MUTATED IRS4 WILD-TYPE 
             6             56 
$`IRS4 MUTATED`
TCGA-2J-AABA TCGA-2J-AABU TCGA-2L-AAQI TCGA-F2-A8YN TCGA-HV-A7OP TCGA-HZ-8637 
       19.96         9.11         3.39        17.00        32.15        17.00 
TCGA-IB-7651 TCGA-US-A77G 
       19.82         0.39 

$`IRS4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
       15.22        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
        8.28        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J 
       15.32         9.40         0.30        39.98        16.80        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  IRS4 MUTATED IRS4 WILD-TYPE 
          0.39           0.23 
  IRS4 MUTATED IRS4 WILD-TYPE 
         32.15          90.12 
  IRS4 MUTATED IRS4 WILD-TYPE 
         17.00          15.19 
[1] "0.4 - 32.1 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D213V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IRS4 MUTATED         0        0        0         1         7         0
  IRS4 WILD-TYPE       1        3       12        18        75         4
                vv
clus             STAGE IV
  IRS4 MUTATED          0
  IRS4 WILD-TYPE        3
D213V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  IRS4 MUTATED    0  0     8
  IRS4 WILD-TYPE  5 17    94
D213V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V5, binary
                cls
clus              0  1
  IRS4 MUTATED    1  7
  IRS4 WILD-TYPE 34 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1    7
  IRS4 WILD-TYPE   34   82
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            1             34
  1            7             82
[1] 2 2
[1] FALSE
D213V6, binary
                cls
clus              0  1
  IRS4 MUTATED    5  0
  IRS4 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      5    0
  IRS4 WILD-TYPE   52    3
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D213V7, binary
                cls
clus              0  1
  IRS4 MUTATED    2  6
  IRS4 WILD-TYPE 49 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2    6
  IRS4 WILD-TYPE   49   69
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            2             49
  MALE              6             69
[1] 2 2
[1] FALSE
D213V8, binary
                cls
clus              0  1
  IRS4 MUTATED    6  2
  IRS4 WILD-TYPE 82 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      6    2
  IRS4 WILD-TYPE   82   28
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO             6             82
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS4 MUTATED                                     7
  IRS4 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS4 MUTATED                                       1
  IRS4 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS4 MUTATED                                                  0
  IRS4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  IRS4 MUTATED                                     0
  IRS4 WILD-TYPE                                   1
D213V9, multiclass
                                                  clus
vv                                                 IRS4 MUTATED IRS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V10, continuous
D213V11, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  IRS4 MUTATED    5  3  0  0
  IRS4 WILD-TYPE 75 32  4  2
D213V12, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0            5             75
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED       1                         0     7
  IRS4 WILD-TYPE     5                         5   107
D213V14, multiclass
                           clus
vv                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V15, binary
                cls
clus              0  1
  IRS4 MUTATED    1  3
  IRS4 WILD-TYPE  4 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1    3
  IRS4 WILD-TYPE    4   88
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(214) Variable = USP4 MUTATION ANALYSIS
D214V1, survival
                sevent
clus2             0  1
  USP4 MUTATED    4  2
  USP4 WILD-TYPE 59 60
  USP4 MUTATED USP4 WILD-TYPE 
             6            119 
  USP4 MUTATED USP4 WILD-TYPE 
             2             60 
$`USP4 MUTATED`
TCGA-3A-A9IL TCGA-FB-AAQ3 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-Q3-A5QY TCGA-YY-A8LH 
       90.12         1.02        19.82        19.82        13.68        66.28 

$`USP4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  USP4 MUTATED USP4 WILD-TYPE 
          1.02           0.23 
  USP4 MUTATED USP4 WILD-TYPE 
         90.12          75.12 
  USP4 MUTATED USP4 WILD-TYPE 
         19.82          15.19 
[1] "1.0 - 90.1 (19.8)" "0.2 - 75.1 (15.2)"
[1] "hr=" "2.1"
D214V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  USP4 MUTATED         1        0        0         0         5         0
  USP4 WILD-TYPE       0        3       12        19        77         4
                vv
clus             STAGE IV
  USP4 MUTATED          1
  USP4 WILD-TYPE        2
D214V3, multiclass
           clus
vv          USP4 MUTATED USP4 WILD-TYPE
  STAGE I              1              0
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  USP4 MUTATED    1  0     6
  USP4 WILD-TYPE  4 17    96
D214V4, multiclass
       clus
vv      USP4 MUTATED USP4 WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V5, binary
                cls
clus              0  1
  USP4 MUTATED    1  5
  USP4 WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP4 MUTATED      1    5
  USP4 WILD-TYPE   34   84
   clus
vv  USP4 MUTATED USP4 WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D214V6, binary
                cls
clus              0  1
  USP4 MUTATED    1  1
  USP4 WILD-TYPE 56  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP4 MUTATED      1    1
  USP4 WILD-TYPE   56    2
   clus
vv  USP4 MUTATED USP4 WILD-TYPE
  0            1             56
  1            1              2
[1] 2 2
[1] FALSE
D214V7, binary
                cls
clus              0  1
  USP4 MUTATED    4  3
  USP4 WILD-TYPE 47 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP4 MUTATED      4    3
  USP4 WILD-TYPE   47   72
        clus
vv       USP4 MUTATED USP4 WILD-TYPE
  FEMALE            4             47
  MALE              3             72
[1] 2 2
[1] FALSE
D214V8, binary
                cls
clus              0  1
  USP4 MUTATED    5  1
  USP4 WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP4 MUTATED      5    1
  USP4 WILD-TYPE   83   29
     clus
vv    USP4 MUTATED USP4 WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  USP4 MUTATED                                     5
  USP4 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  USP4 MUTATED                                       2
  USP4 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  USP4 MUTATED                                                  0
  USP4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  USP4 MUTATED                                     0
  USP4 WILD-TYPE                                   1
D214V9, multiclass
                                                  clus
vv                                                 USP4 MUTATED USP4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V10, continuous
D214V11, continuous
                vv
clus             R0 R1 R2 RX
  USP4 MUTATED    7  0  0  0
  USP4 WILD-TYPE 73 35  4  2
D214V12, multiclass
    clus
vv   USP4 MUTATED USP4 WILD-TYPE
  R0            7             73
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  USP4 MUTATED       0                         0     7
  USP4 WILD-TYPE     6                         5   107
D214V14, multiclass
                           clus
vv                          USP4 MUTATED USP4 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V15, binary
                cls
clus              0  1
  USP4 MUTATED    0  7
  USP4 WILD-TYPE  5 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP4 MUTATED      0    7
  USP4 WILD-TYPE    5   84
                        clus
vv                       USP4 MUTATED USP4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7             84
[1] 2 2
[1] FALSE

Clustering(215) Variable = TGFBR2 MUTATION ANALYSIS
D215V1, survival
                  sevent
clus2               0  1
  TGFBR2 MUTATED    1  7
  TGFBR2 WILD-TYPE 62 55
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              117 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               7               55 
$`TGFBR2 MUTATED`
TCGA-FB-AAQ6 TCGA-2J-AAB1 TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9IC TCGA-IB-7651 
        8.02         2.17        12.95         9.60        24.26        19.82 
TCGA-IB-7885 TCGA-IB-A5SO 
       41.33        12.00 

$`TGFBR2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQM 
        9.11        21.44         4.70        22.49         3.39        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       43.50        20.84         7.36        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            2.17             0.23 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           41.33            90.12 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          12.475           15.320 
[1] "2.2 - 41.3 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D215V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TGFBR2 MUTATED         0        1        0         0         6         1
  TGFBR2 WILD-TYPE       1        2       12        19        76         3
                  vv
clus               STAGE IV
  TGFBR2 MUTATED          0
  TGFBR2 WILD-TYPE        3
D215V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              6               76
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TGFBR2 MUTATED    1  0     7
  TGFBR2 WILD-TYPE  4 17    95
D215V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V5, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    2  6
  TGFBR2 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      2    6
  TGFBR2 WILD-TYPE   33   83
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D215V6, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    4  0
  TGFBR2 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      4    0
  TGFBR2 WILD-TYPE   53    3
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D215V7, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    4  4
  TGFBR2 WILD-TYPE 47 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      4    4
  TGFBR2 WILD-TYPE   47   71
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              4               47
  MALE                4               71
[1] 2 2
[1] FALSE
D215V8, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    7  1
  TGFBR2 WILD-TYPE 81 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      7    1
  TGFBR2 WILD-TYPE   81   29
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               7               81
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR2 MUTATED                                     7
  TGFBR2 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR2 MUTATED                                       1
  TGFBR2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR2 MUTATED                                                  0
  TGFBR2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TGFBR2 MUTATED                                     0
  TGFBR2 WILD-TYPE                                   1
D215V9, multiclass
                                                  clus
vv                                                 TGFBR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TGFBR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V10, continuous
D215V11, continuous
                  vv
clus               R0 R1 R2 RX
  TGFBR2 MUTATED    6  1  0  1
  TGFBR2 WILD-TYPE 74 34  4  1
D215V12, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED       0                         0     8
  TGFBR2 WILD-TYPE     6                         5   106
D215V14, multiclass
                           clus
vv                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V15, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    0  4
  TGFBR2 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    4
  TGFBR2 WILD-TYPE    5   87
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(216) Variable = ZMYND8 MUTATION ANALYSIS
D216V1, survival
                  sevent
clus2               0  1
  ZMYND8 MUTATED    4  4
  ZMYND8 WILD-TYPE 59 58
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               8              117 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               4               58 
$`ZMYND8 MUTATED`
TCGA-FB-AAQ6 TCGA-F2-A7TX TCGA-FB-AAPP TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7651 
        8.02         3.12        15.95        10.85        19.82        19.82 
TCGA-IB-8126 TCGA-YY-A8LH 
       15.19        66.28 

$`ZMYND8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
       19.46        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7652 
       20.19        17.00        10.13         5.26         0.23        36.69 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76        15.35 

  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
            3.12             0.23 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           66.28            90.12 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           15.57            15.22 
[1] "3.1 - 66.3 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D216V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZMYND8 MUTATED         0        1        0         0         5         1
  ZMYND8 WILD-TYPE       1        2       12        19        77         3
                  vv
clus               STAGE IV
  ZMYND8 MUTATED          1
  ZMYND8 WILD-TYPE        2
D216V3, multiclass
           clus
vv          ZMYND8 MUTATED ZMYND8 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZMYND8 MUTATED    1  0     7
  ZMYND8 WILD-TYPE  4 17    95
D216V4, multiclass
       clus
vv      ZMYND8 MUTATED ZMYND8 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V5, binary
                  cls
clus                0  1
  ZMYND8 MUTATED    2  6
  ZMYND8 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      2    6
  ZMYND8 WILD-TYPE   33   83
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D216V6, binary
                  cls
clus                0  1
  ZMYND8 MUTATED    3  1
  ZMYND8 WILD-TYPE 54  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      3    1
  ZMYND8 WILD-TYPE   54    2
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0              3               54
  1              1                2
[1] 2 2
[1] FALSE
D216V7, binary
                  cls
clus                0  1
  ZMYND8 MUTATED    3  5
  ZMYND8 WILD-TYPE 48 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      3    5
  ZMYND8 WILD-TYPE   48   70
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  FEMALE              3               48
  MALE                5               70
[1] 2 2
[1] FALSE
D216V8, binary
                  cls
clus                0  1
  ZMYND8 MUTATED    6  2
  ZMYND8 WILD-TYPE 82 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      6    2
  ZMYND8 WILD-TYPE   82   28
     clus
vv    ZMYND8 MUTATED ZMYND8 WILD-TYPE
  NO               6               82
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYND8 MUTATED                                     6
  ZMYND8 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYND8 MUTATED                                       2
  ZMYND8 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYND8 MUTATED                                                  0
  ZMYND8 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZMYND8 MUTATED                                     0
  ZMYND8 WILD-TYPE                                   1
D216V9, multiclass
                                                  clus
vv                                                 ZMYND8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZMYND8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V10, continuous
D216V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZMYND8 MUTATED    6  2  0  0
  ZMYND8 WILD-TYPE 74 33  4  2
D216V12, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  R0              6               74
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYND8 MUTATED       0                         0     8
  ZMYND8 WILD-TYPE     6                         5   106
D216V14, multiclass
                           clus
vv                          ZMYND8 MUTATED ZMYND8 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V15, binary
                  cls
clus                0  1
  ZMYND8 MUTATED    0  7
  ZMYND8 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED      0    7
  ZMYND8 WILD-TYPE    5   84
                        clus
vv                       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(217) Variable = ATG2B MUTATION ANALYSIS
D217V1, survival
                 sevent
clus2              0  1
  ATG2B MUTATED    4  5
  ATG2B WILD-TYPE 59 57
  ATG2B MUTATED ATG2B WILD-TYPE 
              9             116 
  ATG2B MUTATED ATG2B WILD-TYPE 
              5              57 
$`ATG2B MUTATED`
TCGA-3A-A9IJ TCGA-2J-AAB4 TCGA-3A-A9IU TCGA-FB-AAPS TCGA-FZ-5922 TCGA-FZ-5926 
       60.95        23.97        15.06         7.50        36.20        17.79 
TCGA-IB-7651 TCGA-IB-AAUQ TCGA-XN-A8T3 
       19.82         6.02        31.27 

$`ATG2B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
        2.01         5.10        20.35        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ATG2B MUTATED ATG2B WILD-TYPE 
           6.02            0.23 
  ATG2B MUTATED ATG2B WILD-TYPE 
          60.95           90.12 
  ATG2B MUTATED ATG2B WILD-TYPE 
         19.820          15.155 
[1] "6.0 - 61.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D217V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATG2B MUTATED         0        0        2         1         5         1
  ATG2B WILD-TYPE       1        3       10        18        77         3
                 vv
clus              STAGE IV
  ATG2B MUTATED          0
  ATG2B WILD-TYPE        3
D217V3, multiclass
           clus
vv          ATG2B MUTATED ATG2B WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ATG2B MUTATED    0  4     5
  ATG2B WILD-TYPE  5 13    97
D217V4, multiclass
       clus
vv      ATG2B MUTATED ATG2B WILD-TYPE
  T1                0               5
  T2                4              13
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V5, binary
                 cls
clus               0  1
  ATG2B MUTATED    3  6
  ATG2B WILD-TYPE 32 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      3    6
  ATG2B WILD-TYPE   32   83
   clus
vv  ATG2B MUTATED ATG2B WILD-TYPE
  0             3              32
  1             6              83
[1] 2 2
[1] FALSE
D217V6, binary
                 cls
clus               0  1
  ATG2B MUTATED    6  0
  ATG2B WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      6    0
  ATG2B WILD-TYPE   51    3
   clus
vv  ATG2B MUTATED ATG2B WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D217V7, binary
                 cls
clus               0  1
  ATG2B MUTATED    3  6
  ATG2B WILD-TYPE 48 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      3    6
  ATG2B WILD-TYPE   48   69
        clus
vv       ATG2B MUTATED ATG2B WILD-TYPE
  FEMALE             3              48
  MALE               6              69
[1] 2 2
[1] FALSE
D217V8, binary
                 cls
clus               0  1
  ATG2B MUTATED    7  2
  ATG2B WILD-TYPE 81 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      7    2
  ATG2B WILD-TYPE   81   28
     clus
vv    ATG2B MUTATED ATG2B WILD-TYPE
  NO              7              81
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATG2B MUTATED                                     7
  ATG2B WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATG2B MUTATED                                       2
  ATG2B WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATG2B MUTATED                                                  0
  ATG2B WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATG2B MUTATED                                     0
  ATG2B WILD-TYPE                                   1
D217V9, multiclass
                                                  clus
vv                                                 ATG2B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ATG2B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V10, continuous
D217V11, continuous
                 vv
clus              R0 R1 R2 RX
  ATG2B MUTATED    7  2  0  0
  ATG2B WILD-TYPE 73 33  4  2
D217V12, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  R0             7              73
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATG2B MUTATED       0                         0     9
  ATG2B WILD-TYPE     6                         5   105
D217V14, multiclass
                           clus
vv                          ATG2B MUTATED ATG2B WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V15, binary
                 cls
clus               0  1
  ATG2B MUTATED    1  7
  ATG2B WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      1    7
  ATG2B WILD-TYPE    4   84
                        clus
vv                       ATG2B MUTATED ATG2B WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(218) Variable = CDH10 MUTATION ANALYSIS
D218V1, survival
                 sevent
clus2              0  1
  CDH10 MUTATED    8  5
  CDH10 WILD-TYPE 55 57
  CDH10 MUTATED CDH10 WILD-TYPE 
             13             112 
  CDH10 MUTATED CDH10 WILD-TYPE 
              5              57 
$`CDH10 MUTATED`
TCGA-3A-A9IJ TCGA-FZ-5924 TCGA-LB-A7SX TCGA-2J-AABE TCGA-2J-AABP TCGA-2J-AABV 
       60.95        15.78        12.92        22.22        15.22        21.44 
TCGA-FB-AAPS TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A7M4 TCGA-RB-A7B8 TCGA-US-A776 
        7.50        32.15        19.82        15.88        15.32        39.98 
TCGA-XN-A8T3 
       31.27 

$`CDH10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
        1.08        15.12        17.26        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF 
       23.97         9.63         2.63        20.61        19.96        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE 
       42.31        15.91        14.47         9.11         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
        8.78        13.68         3.12         9.40         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
        0.39        18.67        13.81        12.99        12.03        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  CDH10 MUTATED CDH10 WILD-TYPE 
           7.50            0.23 
  CDH10 MUTATED CDH10 WILD-TYPE 
          60.95           90.12 
  CDH10 MUTATED CDH10 WILD-TYPE 
         19.820          14.435 
[1] "7.5 - 61.0 (19.8)" "0.2 - 90.1 (14.4)"
[1] "hr=" "1.8"
D218V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDH10 MUTATED         0        0        2         3         8         0
  CDH10 WILD-TYPE       1        3       10        16        74         4
                 vv
clus              STAGE IV
  CDH10 MUTATED          0
  CDH10 WILD-TYPE        3
D218V3, multiclass
           clus
vv          CDH10 MUTATED CDH10 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             3              16
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CDH10 MUTATED    0  3    10
  CDH10 WILD-TYPE  5 14    92
D218V4, multiclass
       clus
vv      CDH10 MUTATED CDH10 WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V5, binary
                 cls
clus               0  1
  CDH10 MUTATED    4  9
  CDH10 WILD-TYPE 31 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      4    9
  CDH10 WILD-TYPE   31   80
   clus
vv  CDH10 MUTATED CDH10 WILD-TYPE
  0             4              31
  1             9              80
[1] 2 2
[1] FALSE
D218V6, binary
                 cls
clus               0  1
  CDH10 MUTATED    7  0
  CDH10 WILD-TYPE 50  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      7    0
  CDH10 WILD-TYPE   50    3
   clus
vv  CDH10 MUTATED CDH10 WILD-TYPE
  0             7              50
  1             0               3
[1] 2 2
[1] FALSE
D218V7, binary
                 cls
clus               0  1
  CDH10 MUTATED    5  8
  CDH10 WILD-TYPE 46 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      5    8
  CDH10 WILD-TYPE   46   67
        clus
vv       CDH10 MUTATED CDH10 WILD-TYPE
  FEMALE             5              46
  MALE               8              67
[1] 2 2
[1] FALSE
D218V8, binary
                 cls
clus               0  1
  CDH10 MUTATED    9  4
  CDH10 WILD-TYPE 79 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      9    4
  CDH10 WILD-TYPE   79   26
     clus
vv    CDH10 MUTATED CDH10 WILD-TYPE
  NO              9              79
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDH10 MUTATED                                     8
  CDH10 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDH10 MUTATED                                       3
  CDH10 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDH10 MUTATED                                                  1
  CDH10 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDH10 MUTATED                                     1
  CDH10 WILD-TYPE                                   0
D218V9, multiclass
                                                  clus
vv                                                 CDH10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 CDH10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V10, continuous
D218V11, continuous
                 vv
clus              R0 R1 R2 RX
  CDH10 MUTATED   10  3  0  0
  CDH10 WILD-TYPE 70 32  4  2
D218V12, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  R0            10              70
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH10 MUTATED       1                         1    11
  CDH10 WILD-TYPE     5                         4   103
D218V14, multiclass
                           clus
vv                          CDH10 MUTATED CDH10 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V15, binary
                 cls
clus               0  1
  CDH10 MUTATED    1  8
  CDH10 WILD-TYPE  4 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      1    8
  CDH10 WILD-TYPE    4   83
                        clus
vv                       CDH10 MUTATED CDH10 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(219) Variable = OXR1 MUTATION ANALYSIS
D219V1, survival
                sevent
clus2             0  1
  OXR1 MUTATED    4  1
  OXR1 WILD-TYPE 59 61
  OXR1 MUTATED OXR1 WILD-TYPE 
             5            120 
  OXR1 MUTATED OXR1 WILD-TYPE 
             1             61 
$`OXR1 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IR TCGA-3A-A9IZ TCGA-IB-A7M4 TCGA-IB-AAUU 
        1.08        50.70        10.13        15.88         8.05 

$`OXR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  OXR1 MUTATED OXR1 WILD-TYPE 
          1.08           0.23 
  OXR1 MUTATED OXR1 WILD-TYPE 
         50.70          90.12 
  OXR1 MUTATED OXR1 WILD-TYPE 
         10.13          15.27 
[1] "1.1 - 50.7 (10.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D219V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OXR1 MUTATED         0        0        1         0         4         0
  OXR1 WILD-TYPE       1        3       11        19        78         4
                vv
clus             STAGE IV
  OXR1 MUTATED          0
  OXR1 WILD-TYPE        3
D219V3, multiclass
           clus
vv          OXR1 MUTATED OXR1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  OXR1 MUTATED    0  1     4
  OXR1 WILD-TYPE  5 16    98
D219V4, multiclass
       clus
vv      OXR1 MUTATED OXR1 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V5, binary
                cls
clus              0  1
  OXR1 MUTATED    1  4
  OXR1 WILD-TYPE 34 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    4
  OXR1 WILD-TYPE   34   85
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            1             34
  1            4             85
[1] 2 2
[1] FALSE
D219V6, binary
                cls
clus              0  1
  OXR1 MUTATED    1  0
  OXR1 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    0
  OXR1 WILD-TYPE   56    3
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D219V7, binary
                cls
clus              0  1
  OXR1 MUTATED    2  3
  OXR1 WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      2    3
  OXR1 WILD-TYPE   49   72
        clus
vv       OXR1 MUTATED OXR1 WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D219V8, binary
                cls
clus              0  1
  OXR1 MUTATED    4  0
  OXR1 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      4    0
  OXR1 WILD-TYPE   84   30
     clus
vv    OXR1 MUTATED OXR1 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OXR1 MUTATED                                     3
  OXR1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OXR1 MUTATED                                       2
  OXR1 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OXR1 MUTATED                                                  0
  OXR1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  OXR1 MUTATED                                     0
  OXR1 WILD-TYPE                                   1
D219V9, multiclass
                                                  clus
vv                                                 OXR1 MUTATED OXR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V10, continuous
D219V11, continuous
                vv
clus             R0 R1 R2 RX
  OXR1 MUTATED    4  1  0  0
  OXR1 WILD-TYPE 76 34  4  2
D219V12, multiclass
    clus
vv   OXR1 MUTATED OXR1 WILD-TYPE
  R0            4             76
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXR1 MUTATED       0                         0     5
  OXR1 WILD-TYPE     6                         5   109
D219V14, multiclass
                           clus
vv                          OXR1 MUTATED OXR1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V15, binary
                cls
clus              0  1
  OXR1 MUTATED    1  4
  OXR1 WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    4
  OXR1 WILD-TYPE    4   87
                        clus
vv                       OXR1 MUTATED OXR1 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(220) Variable = SEC31A MUTATION ANALYSIS
D220V1, survival
                  sevent
clus2               0  1
  SEC31A MUTATED    3  3
  SEC31A WILD-TYPE 60 59
  SEC31A MUTATED SEC31A WILD-TYPE 
               6              119 
  SEC31A MUTATED SEC31A WILD-TYPE 
               3               59 
$`SEC31A MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7885 TCGA-YB-A89D 
        4.70        12.95         0.23        19.82        41.33        11.51 

$`SEC31A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  SEC31A MUTATED SEC31A WILD-TYPE 
            0.23             0.26 
  SEC31A MUTATED SEC31A WILD-TYPE 
           41.33            90.12 
  SEC31A MUTATED SEC31A WILD-TYPE 
           12.23            15.32 
[1] "0.2 - 41.3 (12.2)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.3"
D220V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SEC31A MUTATED         0        0        1         0         4         1
  SEC31A WILD-TYPE       1        3       11        19        78         3
                  vv
clus               STAGE IV
  SEC31A MUTATED          0
  SEC31A WILD-TYPE        3
D220V3, multiclass
           clus
vv          SEC31A MUTATED SEC31A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SEC31A MUTATED    0  1     5
  SEC31A WILD-TYPE  5 16    97
D220V4, multiclass
       clus
vv      SEC31A MUTATED SEC31A WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V5, binary
                  cls
clus                0  1
  SEC31A MUTATED    2  4
  SEC31A WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      2    4
  SEC31A WILD-TYPE   33   85
   clus
vv  SEC31A MUTATED SEC31A WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D220V6, binary
                  cls
clus                0  1
  SEC31A MUTATED    2  0
  SEC31A WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      2    0
  SEC31A WILD-TYPE   55    3
   clus
vv  SEC31A MUTATED SEC31A WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D220V7, binary
                  cls
clus                0  1
  SEC31A MUTATED    3  3
  SEC31A WILD-TYPE 48 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      3    3
  SEC31A WILD-TYPE   48   72
        clus
vv       SEC31A MUTATED SEC31A WILD-TYPE
  FEMALE              3               48
  MALE                3               72
[1] 2 2
[1] FALSE
D220V8, binary
                  cls
clus                0  1
  SEC31A MUTATED    4  1
  SEC31A WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      4    1
  SEC31A WILD-TYPE   84   29
     clus
vv    SEC31A MUTATED SEC31A WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEC31A MUTATED                                     6
  SEC31A WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEC31A MUTATED                                       0
  SEC31A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEC31A MUTATED                                                  0
  SEC31A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SEC31A MUTATED                                     0
  SEC31A WILD-TYPE                                   1
D220V9, multiclass
                                                  clus
vv                                                 SEC31A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SEC31A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V10, continuous
D220V11, continuous
                  vv
clus               R0 R1 R2 RX
  SEC31A MUTATED    4  2  0  0
  SEC31A WILD-TYPE 76 33  4  2
D220V12, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  R0              4               76
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEC31A MUTATED       0                         0     6
  SEC31A WILD-TYPE     6                         5   108
D220V14, multiclass
                           clus
vv                          SEC31A MUTATED SEC31A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V15, binary
                  cls
clus                0  1
  SEC31A MUTATED    0  4
  SEC31A WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      0    4
  SEC31A WILD-TYPE    5   87
                        clus
vv                       SEC31A MUTATED SEC31A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(221) Variable = NDEL1 MUTATION ANALYSIS
D221V1, survival
                 sevent
clus2              0  1
  NDEL1 MUTATED    3  2
  NDEL1 WILD-TYPE 60 60
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              5             120 
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              2              60 
$`NDEL1 MUTATED`
TCGA-2J-AABA TCGA-3A-A9IV TCGA-HZ-8637 TCGA-IB-AAUR TCGA-IB-AAUS 
       19.96        36.26        17.00        11.11         7.40 

$`NDEL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  NDEL1 MUTATED NDEL1 WILD-TYPE 
           7.40            0.23 
  NDEL1 MUTATED NDEL1 WILD-TYPE 
          36.26           90.12 
  NDEL1 MUTATED NDEL1 WILD-TYPE 
         17.000          15.205 
[1] "7.4 - 36.3 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D221V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NDEL1 MUTATED         0        0        1         0         4         0
  NDEL1 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  NDEL1 MUTATED          0
  NDEL1 WILD-TYPE        3
D221V3, multiclass
           clus
vv          NDEL1 MUTATED NDEL1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NDEL1 MUTATED    0  1     4
  NDEL1 WILD-TYPE  5 16    98
D221V4, multiclass
       clus
vv      NDEL1 MUTATED NDEL1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V5, binary
                 cls
clus               0  1
  NDEL1 MUTATED    1  4
  NDEL1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDEL1 MUTATED      1    4
  NDEL1 WILD-TYPE   34   85
   clus
vv  NDEL1 MUTATED NDEL1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D221V6, binary
                 cls
clus               0  1
  NDEL1 MUTATED    3  0
  NDEL1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDEL1 MUTATED      3    0
  NDEL1 WILD-TYPE   54    3
   clus
vv  NDEL1 MUTATED NDEL1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D221V7, binary
                 cls
clus               0  1
  NDEL1 MUTATED    3  2
  NDEL1 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDEL1 MUTATED      3    2
  NDEL1 WILD-TYPE   48   73
        clus
vv       NDEL1 MUTATED NDEL1 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D221V8, binary
                 cls
clus               0  1
  NDEL1 MUTATED    4  1
  NDEL1 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDEL1 MUTATED      4    1
  NDEL1 WILD-TYPE   84   29
     clus
vv    NDEL1 MUTATED NDEL1 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NDEL1 MUTATED                                     4
  NDEL1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NDEL1 MUTATED                                       1
  NDEL1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NDEL1 MUTATED                                                  0
  NDEL1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NDEL1 MUTATED                                     0
  NDEL1 WILD-TYPE                                   1
D221V9, multiclass
                                                  clus
vv                                                 NDEL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NDEL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V10, continuous
[1] "Remove cluster labels:" "NDEL1 MUTATED"         
clus
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUU 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-YY-A8LH 
"NDEL1 WILD-TYPE" 
D221V11, continuous
[1] "Remove cluster labels:" "NDEL1 MUTATED"         
clus
  NDEL1 MUTATED NDEL1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" "NDEL1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NDEL1 MUTATED    2  3  0  0
  NDEL1 WILD-TYPE 78 32  4  2
D221V12, multiclass
    clus
vv   NDEL1 MUTATED NDEL1 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NDEL1 MUTATED       0                         0     5
  NDEL1 WILD-TYPE     6                         5   109
D221V14, multiclass
                           clus
vv                          NDEL1 MUTATED NDEL1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V15, binary
                 cls
clus               0  1
  NDEL1 MUTATED    1  3
  NDEL1 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDEL1 MUTATED      1    3
  NDEL1 WILD-TYPE    4   88
                        clus
vv                       NDEL1 MUTATED NDEL1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(222) Variable = SHROOM4 MUTATION ANALYSIS
D222V1, survival
                   sevent
clus2                0  1
  SHROOM4 MUTATED    5  5
  SHROOM4 WILD-TYPE 58 57
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               10               115 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                5                57 
$`SHROOM4 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IU TCGA-FB-AAPU TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7M4 
        1.08        15.06        12.53        19.82         1.35        15.88 
TCGA-RB-AA9M TCGA-US-A77J TCGA-XN-A8T5 TCGA-YY-A8LH 
        9.40        18.67        23.67        66.28 

$`SHROOM4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        32.81        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
        7.20        20.88        21.90         8.22         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         0.30        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             1.08              0.23 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            66.28             90.12 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            15.47             15.22 
[1] "1.1 - 66.3 (15.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D222V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SHROOM4 MUTATED         0        0        1         1         8         0
  SHROOM4 WILD-TYPE       1        3       11        18        74         4
                   vv
clus                STAGE IV
  SHROOM4 MUTATED          0
  SHROOM4 WILD-TYPE        3
D222V3, multiclass
           clus
vv          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               8                74
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SHROOM4 MUTATED    1  1     8
  SHROOM4 WILD-TYPE  4 16    94
D222V4, multiclass
       clus
vv      SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               8                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V5, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    2  8
  SHROOM4 WILD-TYPE 33 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      2    8
  SHROOM4 WILD-TYPE   33   81
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               2                33
  1               8                81
[1] 2 2
[1] FALSE
D222V6, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    3  0
  SHROOM4 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    0
  SHROOM4 WILD-TYPE   54    3
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D222V7, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    6  4
  SHROOM4 WILD-TYPE 45 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      6    4
  SHROOM4 WILD-TYPE   45   71
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               6                45
  MALE                 4                71
[1] 2 2
[1] FALSE
D222V8, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    5  3
  SHROOM4 WILD-TYPE 83 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      5    3
  SHROOM4 WILD-TYPE   83   27
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                5                83
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SHROOM4 MUTATED                                     8
  SHROOM4 WILD-TYPE                                  97
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SHROOM4 MUTATED                                       2
  SHROOM4 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SHROOM4 MUTATED                                                  0
  SHROOM4 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SHROOM4 MUTATED                                     0
  SHROOM4 WILD-TYPE                                   1
D222V9, multiclass
                                                  clus
vv                                                 SHROOM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SHROOM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V10, continuous
D222V11, continuous
                   vv
clus                R0 R1 R2 RX
  SHROOM4 MUTATED    7  3  0  0
  SHROOM4 WILD-TYPE 73 32  4  2
D222V12, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0               7                73
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED       1                         0     9
  SHROOM4 WILD-TYPE     5                         5   105
D222V14, multiclass
                           clus
vv                          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   9               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V15, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    1  9
  SHROOM4 WILD-TYPE  4 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    9
  SHROOM4 WILD-TYPE    4   82
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               9                82
[1] 2 2
[1] FALSE

Clustering(223) Variable = HIRA MUTATION ANALYSIS
D223V1, survival
                sevent
clus2             0  1
  HIRA MUTATED    2  3
  HIRA WILD-TYPE 61 59
  HIRA MUTATED HIRA WILD-TYPE 
             5            120 
  HIRA MUTATED HIRA WILD-TYPE 
             3             59 
$`HIRA MUTATED`
TCGA-LB-A7SX TCGA-US-A77E TCGA-IB-A5SP TCGA-US-A77J TCGA-XD-AAUG 
       12.92        14.14        15.85        18.67        13.81 

$`HIRA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-XD-AAUL 
        8.02        15.78         1.08        15.12        17.26        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUH TCGA-XD-AAUI 
        0.30        39.98        16.80         0.39        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  HIRA MUTATED HIRA WILD-TYPE 
         12.92           0.23 
  HIRA MUTATED HIRA WILD-TYPE 
         18.67          90.12 
  HIRA MUTATED HIRA WILD-TYPE 
         14.14          15.27 
[1] "12.9 - 18.7 (14.1)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.5"
D223V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIRA MUTATED         0        0        0         1         3         0
  HIRA WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  HIRA MUTATED          1
  HIRA WILD-TYPE        2
D223V3, multiclass
           clus
vv          HIRA MUTATED HIRA WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  HIRA MUTATED    0  0     5
  HIRA WILD-TYPE  5 17    97
D223V4, multiclass
       clus
vv      HIRA MUTATED HIRA WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V5, binary
                cls
clus              0  1
  HIRA MUTATED    1  4
  HIRA WILD-TYPE 34 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIRA MUTATED      1    4
  HIRA WILD-TYPE   34   85
   clus
vv  HIRA MUTATED HIRA WILD-TYPE
  0            1             34
  1            4             85
[1] 2 2
[1] FALSE
D223V6, binary
                cls
clus              0  1
  HIRA MUTATED    1  1
  HIRA WILD-TYPE 56  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIRA MUTATED      1    1
  HIRA WILD-TYPE   56    2
   clus
vv  HIRA MUTATED HIRA WILD-TYPE
  0            1             56
  1            1              2
[1] 2 2
[1] FALSE
D223V7, binary
                cls
clus              0  1
  HIRA MUTATED    3  2
  HIRA WILD-TYPE 48 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIRA MUTATED      3    2
  HIRA WILD-TYPE   48   73
        clus
vv       HIRA MUTATED HIRA WILD-TYPE
  FEMALE            3             48
  MALE              2             73
[1] 2 2
[1] FALSE
D223V8, binary
                cls
clus              0  1
  HIRA MUTATED    4  0
  HIRA WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIRA MUTATED      4    0
  HIRA WILD-TYPE   84   30
     clus
vv    HIRA MUTATED HIRA WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIRA MUTATED                                     4
  HIRA WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIRA MUTATED                                       1
  HIRA WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIRA MUTATED                                                  0
  HIRA WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIRA MUTATED                                     0
  HIRA WILD-TYPE                                   1
D223V9, multiclass
                                                  clus
vv                                                 HIRA MUTATED HIRA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V10, continuous
[1] "Remove cluster labels:" "HIRA MUTATED"          
clus
  HIRA MUTATED HIRA WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" 
D223V11, continuous
[1] "Remove cluster labels:" "HIRA MUTATED"          
clus
  HIRA MUTATED HIRA WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" "HIRA WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  HIRA MUTATED    2  3  0  0
  HIRA WILD-TYPE 78 32  4  2
D223V12, multiclass
    clus
vv   HIRA MUTATED HIRA WILD-TYPE
  R0            2             78
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIRA MUTATED       0                         1     4
  HIRA WILD-TYPE     6                         4   110
D223V14, multiclass
                           clus
vv                          HIRA MUTATED HIRA WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V15, binary
                cls
clus              0  1
  HIRA MUTATED    0  4
  HIRA WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIRA MUTATED      0    4
  HIRA WILD-TYPE    5   87
                        clus
vv                       HIRA MUTATED HIRA WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(224) Variable = XRCC2 MUTATION ANALYSIS
D224V1, survival
                 sevent
clus2              0  1
  XRCC2 MUTATED    1  3
  XRCC2 WILD-TYPE 62 59
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              4             121 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
              3              59 
$`XRCC2 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABE TCGA-2L-AAQI TCGA-IB-A6UG 
       12.92        22.22         3.39         1.35 

$`XRCC2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  XRCC2 MUTATED XRCC2 WILD-TYPE 
           1.35            0.23 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
          22.22           90.12 
  XRCC2 MUTATED XRCC2 WILD-TYPE 
          8.155          15.320 
[1] "1.4 - 22.2 (8.2)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.6"
D224V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XRCC2 MUTATED         0        0        0         1         3         0
  XRCC2 WILD-TYPE       1        3       12        18        79         4
                 vv
clus              STAGE IV
  XRCC2 MUTATED          0
  XRCC2 WILD-TYPE        3
D224V3, multiclass
           clus
vv          XRCC2 MUTATED XRCC2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  XRCC2 MUTATED    0  0     4
  XRCC2 WILD-TYPE  5 17    98
D224V4, multiclass
       clus
vv      XRCC2 MUTATED XRCC2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V5, binary
                 cls
clus               0  1
  XRCC2 MUTATED    1  3
  XRCC2 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      1    3
  XRCC2 WILD-TYPE   34   86
   clus
vv  XRCC2 MUTATED XRCC2 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D224V6, binary
                 cls
clus               0  1
  XRCC2 MUTATED    2  0
  XRCC2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      2    0
  XRCC2 WILD-TYPE   55    3
   clus
vv  XRCC2 MUTATED XRCC2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D224V7, binary
                 cls
clus               0  1
  XRCC2 MUTATED    1  3
  XRCC2 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      1    3
  XRCC2 WILD-TYPE   50   72
        clus
vv       XRCC2 MUTATED XRCC2 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D224V8, binary
                 cls
clus               0  1
  XRCC2 MUTATED    3  1
  XRCC2 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      3    1
  XRCC2 WILD-TYPE   85   29
     clus
vv    XRCC2 MUTATED XRCC2 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XRCC2 MUTATED                                     4
  XRCC2 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XRCC2 MUTATED                                       0
  XRCC2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XRCC2 MUTATED                                                  0
  XRCC2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  XRCC2 MUTATED                                     0
  XRCC2 WILD-TYPE                                   1
D224V9, multiclass
                                                  clus
vv                                                 XRCC2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 XRCC2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V10, continuous
D224V11, continuous
                 vv
clus              R0 R1 R2 RX
  XRCC2 MUTATED    1  3  0  0
  XRCC2 WILD-TYPE 79 32  4  2
D224V12, multiclass
    clus
vv   XRCC2 MUTATED XRCC2 WILD-TYPE
  R0             1              79
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XRCC2 MUTATED       0                         1     3
  XRCC2 WILD-TYPE     6                         4   111
D224V14, multiclass
                           clus
vv                          XRCC2 MUTATED XRCC2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V15, binary
                 cls
clus               0  1
  XRCC2 MUTATED    0  2
  XRCC2 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC2 MUTATED      0    2
  XRCC2 WILD-TYPE    5   89
                        clus
vv                       XRCC2 MUTATED XRCC2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(225) Variable = APEX1 MUTATION ANALYSIS
D225V1, survival
                 sevent
clus2              0  1
  APEX1 MUTATED    2  1
  APEX1 WILD-TYPE 61 61
  APEX1 MUTATED APEX1 WILD-TYPE 
              3             122 
  APEX1 MUTATED APEX1 WILD-TYPE 
              1              61 
$`APEX1 MUTATED`
TCGA-3A-A9IJ TCGA-XD-AAUL TCGA-2L-AAQE 
       60.95        16.37        22.49 

$`APEX1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  APEX1 MUTATED APEX1 WILD-TYPE 
          16.37            0.23 
  APEX1 MUTATED APEX1 WILD-TYPE 
          60.95           90.12 
  APEX1 MUTATED APEX1 WILD-TYPE 
         22.490          15.155 
[1] "16.4 - 61.0 (22.5)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.4"
D225V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  APEX1 MUTATED         0        0        1         1         2         0
  APEX1 WILD-TYPE       1        3       11        18        80         4
                 vv
clus              STAGE IV
  APEX1 MUTATED          0
  APEX1 WILD-TYPE        3
D225V3, multiclass
           clus
vv          APEX1 MUTATED APEX1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  APEX1 MUTATED    0  1     3
  APEX1 WILD-TYPE  5 16    99
D225V4, multiclass
       clus
vv      APEX1 MUTATED APEX1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V5, binary
                 cls
clus               0  1
  APEX1 MUTATED    2  2
  APEX1 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APEX1 MUTATED      2    2
  APEX1 WILD-TYPE   33   87
   clus
vv  APEX1 MUTATED APEX1 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D225V6, binary
                 cls
clus               0  1
  APEX1 MUTATED    1  0
  APEX1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APEX1 MUTATED      1    0
  APEX1 WILD-TYPE   56    3
   clus
vv  APEX1 MUTATED APEX1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D225V7, binary
                 cls
clus               0  1
  APEX1 MUTATED    0  4
  APEX1 WILD-TYPE 51 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APEX1 MUTATED      0    4
  APEX1 WILD-TYPE   51   71
        clus
vv       APEX1 MUTATED APEX1 WILD-TYPE
  FEMALE             0              51
  MALE               4              71
[1] 2 2
[1] FALSE
D225V8, binary
                 cls
clus               0  1
  APEX1 MUTATED    3  0
  APEX1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APEX1 MUTATED      3    0
  APEX1 WILD-TYPE   85   30
     clus
vv    APEX1 MUTATED APEX1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  APEX1 MUTATED                                     3
  APEX1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  APEX1 MUTATED                                       1
  APEX1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  APEX1 MUTATED                                                  0
  APEX1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  APEX1 MUTATED                                     0
  APEX1 WILD-TYPE                                   1
D225V9, multiclass
                                                  clus
vv                                                 APEX1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 APEX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V10, continuous
D225V11, continuous
                 vv
clus              R0 R1 R2 RX
  APEX1 MUTATED    4  0  0  0
  APEX1 WILD-TYPE 76 35  4  2
D225V12, multiclass
    clus
vv   APEX1 MUTATED APEX1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APEX1 MUTATED       0                         0     4
  APEX1 WILD-TYPE     6                         5   110
D225V14, multiclass
                           clus
vv                          APEX1 MUTATED APEX1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V15, binary
                 cls
clus               0  1
  APEX1 MUTATED    0  3
  APEX1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APEX1 MUTATED      0    3
  APEX1 WILD-TYPE    5   88
                        clus
vv                       APEX1 MUTATED APEX1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(226) Variable = TMEM90B MUTATION ANALYSIS
D226V1, survival
                   sevent
clus2                0  1
  TMEM90B MUTATED    3  3
  TMEM90B WILD-TYPE 60 59
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                6               119 
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                3                59 
$`TMEM90B MUTATED`
TCGA-FB-AAQ6 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-3A-A9IS TCGA-IB-7651 TCGA-IB-A5ST 
        8.02        12.92        17.26        32.81        19.82        20.88 

$`TMEM90B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        15.12        14.14        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TMEM90B MUTATED TMEM90B WILD-TYPE 
             8.02              0.23 
  TMEM90B MUTATED TMEM90B WILD-TYPE 
            32.81             90.12 
  TMEM90B MUTATED TMEM90B WILD-TYPE 
            18.54             15.19 
[1] "8.0 - 32.8 (18.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D226V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM90B MUTATED         0        1        1         0         4         0
  TMEM90B WILD-TYPE       1        2       11        19        78         4
                   vv
clus                STAGE IV
  TMEM90B MUTATED          0
  TMEM90B WILD-TYPE        3
D226V3, multiclass
           clus
vv          TMEM90B MUTATED TMEM90B WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TMEM90B MUTATED    1  1     4
  TMEM90B WILD-TYPE  4 16    98
D226V4, multiclass
       clus
vv      TMEM90B MUTATED TMEM90B WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V5, binary
                   cls
clus                 0  1
  TMEM90B MUTATED    2  4
  TMEM90B WILD-TYPE 33 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM90B MUTATED      2    4
  TMEM90B WILD-TYPE   33   85
   clus
vv  TMEM90B MUTATED TMEM90B WILD-TYPE
  0               2                33
  1               4                85
[1] 2 2
[1] FALSE
D226V6, binary
                   cls
clus                 0  1
  TMEM90B MUTATED    2  0
  TMEM90B WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM90B MUTATED      2    0
  TMEM90B WILD-TYPE   55    3
   clus
vv  TMEM90B MUTATED TMEM90B WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D226V7, binary
                   cls
clus                 0  1
  TMEM90B MUTATED    4  2
  TMEM90B WILD-TYPE 47 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM90B MUTATED      4    2
  TMEM90B WILD-TYPE   47   73
        clus
vv       TMEM90B MUTATED TMEM90B WILD-TYPE
  FEMALE               4                47
  MALE                 2                73
[1] 2 2
[1] FALSE
D226V8, binary
                   cls
clus                 0  1
  TMEM90B MUTATED    5  1
  TMEM90B WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM90B MUTATED      5    1
  TMEM90B WILD-TYPE   83   29
     clus
vv    TMEM90B MUTATED TMEM90B WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM90B MUTATED                                     5
  TMEM90B WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM90B MUTATED                                       1
  TMEM90B WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM90B MUTATED                                                  0
  TMEM90B WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM90B MUTATED                                     0
  TMEM90B WILD-TYPE                                   1
D226V9, multiclass
                                                  clus
vv                                                 TMEM90B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TMEM90B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V10, continuous
[1] "Remove cluster labels:" "TMEM90B MUTATED"       
clus
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-YY-A8LH 
"TMEM90B WILD-TYPE" 
D226V11, continuous
[1] "Remove cluster labels:" "TMEM90B MUTATED"       
clus
  TMEM90B MUTATED TMEM90B WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" "TMEM90B WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TMEM90B MUTATED    4  2  0  0
  TMEM90B WILD-TYPE 76 33  4  2
D226V12, multiclass
    clus
vv   TMEM90B MUTATED TMEM90B WILD-TYPE
  R0               4                76
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM90B MUTATED       0                         1     5
  TMEM90B WILD-TYPE     6                         4   109
D226V14, multiclass
                           clus
vv                          TMEM90B MUTATED TMEM90B WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V15, binary
                   cls
clus                 0  1
  TMEM90B MUTATED    0  6
  TMEM90B WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM90B MUTATED      0    6
  TMEM90B WILD-TYPE    5   85
                        clus
vv                       TMEM90B MUTATED TMEM90B WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(227) Variable = RAB11FIP1 MUTATION ANALYSIS
D227V1, survival
                     sevent
clus2                  0  1
  RAB11FIP1 MUTATED    2  5
  RAB11FIP1 WILD-TYPE 61 57
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  7                 118 
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  5                  57 
$`RAB11FIP1 MUTATED`
TCGA-FB-AAQ6 TCGA-2L-AAQI TCGA-3A-A9IC TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-AAUU 
        8.02         3.39        24.26        17.49        19.82         8.05 
TCGA-Q3-A5QY 
       13.68 

$`RAB11FIP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
               3.39                0.23 
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
              24.26               90.12 
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
              13.68               15.27 
[1] "3.4 - 24.3 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D227V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RAB11FIP1 MUTATED         0        1        0         0         6         0
  RAB11FIP1 WILD-TYPE       1        2       12        19        76         4
                     vv
clus                  STAGE IV
  RAB11FIP1 MUTATED          0
  RAB11FIP1 WILD-TYPE        3
D227V3, multiclass
           clus
vv          RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  1                   2
  STAGE IB                  0                  12
  STAGE IIA                 0                  19
  STAGE IIB                 6                  76
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3+T4
  RAB11FIP1 MUTATED    1  1     5
  RAB11FIP1 WILD-TYPE  4 16    97
D227V4, multiclass
       clus
vv      RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  T1                    1                   4
  T2                    1                  16
  T3+T4                 5                  97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V5, binary
                     cls
clus                   0  1
  RAB11FIP1 MUTATED    1  6
  RAB11FIP1 WILD-TYPE 34 83
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP1 MUTATED      1    6
  RAB11FIP1 WILD-TYPE   34   83
   clus
vv  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  0                 1                  34
  1                 6                  83
[1] 2 2
[1] FALSE
D227V6, binary
                     cls
clus                   0  1
  RAB11FIP1 MUTATED    2  0
  RAB11FIP1 WILD-TYPE 55  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP1 MUTATED      2    0
  RAB11FIP1 WILD-TYPE   55    3
   clus
vv  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  0                 2                  55
  1                 0                   3
[1] 2 2
[1] FALSE
D227V7, binary
                     cls
clus                   0  1
  RAB11FIP1 MUTATED    3  4
  RAB11FIP1 WILD-TYPE 48 71
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP1 MUTATED      3    4
  RAB11FIP1 WILD-TYPE   48   71
        clus
vv       RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  FEMALE                 3                  48
  MALE                   4                  71
[1] 2 2
[1] FALSE
D227V8, binary
                     cls
clus                   0  1
  RAB11FIP1 MUTATED    6  1
  RAB11FIP1 WILD-TYPE 82 29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP1 MUTATED      6    1
  RAB11FIP1 WILD-TYPE   82   29
     clus
vv    RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  NO                  6                  82
  YES                 1                  29
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAB11FIP1 MUTATED                                     7
  RAB11FIP1 WILD-TYPE                                  98
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAB11FIP1 MUTATED                                       0
  RAB11FIP1 WILD-TYPE                                    18
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAB11FIP1 MUTATED                                                  0
  RAB11FIP1 WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  RAB11FIP1 MUTATED                                     0
  RAB11FIP1 WILD-TYPE                                   1
D227V9, multiclass
                                                  clus
vv                                                 RAB11FIP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 RAB11FIP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                               98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V10, continuous
[1] "Remove cluster labels:" "RAB11FIP1 MUTATED"     
clus
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  2                  37 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2J-AABV 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-2L-AAQA          TCGA-2L-AAQE          TCGA-3A-A9I9 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IX          TCGA-F2-A8YN 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-FB-A5VM          TCGA-FB-A78T          TCGA-FB-AAPQ 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-H8-A6C1          TCGA-HV-AA8V 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XN-A8T5 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-YY-A8LH 
"RAB11FIP1 WILD-TYPE" 
D227V11, continuous
[1] "Remove cluster labels:" "RAB11FIP1 MUTATED"     
clus
  RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE 
                  1                  32 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABE          TCGA-2J-AABF 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-2J-AABO          TCGA-3A-A9IB          TCGA-3A-A9IR 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-FB-A5VM          TCGA-FB-A78T 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-FB-AAPQ          TCGA-FB-AAPS          TCGA-H8-A6C1 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XD-AAUI 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"RAB11FIP1 WILD-TYPE" "RAB11FIP1 WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  RAB11FIP1 MUTATED    5  1  1  0
  RAB11FIP1 WILD-TYPE 75 34  3  2
D227V12, multiclass
    clus
vv   RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  R0                 5                  75
  R1                 1                  34
  R2                 1                   3
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAB11FIP1 MUTATED       1                         0     6
  RAB11FIP1 WILD-TYPE     5                         5   108
D227V14, multiclass
                           clus
vv                          RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  ASIAN                                     1                   5
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     6                 108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V15, binary
                     cls
clus                   0  1
  RAB11FIP1 MUTATED    0  5
  RAB11FIP1 WILD-TYPE  5 86
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP1 MUTATED      0    5
  RAB11FIP1 WILD-TYPE    5   86
                        clus
vv                       RAB11FIP1 MUTATED RAB11FIP1 WILD-TYPE
  HISPANIC OR LATINO                     0                   5
  NOT HISPANIC OR LATINO                 5                  86
[1] 2 2
[1] FALSE

Clustering(228) Variable = MPP6 MUTATION ANALYSIS
D228V1, survival
                sevent
clus2             0  1
  MPP6 MUTATED    1  3
  MPP6 WILD-TYPE 62 59
  MPP6 MUTATED MPP6 WILD-TYPE 
             4            121 
  MPP6 MUTATED MPP6 WILD-TYPE 
             3             59 
$`MPP6 MUTATED`
TCGA-FZ-5924 TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-AAUW 
       15.78         7.50        19.82         7.56 

$`MPP6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MPP6 MUTATED MPP6 WILD-TYPE 
          7.50           0.23 
  MPP6 MUTATED MPP6 WILD-TYPE 
         19.82          90.12 
  MPP6 MUTATED MPP6 WILD-TYPE 
         11.67          15.22 
[1] "7.5 - 19.8 (11.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.3"
D228V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MPP6 MUTATED         0        0        0         1         4         0
  MPP6 WILD-TYPE       1        3       12        18        78         4
                vv
clus             STAGE IV
  MPP6 MUTATED          0
  MPP6 WILD-TYPE        3
D228V3, multiclass
           clus
vv          MPP6 MUTATED MPP6 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  MPP6 MUTATED    0  1     4
  MPP6 WILD-TYPE  5 16    98
D228V4, multiclass
       clus
vv      MPP6 MUTATED MPP6 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V5, binary
                cls
clus              0  1
  MPP6 MUTATED    0  5
  MPP6 WILD-TYPE 35 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP6 MUTATED      0    5
  MPP6 WILD-TYPE   35   84
   clus
vv  MPP6 MUTATED MPP6 WILD-TYPE
  0            0             35
  1            5             84
[1] 2 2
[1] FALSE
D228V6, binary
                cls
clus              0  1
  MPP6 MUTATED    3  0
  MPP6 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP6 MUTATED      3    0
  MPP6 WILD-TYPE   54    3
   clus
vv  MPP6 MUTATED MPP6 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D228V7, binary
                cls
clus              0  1
  MPP6 MUTATED    3  2
  MPP6 WILD-TYPE 48 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP6 MUTATED      3    2
  MPP6 WILD-TYPE   48   73
        clus
vv       MPP6 MUTATED MPP6 WILD-TYPE
  FEMALE            3             48
  MALE              2             73
[1] 2 2
[1] FALSE
D228V8, binary
                cls
clus              0  1
  MPP6 MUTATED    3  1
  MPP6 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP6 MUTATED      3    1
  MPP6 WILD-TYPE   85   29
     clus
vv    MPP6 MUTATED MPP6 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MPP6 MUTATED                                     5
  MPP6 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MPP6 MUTATED                                       0
  MPP6 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MPP6 MUTATED                                                  0
  MPP6 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MPP6 MUTATED                                     0
  MPP6 WILD-TYPE                                   1
D228V9, multiclass
                                                  clus
vv                                                 MPP6 MUTATED MPP6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V10, continuous
D228V11, continuous
                vv
clus             R0 R1 R2 RX
  MPP6 MUTATED    5  0  0  0
  MPP6 WILD-TYPE 75 35  4  2
D228V12, multiclass
    clus
vv   MPP6 MUTATED MPP6 WILD-TYPE
  R0            5             75
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MPP6 MUTATED       0                         0     5
  MPP6 WILD-TYPE     6                         5   109
D228V14, multiclass
                           clus
vv                          MPP6 MUTATED MPP6 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V15, binary
                cls
clus              0  1
  MPP6 MUTATED    0  5
  MPP6 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  MPP6 MUTATED      0    5
  MPP6 WILD-TYPE    5   86
                        clus
vv                       MPP6 MUTATED MPP6 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(229) Variable = KIAA2018 MUTATION ANALYSIS
D229V1, survival
                    sevent
clus2                 0  1
  KIAA2018 MUTATED    2  6
  KIAA2018 WILD-TYPE 61 56
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 8                117 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 6                 56 
$`KIAA2018 MUTATED`
TCGA-2L-AAQJ TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A6UG 
       12.95        17.49        20.19         5.26        19.82         1.35 
TCGA-IB-AAUU TCGA-IB-AAUV 
        8.05        13.28 

$`KIAA2018 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        17.00        10.13        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUW 
        7.86        14.17         6.02        11.11         7.40         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
              1.35               0.23 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
             20.19              90.12 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
            13.115             15.320 
[1] "1.4 - 20.2 (13.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.3"
D229V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA2018 MUTATED         0        0        0         0         7         1
  KIAA2018 WILD-TYPE       1        3       12        19        75         3
                    vv
clus                 STAGE IV
  KIAA2018 MUTATED          0
  KIAA2018 WILD-TYPE        3
D229V3, multiclass
           clus
vv          KIAA2018 MUTATED KIAA2018 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                7                 75
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA2018 MUTATED    0  2     6
  KIAA2018 WILD-TYPE  5 15    96
D229V4, multiclass
       clus
vv      KIAA2018 MUTATED KIAA2018 WILD-TYPE
  T1                   0                  5
  T2                   2                 15
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V5, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    1  7
  KIAA2018 WILD-TYPE 34 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      1    7
  KIAA2018 WILD-TYPE   34   82
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0                1                 34
  1                7                 82
[1] 2 2
[1] FALSE
D229V6, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    4  0
  KIAA2018 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      4    0
  KIAA2018 WILD-TYPE   53    3
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D229V7, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    4  4
  KIAA2018 WILD-TYPE 47 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      4    4
  KIAA2018 WILD-TYPE   47   71
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  FEMALE                4                 47
  MALE                  4                 71
[1] 2 2
[1] FALSE
D229V8, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    8  0
  KIAA2018 WILD-TYPE 80 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      8    0
  KIAA2018 WILD-TYPE   80   30
     clus
vv    KIAA2018 MUTATED KIAA2018 WILD-TYPE
  NO                 8                 80
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA2018 MUTATED                                     8
  KIAA2018 WILD-TYPE                                  97
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA2018 MUTATED                                       0
  KIAA2018 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA2018 MUTATED                                                  0
  KIAA2018 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA2018 MUTATED                                     0
  KIAA2018 WILD-TYPE                                   1
D229V9, multiclass
                                                  clus
vv                                                 KIAA2018 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA2018 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V10, continuous
D229V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA2018 MUTATED    5  2  1  0
  KIAA2018 WILD-TYPE 75 33  3  2
D229V12, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  R0                5                 75
  R1                2                 33
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA2018 MUTATED       1                         0     7
  KIAA2018 WILD-TYPE     5                         5   107
D229V14, multiclass
                           clus
vv                          KIAA2018 MUTATED KIAA2018 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V15, binary
                    cls
clus                  0  1
  KIAA2018 MUTATED    0  6
  KIAA2018 WILD-TYPE  5 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      0    6
  KIAA2018 WILD-TYPE    5   85
                        clus
vv                       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                6                 85
[1] 2 2
[1] FALSE

Clustering(230) Variable = CEP72 MUTATION ANALYSIS
D230V1, survival
                 sevent
clus2              0  1
  CEP72 MUTATED    2  4
  CEP72 WILD-TYPE 61 58
  CEP72 MUTATED CEP72 WILD-TYPE 
              6             119 
  CEP72 MUTATED CEP72 WILD-TYPE 
              4              58 
$`CEP72 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-OE-A75W 
       22.06        20.19        19.82        15.85         1.35         8.78 

$`CEP72 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CEP72 MUTATED CEP72 WILD-TYPE 
           1.35            0.23 
  CEP72 MUTATED CEP72 WILD-TYPE 
          22.06           90.12 
  CEP72 MUTATED CEP72 WILD-TYPE 
         17.835          15.190 
[1] "1.4 - 22.1 (17.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D230V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CEP72 MUTATED         0        0        0         3         3         0
  CEP72 WILD-TYPE       1        3       12        16        79         4
                 vv
clus              STAGE IV
  CEP72 MUTATED          0
  CEP72 WILD-TYPE        3
D230V3, multiclass
           clus
vv          CEP72 MUTATED CEP72 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CEP72 MUTATED    0  0     6
  CEP72 WILD-TYPE  5 17    96
D230V4, multiclass
       clus
vv      CEP72 MUTATED CEP72 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V5, binary
                 cls
clus               0  1
  CEP72 MUTATED    3  3
  CEP72 WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      3    3
  CEP72 WILD-TYPE   32   86
   clus
vv  CEP72 MUTATED CEP72 WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D230V6, binary
                 cls
clus               0  1
  CEP72 MUTATED    4  0
  CEP72 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      4    0
  CEP72 WILD-TYPE   53    3
   clus
vv  CEP72 MUTATED CEP72 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D230V7, binary
                 cls
clus               0  1
  CEP72 MUTATED    1  5
  CEP72 WILD-TYPE 50 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      1    5
  CEP72 WILD-TYPE   50   70
        clus
vv       CEP72 MUTATED CEP72 WILD-TYPE
  FEMALE             1              50
  MALE               5              70
[1] 2 2
[1] FALSE
D230V8, binary
                 cls
clus               0  1
  CEP72 MUTATED    5  1
  CEP72 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      5    1
  CEP72 WILD-TYPE   83   29
     clus
vv    CEP72 MUTATED CEP72 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEP72 MUTATED                                     5
  CEP72 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEP72 MUTATED                                       1
  CEP72 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEP72 MUTATED                                                  0
  CEP72 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CEP72 MUTATED                                     0
  CEP72 WILD-TYPE                                   1
D230V9, multiclass
                                                  clus
vv                                                 CEP72 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CEP72 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V10, continuous
D230V11, continuous
                 vv
clus              R0 R1 R2 RX
  CEP72 MUTATED    4  2  0  0
  CEP72 WILD-TYPE 76 33  4  2
D230V12, multiclass
    clus
vv   CEP72 MUTATED CEP72 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP72 MUTATED       0                         0     6
  CEP72 WILD-TYPE     6                         5   108
D230V14, multiclass
                           clus
vv                          CEP72 MUTATED CEP72 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V15, binary
                 cls
clus               0  1
  CEP72 MUTATED    0  5
  CEP72 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      0    5
  CEP72 WILD-TYPE    5   86
                        clus
vv                       CEP72 MUTATED CEP72 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(231) Variable = AJAP1 MUTATION ANALYSIS
D231V1, survival
                 sevent
clus2              0  1
  AJAP1 MUTATED    4  4
  AJAP1 WILD-TYPE 59 58
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              8             117 
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              4              58 
$`AJAP1 MUTATED`
TCGA-2J-AABK TCGA-2J-AABP TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-HZ-A77P TCGA-IB-7651 
       15.91        15.22        23.54         5.03        10.85        19.82 
TCGA-IB-AAUO TCGA-US-A779 
        7.86        16.80 

$`AJAP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 
        7.50        12.53        15.55         4.04         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13         5.26         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        39.98         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  AJAP1 MUTATED AJAP1 WILD-TYPE 
           5.03            0.23 
  AJAP1 MUTATED AJAP1 WILD-TYPE 
          23.54           90.12 
  AJAP1 MUTATED AJAP1 WILD-TYPE 
         15.565          15.190 
[1] "5.0 - 23.5 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D231V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AJAP1 MUTATED         0        0        0         0         8         0
  AJAP1 WILD-TYPE       1        3       12        19        74         4
                 vv
clus              STAGE IV
  AJAP1 MUTATED          0
  AJAP1 WILD-TYPE        3
D231V3, multiclass
           clus
vv          AJAP1 MUTATED AJAP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AJAP1 MUTATED    0  1     7
  AJAP1 WILD-TYPE  5 16    95
D231V4, multiclass
       clus
vv      AJAP1 MUTATED AJAP1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V5, binary
                 cls
clus               0  1
  AJAP1 MUTATED    0  8
  AJAP1 WILD-TYPE 35 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AJAP1 MUTATED      0    8
  AJAP1 WILD-TYPE   35   81
   clus
vv  AJAP1 MUTATED AJAP1 WILD-TYPE
  0             0              35
  1             8              81
[1] 2 2
[1] FALSE
D231V6, binary
                 cls
clus               0  1
  AJAP1 MUTATED    4  0
  AJAP1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AJAP1 MUTATED      4    0
  AJAP1 WILD-TYPE   53    3
   clus
vv  AJAP1 MUTATED AJAP1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D231V7, binary
                 cls
clus               0  1
  AJAP1 MUTATED    5  3
  AJAP1 WILD-TYPE 46 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AJAP1 MUTATED      5    3
  AJAP1 WILD-TYPE   46   72
        clus
vv       AJAP1 MUTATED AJAP1 WILD-TYPE
  FEMALE             5              46
  MALE               3              72
[1] 2 2
[1] FALSE
D231V8, binary
                 cls
clus               0  1
  AJAP1 MUTATED    6  1
  AJAP1 WILD-TYPE 82 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AJAP1 MUTATED      6    1
  AJAP1 WILD-TYPE   82   29
     clus
vv    AJAP1 MUTATED AJAP1 WILD-TYPE
  NO              6              82
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AJAP1 MUTATED                                     6
  AJAP1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AJAP1 MUTATED                                       1
  AJAP1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AJAP1 MUTATED                                                  0
  AJAP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AJAP1 MUTATED                                     1
  AJAP1 WILD-TYPE                                   0
D231V9, multiclass
                                                  clus
vv                                                 AJAP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 AJAP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V10, continuous
[1] "Remove cluster labels:" "AJAP1 MUTATED"         
clus
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
D231V11, continuous
[1] "Remove cluster labels:" "AJAP1 MUTATED"         
clus
  AJAP1 MUTATED AJAP1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" "AJAP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  AJAP1 MUTATED    5  3  0  0
  AJAP1 WILD-TYPE 75 32  4  2
D231V12, multiclass
    clus
vv   AJAP1 MUTATED AJAP1 WILD-TYPE
  R0             5              75
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AJAP1 MUTATED       0                         0     8
  AJAP1 WILD-TYPE     6                         5   106
D231V14, multiclass
                           clus
vv                          AJAP1 MUTATED AJAP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V15, binary
                 cls
clus               0  1
  AJAP1 MUTATED    0  6
  AJAP1 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AJAP1 MUTATED      0    6
  AJAP1 WILD-TYPE    5   85
                        clus
vv                       AJAP1 MUTATED AJAP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(232) Variable = GABBR1 MUTATION ANALYSIS
D232V1, survival
                  sevent
clus2               0  1
  GABBR1 MUTATED    7  3
  GABBR1 WILD-TYPE 56 59
  GABBR1 MUTATED GABBR1 WILD-TYPE 
              10              115 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               3               59 
$`GABBR1 MUTATED`
TCGA-3A-A9IJ TCGA-FB-AAQ6 TCGA-2J-AAB4 TCGA-2J-AABP TCGA-3A-A9IU TCGA-HV-A7OP 
       60.95         8.02        23.97        15.22        15.06        32.15 
TCGA-IB-7651 TCGA-IB-8126 TCGA-US-A776 TCGA-XN-A8T5 
       19.82        15.19        39.98        23.67 

$`GABBR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FZ-5924 
       14.40        10.49        58.98        90.12         7.66        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV 
       22.72        42.31        15.91        14.47         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GABBR1 MUTATED GABBR1 WILD-TYPE 
            8.02             0.23 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
           60.95            90.12 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
          21.745           14.470 
[1] "8.0 - 61.0 (21.7)" "0.2 - 90.1 (14.5)"
[1] "hr=" "2.4"
D232V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GABBR1 MUTATED         0        1        2         1         5         1
  GABBR1 WILD-TYPE       1        2       10        18        77         3
                  vv
clus               STAGE IV
  GABBR1 MUTATED          0
  GABBR1 WILD-TYPE        3
D232V3, multiclass
           clus
vv          GABBR1 MUTATED GABBR1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               2               10
  STAGE IIA              1               18
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GABBR1 MUTATED    1  3     6
  GABBR1 WILD-TYPE  4 14    96
D232V4, multiclass
       clus
vv      GABBR1 MUTATED GABBR1 WILD-TYPE
  T1                 1                4
  T2                 3               14
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V5, binary
                  cls
clus                0  1
  GABBR1 MUTATED    4  6
  GABBR1 WILD-TYPE 31 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      4    6
  GABBR1 WILD-TYPE   31   83
   clus
vv  GABBR1 MUTATED GABBR1 WILD-TYPE
  0              4               31
  1              6               83
[1] 2 2
[1] FALSE
D232V6, binary
                  cls
clus                0  1
  GABBR1 MUTATED    6  0
  GABBR1 WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      6    0
  GABBR1 WILD-TYPE   51    3
   clus
vv  GABBR1 MUTATED GABBR1 WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D232V7, binary
                  cls
clus                0  1
  GABBR1 MUTATED    4  6
  GABBR1 WILD-TYPE 47 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      4    6
  GABBR1 WILD-TYPE   47   69
        clus
vv       GABBR1 MUTATED GABBR1 WILD-TYPE
  FEMALE              4               47
  MALE                6               69
[1] 2 2
[1] FALSE
D232V8, binary
                  cls
clus                0  1
  GABBR1 MUTATED    8  2
  GABBR1 WILD-TYPE 80 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      8    2
  GABBR1 WILD-TYPE   80   28
     clus
vv    GABBR1 MUTATED GABBR1 WILD-TYPE
  NO               8               80
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GABBR1 MUTATED                                     4
  GABBR1 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GABBR1 MUTATED                                       4
  GABBR1 WILD-TYPE                                    14
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GABBR1 MUTATED                                                  1
  GABBR1 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GABBR1 MUTATED                                     1
  GABBR1 WILD-TYPE                                   0
D232V9, multiclass
                                                  clus
vv                                                 GABBR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 GABBR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          14
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V10, continuous
D232V11, continuous
                  vv
clus               R0 R1 R2 RX
  GABBR1 MUTATED    8  2  0  0
  GABBR1 WILD-TYPE 72 33  4  2
D232V12, multiclass
    clus
vv   GABBR1 MUTATED GABBR1 WILD-TYPE
  R0              8               72
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GABBR1 MUTATED       1                         0     9
  GABBR1 WILD-TYPE     5                         5   105
D232V14, multiclass
                           clus
vv                          GABBR1 MUTATED GABBR1 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V15, binary
                  cls
clus                0  1
  GABBR1 MUTATED    1  6
  GABBR1 WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      1    6
  GABBR1 WILD-TYPE    4   85
                        clus
vv                       GABBR1 MUTATED GABBR1 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(233) Variable = PAMR1 MUTATION ANALYSIS
D233V1, survival
                 sevent
clus2              0  1
  PAMR1 MUTATED    4  3
  PAMR1 WILD-TYPE 59 59
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              7             118 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              3              59 
$`PAMR1 MUTATED`
TCGA-2J-AAB4 TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-IB-7651 TCGA-IB-AAUP TCGA-RB-AA9M 
       23.97         4.70        12.95        19.82        14.17         9.40 
TCGA-YY-A8LH 
       66.28 

$`PAMR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
       15.22         9.11        21.44        22.49         3.39         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  PAMR1 MUTATED PAMR1 WILD-TYPE 
           4.70            0.23 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          66.28           90.12 
  PAMR1 MUTATED PAMR1 WILD-TYPE 
          14.17           15.27 
[1] "4.7 - 66.3 (14.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D233V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PAMR1 MUTATED         0        0        0         0         6         1
  PAMR1 WILD-TYPE       1        3       12        19        76         3
                 vv
clus              STAGE IV
  PAMR1 MUTATED          0
  PAMR1 WILD-TYPE        3
D233V3, multiclass
           clus
vv          PAMR1 MUTATED PAMR1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PAMR1 MUTATED    1  1     5
  PAMR1 WILD-TYPE  4 16    97
D233V4, multiclass
       clus
vv      PAMR1 MUTATED PAMR1 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V5, binary
                 cls
clus               0  1
  PAMR1 MUTATED    1  6
  PAMR1 WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      1    6
  PAMR1 WILD-TYPE   34   83
   clus
vv  PAMR1 MUTATED PAMR1 WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D233V6, binary
                 cls
clus               0  1
  PAMR1 MUTATED    3  0
  PAMR1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      3    0
  PAMR1 WILD-TYPE   54    3
   clus
vv  PAMR1 MUTATED PAMR1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D233V7, binary
                 cls
clus               0  1
  PAMR1 MUTATED    3  4
  PAMR1 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      3    4
  PAMR1 WILD-TYPE   48   71
        clus
vv       PAMR1 MUTATED PAMR1 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D233V8, binary
                 cls
clus               0  1
  PAMR1 MUTATED    5  2
  PAMR1 WILD-TYPE 83 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      5    2
  PAMR1 WILD-TYPE   83   28
     clus
vv    PAMR1 MUTATED PAMR1 WILD-TYPE
  NO              5              83
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PAMR1 MUTATED                                     6
  PAMR1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PAMR1 MUTATED                                       1
  PAMR1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PAMR1 MUTATED                                                  0
  PAMR1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PAMR1 MUTATED                                     0
  PAMR1 WILD-TYPE                                   1
D233V9, multiclass
                                                  clus
vv                                                 PAMR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PAMR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V10, continuous
D233V11, continuous
[1] "Remove cluster labels:" "PAMR1 MUTATED"         
clus
  PAMR1 MUTATED PAMR1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" "PAMR1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PAMR1 MUTATED    4  3  0  0
  PAMR1 WILD-TYPE 76 32  4  2
D233V12, multiclass
    clus
vv   PAMR1 MUTATED PAMR1 WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAMR1 MUTATED       0                         0     7
  PAMR1 WILD-TYPE     6                         5   107
D233V14, multiclass
                           clus
vv                          PAMR1 MUTATED PAMR1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V15, binary
                 cls
clus               0  1
  PAMR1 MUTATED    0  4
  PAMR1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAMR1 MUTATED      0    4
  PAMR1 WILD-TYPE    5   87
                        clus
vv                       PAMR1 MUTATED PAMR1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(234) Variable = GRHPR MUTATION ANALYSIS
D234V1, survival
                 sevent
clus2              0  1
  GRHPR MUTATED    2  3
  GRHPR WILD-TYPE 61 59
  GRHPR MUTATED GRHPR WILD-TYPE 
              5             120 
  GRHPR MUTATED GRHPR WILD-TYPE 
              3              59 
$`GRHPR MUTATED`
TCGA-HZ-A77Q TCGA-FZ-5919 TCGA-HV-AA8X TCGA-US-A77J TCGA-YB-A89D 
        1.08        24.36        17.49        18.67        11.51 

$`GRHPR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 
       17.79        22.06         8.28        32.15        30.25        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  GRHPR MUTATED GRHPR WILD-TYPE 
           1.08            0.23 
  GRHPR MUTATED GRHPR WILD-TYPE 
          24.36           90.12 
  GRHPR MUTATED GRHPR WILD-TYPE 
         17.490          15.205 
[1] "1.1 - 24.4 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D234V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GRHPR MUTATED         0        0        0         0         5         0
  GRHPR WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  GRHPR MUTATED          0
  GRHPR WILD-TYPE        3
D234V3, multiclass
           clus
vv          GRHPR MUTATED GRHPR WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  GRHPR MUTATED    0  1     4
  GRHPR WILD-TYPE  5 16    98
D234V4, multiclass
       clus
vv      GRHPR MUTATED GRHPR WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V5, binary
                 cls
clus               0  1
  GRHPR MUTATED    0  5
  GRHPR WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHPR MUTATED      0    5
  GRHPR WILD-TYPE   35   84
   clus
vv  GRHPR MUTATED GRHPR WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D234V6, binary
                 cls
clus               0  1
  GRHPR MUTATED    0  0
  GRHPR WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHPR MUTATED      0    0
  GRHPR WILD-TYPE   57    3
D234V7, binary
                 cls
clus               0  1
  GRHPR MUTATED    4  1
  GRHPR WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHPR MUTATED      4    1
  GRHPR WILD-TYPE   47   74
        clus
vv       GRHPR MUTATED GRHPR WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D234V8, binary
                 cls
clus               0  1
  GRHPR MUTATED    2  1
  GRHPR WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHPR MUTATED      2    1
  GRHPR WILD-TYPE   86   29
     clus
vv    GRHPR MUTATED GRHPR WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GRHPR MUTATED                                     4
  GRHPR WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GRHPR MUTATED                                       1
  GRHPR WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GRHPR MUTATED                                                  0
  GRHPR WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  GRHPR MUTATED                                     0
  GRHPR WILD-TYPE                                   1
D234V9, multiclass
                                                  clus
vv                                                 GRHPR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 GRHPR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V10, continuous
[1] "Remove cluster labels:" "GRHPR MUTATED"         
clus
  GRHPR MUTATED GRHPR WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
D234V11, continuous
[1] "Remove cluster labels:" "GRHPR MUTATED"         
clus
  GRHPR MUTATED GRHPR WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" "GRHPR WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  GRHPR MUTATED    3  0  1  0
  GRHPR WILD-TYPE 77 35  3  2
D234V12, multiclass
    clus
vv   GRHPR MUTATED GRHPR WILD-TYPE
  R0             3              77
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GRHPR MUTATED       1                         0     4
  GRHPR WILD-TYPE     5                         5   110
D234V14, multiclass
                           clus
vv                          GRHPR MUTATED GRHPR WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V15, binary
                 cls
clus               0  1
  GRHPR MUTATED    0  4
  GRHPR WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRHPR MUTATED      0    4
  GRHPR WILD-TYPE    5   87
                        clus
vv                       GRHPR MUTATED GRHPR WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(235) Variable = CYP20A1 MUTATION ANALYSIS
D235V1, survival
                   sevent
clus2                0  1
  CYP20A1 MUTATED    4  2
  CYP20A1 WILD-TYPE 59 60
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                6               119 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                2                60 
$`CYP20A1 MUTATED`
TCGA-3A-A9IL TCGA-HZ-A77Q TCGA-3A-A9IC TCGA-IB-7651 TCGA-IB-7885 TCGA-RB-AA9M 
       90.12         1.08        24.26        19.82        41.33         9.40 

$`CYP20A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
             1.08              0.23 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            90.12             75.12 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            22.04             15.19 
[1] "1.1 - 90.1 (22.0)" "0.2 - 75.1 (15.2)"
[1] "hr=" "2.2"
D235V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CYP20A1 MUTATED         1        0        0         0         5         0
  CYP20A1 WILD-TYPE       0        3       12        19        77         4
                   vv
clus                STAGE IV
  CYP20A1 MUTATED          0
  CYP20A1 WILD-TYPE        3
D235V3, multiclass
           clus
vv          CYP20A1 MUTATED CYP20A1 WILD-TYPE
  STAGE I                 1                 0
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CYP20A1 MUTATED    2  0     4
  CYP20A1 WILD-TYPE  3 17    98
D235V4, multiclass
       clus
vv      CYP20A1 MUTATED CYP20A1 WILD-TYPE
  T1                  2                 3
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V5, binary
                   cls
clus                 0  1
  CYP20A1 MUTATED    0  5
  CYP20A1 WILD-TYPE 35 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      0    5
  CYP20A1 WILD-TYPE   35   84
   clus
vv  CYP20A1 MUTATED CYP20A1 WILD-TYPE
  0               0                35
  1               5                84
[1] 2 2
[1] FALSE
D235V6, binary
                   cls
clus                 0  1
  CYP20A1 MUTATED    2  0
  CYP20A1 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      2    0
  CYP20A1 WILD-TYPE   55    3
   clus
vv  CYP20A1 MUTATED CYP20A1 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D235V7, binary
                   cls
clus                 0  1
  CYP20A1 MUTATED    5  1
  CYP20A1 WILD-TYPE 46 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      5    1
  CYP20A1 WILD-TYPE   46   74
        clus
vv       CYP20A1 MUTATED CYP20A1 WILD-TYPE
  FEMALE               5                46
  MALE                 1                74
[1] 2 2
[1] FALSE
D235V8, binary
                   cls
clus                 0  1
  CYP20A1 MUTATED    3  2
  CYP20A1 WILD-TYPE 85 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      3    2
  CYP20A1 WILD-TYPE   85   28
     clus
vv    CYP20A1 MUTATED CYP20A1 WILD-TYPE
  NO                3                85
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CYP20A1 MUTATED                                     4
  CYP20A1 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CYP20A1 MUTATED                                       2
  CYP20A1 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CYP20A1 MUTATED                                                  0
  CYP20A1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CYP20A1 MUTATED                                     0
  CYP20A1 WILD-TYPE                                   1
D235V9, multiclass
                                                  clus
vv                                                 CYP20A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CYP20A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V10, continuous
D235V11, continuous
                   vv
clus                R0 R1 R2 RX
  CYP20A1 MUTATED    6  0  0  0
  CYP20A1 WILD-TYPE 74 35  4  2
D235V12, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  R0               6                74
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP20A1 MUTATED       0                         0     6
  CYP20A1 WILD-TYPE     6                         5   108
D235V14, multiclass
                           clus
vv                          CYP20A1 MUTATED CYP20A1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V15, binary
                   cls
clus                 0  1
  CYP20A1 MUTATED    0  6
  CYP20A1 WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      0    6
  CYP20A1 WILD-TYPE    5   85
                        clus
vv                       CYP20A1 MUTATED CYP20A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(236) Variable = ARMCX3 MUTATION ANALYSIS
D236V1, survival
                  sevent
clus2               0  1
  ARMCX3 MUTATED    1  4
  ARMCX3 WILD-TYPE 62 58
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               5              120 
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               4               58 
$`ARMCX3 MUTATED`
TCGA-FB-A78T TCGA-FB-AAPP TCGA-IB-A5SQ TCGA-RB-A7B8 TCGA-XD-AAUH 
       12.33        15.95         7.20        15.32        12.99 

$`ARMCX3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPQ 
       71.74        19.46         3.12        17.00        16.37        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI 
       39.98        16.80         0.39        18.67        13.81        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
            7.20             0.23 
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
           15.95            90.12 
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
          12.990           15.285 
[1] "7.2 - 15.9 (13.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.6"
D236V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ARMCX3 MUTATED         0        0        1         0         4         0
  ARMCX3 WILD-TYPE       1        3       11        19        78         4
                  vv
clus               STAGE IV
  ARMCX3 MUTATED          0
  ARMCX3 WILD-TYPE        3
D236V3, multiclass
           clus
vv          ARMCX3 MUTATED ARMCX3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ARMCX3 MUTATED    0  1     4
  ARMCX3 WILD-TYPE  5 16    98
D236V4, multiclass
       clus
vv      ARMCX3 MUTATED ARMCX3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V5, binary
                  cls
clus                0  1
  ARMCX3 MUTATED    1  4
  ARMCX3 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX3 MUTATED      1    4
  ARMCX3 WILD-TYPE   34   85
   clus
vv  ARMCX3 MUTATED ARMCX3 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D236V6, binary
                  cls
clus                0  1
  ARMCX3 MUTATED    3  0
  ARMCX3 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX3 MUTATED      3    0
  ARMCX3 WILD-TYPE   54    3
   clus
vv  ARMCX3 MUTATED ARMCX3 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D236V7, binary
                  cls
clus                0  1
  ARMCX3 MUTATED    4  1
  ARMCX3 WILD-TYPE 47 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX3 MUTATED      4    1
  ARMCX3 WILD-TYPE   47   74
        clus
vv       ARMCX3 MUTATED ARMCX3 WILD-TYPE
  FEMALE              4               47
  MALE                1               74
[1] 2 2
[1] FALSE
D236V8, binary
                  cls
clus                0  1
  ARMCX3 MUTATED    3  2
  ARMCX3 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX3 MUTATED      3    2
  ARMCX3 WILD-TYPE   85   28
     clus
vv    ARMCX3 MUTATED ARMCX3 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARMCX3 MUTATED                                     4
  ARMCX3 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARMCX3 MUTATED                                       1
  ARMCX3 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARMCX3 MUTATED                                                  0
  ARMCX3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ARMCX3 MUTATED                                     0
  ARMCX3 WILD-TYPE                                   1
D236V9, multiclass
                                                  clus
vv                                                 ARMCX3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ARMCX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V10, continuous
[1] "Remove cluster labels:" "ARMCX3 MUTATED"        
clus
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-AAPQ 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
D236V11, continuous
[1] "Remove cluster labels:" "ARMCX3 MUTATED"        
clus
  ARMCX3 MUTATED ARMCX3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" "ARMCX3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ARMCX3 MUTATED    4  0  1  0
  ARMCX3 WILD-TYPE 76 35  3  2
D236V12, multiclass
    clus
vv   ARMCX3 MUTATED ARMCX3 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARMCX3 MUTATED       0                         0     5
  ARMCX3 WILD-TYPE     6                         5   109
D236V14, multiclass
                           clus
vv                          ARMCX3 MUTATED ARMCX3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V15, binary
                  cls
clus                0  1
  ARMCX3 MUTATED    0  5
  ARMCX3 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX3 MUTATED      0    5
  ARMCX3 WILD-TYPE    5   86
                        clus
vv                       ARMCX3 MUTATED ARMCX3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(237) Variable = MED23 MUTATION ANALYSIS
D237V1, survival
                 sevent
clus2              0  1
  MED23 MUTATED    2  4
  MED23 WILD-TYPE 61 58
  MED23 MUTATED MED23 WILD-TYPE 
              6             119 
  MED23 MUTATED MED23 WILD-TYPE 
              4              58 
$`MED23 MUTATED`
TCGA-3A-A9I9 TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-A7M4 TCGA-OE-A75W TCGA-XD-AAUH 
       20.84        19.46        19.82        15.88         8.78        12.99 

$`MED23 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  MED23 MUTATED MED23 WILD-TYPE 
           8.78            0.23 
  MED23 MUTATED MED23 WILD-TYPE 
          20.84           90.12 
  MED23 MUTATED MED23 WILD-TYPE 
          17.67           15.19 
[1] "8.8 - 20.8 (17.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D237V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MED23 MUTATED         0        0        0         2         4         0
  MED23 WILD-TYPE       1        3       12        17        78         4
                 vv
clus              STAGE IV
  MED23 MUTATED          0
  MED23 WILD-TYPE        3
D237V3, multiclass
           clus
vv          MED23 MUTATED MED23 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MED23 MUTATED    0  0     6
  MED23 WILD-TYPE  5 17    96
D237V4, multiclass
       clus
vv      MED23 MUTATED MED23 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V5, binary
                 cls
clus               0  1
  MED23 MUTATED    2  4
  MED23 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      2    4
  MED23 WILD-TYPE   33   85
   clus
vv  MED23 MUTATED MED23 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D237V6, binary
                 cls
clus               0  1
  MED23 MUTATED    4  0
  MED23 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      4    0
  MED23 WILD-TYPE   53    3
   clus
vv  MED23 MUTATED MED23 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D237V7, binary
                 cls
clus               0  1
  MED23 MUTATED    2  4
  MED23 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      2    4
  MED23 WILD-TYPE   49   71
        clus
vv       MED23 MUTATED MED23 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D237V8, binary
                 cls
clus               0  1
  MED23 MUTATED    2  4
  MED23 WILD-TYPE 86 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      2    4
  MED23 WILD-TYPE   86   26
     clus
vv    MED23 MUTATED MED23 WILD-TYPE
  NO              2              86
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED23 MUTATED                                     6
  MED23 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED23 MUTATED                                       0
  MED23 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED23 MUTATED                                                  0
  MED23 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MED23 MUTATED                                     0
  MED23 WILD-TYPE                                   1
D237V9, multiclass
                                                  clus
vv                                                 MED23 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MED23 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V10, continuous
D237V11, continuous
                 vv
clus              R0 R1 R2 RX
  MED23 MUTATED    4  1  1  0
  MED23 WILD-TYPE 76 34  3  2
D237V12, multiclass
    clus
vv   MED23 MUTATED MED23 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED23 MUTATED       0                         1     5
  MED23 WILD-TYPE     6                         4   109
D237V14, multiclass
                           clus
vv                          MED23 MUTATED MED23 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V15, binary
                 cls
clus               0  1
  MED23 MUTATED    0  6
  MED23 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED23 MUTATED      0    6
  MED23 WILD-TYPE    5   85
                        clus
vv                       MED23 MUTATED MED23 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(238) Variable = AR MUTATION ANALYSIS
D238V1, survival
              sevent
clus2           0  1
  AR MUTATED    4  4
  AR WILD-TYPE 59 58
  AR MUTATED AR WILD-TYPE 
           8          117 
  AR MUTATED AR WILD-TYPE 
           4           58 
$`AR MUTATED`
TCGA-3A-A9IJ TCGA-FB-AAPS TCGA-FB-AAQ3 TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-8126 
       60.95         7.50         1.02        17.49        19.82        15.19 
TCGA-IB-A6UG TCGA-LB-A8F3 
        1.35        12.46 

$`AR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  AR MUTATED AR WILD-TYPE 
        1.02         0.23 
  AR MUTATED AR WILD-TYPE 
       60.95        90.12 
  AR MUTATED AR WILD-TYPE 
      13.825       15.320 
[1] "1.0 - 61.0 (13.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D238V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AR MUTATED         0        0        1         1         5         1        0
  AR WILD-TYPE       1        3       11        18        77         3        3
D238V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            0            1
  STAGE IA           0            3
  STAGE IB           1           11
  STAGE IIA          1           18
  STAGE IIB          5           77
  STAGE III          1            3
  STAGE IV           0            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T1 T2 T3+T4
  AR MUTATED    0  3     5
  AR WILD-TYPE  5 14    97
D238V4, multiclass
       clus
vv      AR MUTATED AR WILD-TYPE
  T1             0            5
  T2             3           14
  T3+T4          5           97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V5, binary
              cls
clus            0  1
  AR MUTATED    2  6
  AR WILD-TYPE 33 83
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      2    6
  AR WILD-TYPE   33   83
   clus
vv  AR MUTATED AR WILD-TYPE
  0          2           33
  1          6           83
[1] 2 2
[1] FALSE
D238V6, binary
              cls
clus            0  1
  AR MUTATED    3  0
  AR WILD-TYPE 54  3
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      3    0
  AR WILD-TYPE   54    3
   clus
vv  AR MUTATED AR WILD-TYPE
  0          3           54
  1          0            3
[1] 2 2
[1] FALSE
D238V7, binary
              cls
clus            0  1
  AR MUTATED    6  2
  AR WILD-TYPE 45 73
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    2
  AR WILD-TYPE   45   73
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          6           45
  MALE            2           73
[1] 2 2
[1] FALSE
D238V8, binary
              cls
clus            0  1
  AR MUTATED    6  2
  AR WILD-TYPE 82 28
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    2
  AR WILD-TYPE   82   28
     clus
vv    AR MUTATED AR WILD-TYPE
  NO           6           82
  YES          2           28
[1] 2 2
[1] FALSE
              vv
clus           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AR MUTATED                                     7
  AR WILD-TYPE                                  98
              vv
clus           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AR MUTATED                                       1
  AR WILD-TYPE                                    17
              vv
clus           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AR MUTATED                                                  0
  AR WILD-TYPE                                                1
              vv
clus           PANCREAS-UNDIFFERENTIATED CARCINOMA
  AR MUTATED                                     0
  AR WILD-TYPE                                   1
D238V9, multiclass
                                                  clus
vv                                                 AR MUTATED AR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       7           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                     1           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA          0            1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                       0            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V10, continuous
D238V11, continuous
              vv
clus           R0 R1 R2 RX
  AR MUTATED    5  2  1  0
  AR WILD-TYPE 75 33  3  2
D238V12, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  R0          5           75
  R1          2           33
  R2          1            3
  RX          0            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V13, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AR MUTATED       1                         1     6
  AR WILD-TYPE     5                         4   108
D238V14, multiclass
                           clus
vv                          AR MUTATED AR WILD-TYPE
  ASIAN                              1            5
  BLACK OR AFRICAN AMERICAN          1            4
  WHITE                              6          108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V15, binary
              cls
clus            0  1
  AR MUTATED    0  7
  AR WILD-TYPE  5 84
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      0    7
  AR WILD-TYPE    5   84
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              0            5
  NOT HISPANIC OR LATINO          7           84
[1] 2 2
[1] FALSE

Clustering(239) Variable = NKTR MUTATION ANALYSIS
D239V1, survival
                sevent
clus2             0  1
  NKTR MUTATED    4  2
  NKTR WILD-TYPE 59 60
  NKTR MUTATED NKTR WILD-TYPE 
             6            119 
  NKTR MUTATED NKTR WILD-TYPE 
             2             60 
$`NKTR MUTATED`
TCGA-3A-A9IV TCGA-FB-AAQ1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-YY-A8LH 
       36.26         4.04        19.82        36.69        15.19        66.28 

$`NKTR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        0.23        19.82        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  NKTR MUTATED NKTR WILD-TYPE 
          4.04           0.23 
  NKTR MUTATED NKTR WILD-TYPE 
         66.28          90.12 
  NKTR MUTATED NKTR WILD-TYPE 
         28.04          15.12 
[1] "4.0 - 66.3 (28.0)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2.1"
D239V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NKTR MUTATED         0        0        1         0         4         1
  NKTR WILD-TYPE       1        3       11        19        78         3
                vv
clus             STAGE IV
  NKTR MUTATED          0
  NKTR WILD-TYPE        3
D239V3, multiclass
           clus
vv          NKTR MUTATED NKTR WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NKTR MUTATED    0  1     5
  NKTR WILD-TYPE  5 16    97
D239V4, multiclass
       clus
vv      NKTR MUTATED NKTR WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V5, binary
                cls
clus              0  1
  NKTR MUTATED    1  5
  NKTR WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      1    5
  NKTR WILD-TYPE   34   84
   clus
vv  NKTR MUTATED NKTR WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D239V6, binary
                cls
clus              0  1
  NKTR MUTATED    3  0
  NKTR WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      3    0
  NKTR WILD-TYPE   54    3
   clus
vv  NKTR MUTATED NKTR WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D239V7, binary
                cls
clus              0  1
  NKTR MUTATED    5  1
  NKTR WILD-TYPE 46 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      5    1
  NKTR WILD-TYPE   46   74
        clus
vv       NKTR MUTATED NKTR WILD-TYPE
  FEMALE            5             46
  MALE              1             74
[1] 2 2
[1] FALSE
D239V8, binary
                cls
clus              0  1
  NKTR MUTATED    5  1
  NKTR WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      5    1
  NKTR WILD-TYPE   83   29
     clus
vv    NKTR MUTATED NKTR WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NKTR MUTATED                                     5
  NKTR WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NKTR MUTATED                                       1
  NKTR WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NKTR MUTATED                                                  0
  NKTR WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NKTR MUTATED                                     0
  NKTR WILD-TYPE                                   1
D239V9, multiclass
                                                  clus
vv                                                 NKTR MUTATED NKTR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V10, continuous
D239V11, continuous
                vv
clus             R0 R1 R2 RX
  NKTR MUTATED    3  3  0  0
  NKTR WILD-TYPE 77 32  4  2
D239V12, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  R0            3             77
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NKTR MUTATED       1                         0     5
  NKTR WILD-TYPE     5                         5   109
D239V14, multiclass
                           clus
vv                          NKTR MUTATED NKTR WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V15, binary
                cls
clus              0  1
  NKTR MUTATED    0  6
  NKTR WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      0    6
  NKTR WILD-TYPE    5   85
                        clus
vv                       NKTR MUTATED NKTR WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(240) Variable = VDAC1 MUTATION ANALYSIS
D240V1, survival
                 sevent
clus2              0  1
  VDAC1 MUTATED    3  2
  VDAC1 WILD-TYPE 60 60
  VDAC1 MUTATED VDAC1 WILD-TYPE 
              5             120 
  VDAC1 MUTATED VDAC1 WILD-TYPE 
              2              60 
$`VDAC1 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IS TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-A7M4 
       22.49        32.81         7.50        19.82        15.88 

$`VDAC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  VDAC1 MUTATED VDAC1 WILD-TYPE 
           7.50            0.23 
  VDAC1 MUTATED VDAC1 WILD-TYPE 
          32.81           90.12 
  VDAC1 MUTATED VDAC1 WILD-TYPE 
         19.820          15.155 
[1] "7.5 - 32.8 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D240V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  VDAC1 MUTATED         0        0        1         0         4         0
  VDAC1 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  VDAC1 MUTATED          0
  VDAC1 WILD-TYPE        3
D240V3, multiclass
           clus
vv          VDAC1 MUTATED VDAC1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  VDAC1 MUTATED    0  2     3
  VDAC1 WILD-TYPE  5 15    99
D240V4, multiclass
       clus
vv      VDAC1 MUTATED VDAC1 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V5, binary
                 cls
clus               0  1
  VDAC1 MUTATED    1  4
  VDAC1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VDAC1 MUTATED      1    4
  VDAC1 WILD-TYPE   34   85
   clus
vv  VDAC1 MUTATED VDAC1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D240V6, binary
                 cls
clus               0  1
  VDAC1 MUTATED    2  0
  VDAC1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VDAC1 MUTATED      2    0
  VDAC1 WILD-TYPE   55    3
   clus
vv  VDAC1 MUTATED VDAC1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D240V7, binary
                 cls
clus               0  1
  VDAC1 MUTATED    2  3
  VDAC1 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VDAC1 MUTATED      2    3
  VDAC1 WILD-TYPE   49   72
        clus
vv       VDAC1 MUTATED VDAC1 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D240V8, binary
                 cls
clus               0  1
  VDAC1 MUTATED    4  1
  VDAC1 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VDAC1 MUTATED      4    1
  VDAC1 WILD-TYPE   84   29
     clus
vv    VDAC1 MUTATED VDAC1 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VDAC1 MUTATED                                     4
  VDAC1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VDAC1 MUTATED                                       1
  VDAC1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VDAC1 MUTATED                                                  0
  VDAC1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  VDAC1 MUTATED                                     0
  VDAC1 WILD-TYPE                                   1
D240V9, multiclass
                                                  clus
vv                                                 VDAC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 VDAC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V10, continuous
D240V11, continuous
                 vv
clus              R0 R1 R2 RX
  VDAC1 MUTATED    5  0  0  0
  VDAC1 WILD-TYPE 75 35  4  2
D240V12, multiclass
    clus
vv   VDAC1 MUTATED VDAC1 WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VDAC1 MUTATED       0                         0     5
  VDAC1 WILD-TYPE     6                         5   109
D240V14, multiclass
                           clus
vv                          VDAC1 MUTATED VDAC1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V15, binary
                 cls
clus               0  1
  VDAC1 MUTATED    0  4
  VDAC1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VDAC1 MUTATED      0    4
  VDAC1 WILD-TYPE    5   87
                        clus
vv                       VDAC1 MUTATED VDAC1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(241) Variable = RIT1 MUTATION ANALYSIS
D241V1, survival
                sevent
clus2             0  1
  RIT1 MUTATED    3  1
  RIT1 WILD-TYPE 60 61
  RIT1 MUTATED RIT1 WILD-TYPE 
             4            121 
  RIT1 MUTATED RIT1 WILD-TYPE 
             1             61 
$`RIT1 MUTATED`
TCGA-3A-A9I5 TCGA-2L-AAQI TCGA-H8-A6C1 TCGA-US-A776 
       58.98         3.39        22.06        39.98 

$`RIT1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RIT1 MUTATED RIT1 WILD-TYPE 
          3.39           0.23 
  RIT1 MUTATED RIT1 WILD-TYPE 
         58.98          90.12 
  RIT1 MUTATED RIT1 WILD-TYPE 
         31.02          15.19 
[1] "3.4 - 59.0 (31.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.1"
D241V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RIT1 MUTATED         0        0        0         2         1         0
  RIT1 WILD-TYPE       1        3       12        17        81         4
                vv
clus             STAGE IV
  RIT1 MUTATED          0
  RIT1 WILD-TYPE        3
D241V3, multiclass
           clus
vv          RIT1 MUTATED RIT1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            1             81
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RIT1 MUTATED    0  0     3
  RIT1 WILD-TYPE  5 17    99
D241V4, multiclass
       clus
vv      RIT1 MUTATED RIT1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V5, binary
                cls
clus              0  1
  RIT1 MUTATED    3  1
  RIT1 WILD-TYPE 32 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      3    1
  RIT1 WILD-TYPE   32   88
   clus
vv  RIT1 MUTATED RIT1 WILD-TYPE
  0            3             32
  1            1             88
[1] 2 2
[1] FALSE
D241V6, binary
                cls
clus              0  1
  RIT1 MUTATED    0  0
  RIT1 WILD-TYPE 57  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    0
  RIT1 WILD-TYPE   57    3
D241V7, binary
                cls
clus              0  1
  RIT1 MUTATED    0  4
  RIT1 WILD-TYPE 51 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    4
  RIT1 WILD-TYPE   51   71
        clus
vv       RIT1 MUTATED RIT1 WILD-TYPE
  FEMALE            0             51
  MALE              4             71
[1] 2 2
[1] FALSE
D241V8, binary
                cls
clus              0  1
  RIT1 MUTATED    3  1
  RIT1 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      3    1
  RIT1 WILD-TYPE   85   29
     clus
vv    RIT1 MUTATED RIT1 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RIT1 MUTATED                                     2
  RIT1 WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RIT1 MUTATED                                       1
  RIT1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RIT1 MUTATED                                                  1
  RIT1 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RIT1 MUTATED                                     0
  RIT1 WILD-TYPE                                   1
D241V9, multiclass
                                                  clus
vv                                                 RIT1 MUTATED RIT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V10, continuous
[1] "Remove cluster labels:" "RIT1 MUTATED"          
clus
  RIT1 MUTATED RIT1 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
D241V11, continuous
[1] "Remove cluster labels:" "RIT1 MUTATED"          
clus
  RIT1 MUTATED RIT1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RIT1 MUTATED    3  1  0  0
  RIT1 WILD-TYPE 77 34  4  2
D241V12, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIT1 MUTATED       0                         0     4
  RIT1 WILD-TYPE     6                         5   110
D241V14, multiclass
                           clus
vv                          RIT1 MUTATED RIT1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V15, binary
                cls
clus              0  1
  RIT1 MUTATED    0  3
  RIT1 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    3
  RIT1 WILD-TYPE    5   88
                        clus
vv                       RIT1 MUTATED RIT1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(242) Variable = FAM47C MUTATION ANALYSIS
D242V1, survival
                  sevent
clus2               0  1
  FAM47C MUTATED   12  8
  FAM47C WILD-TYPE 51 54
  FAM47C MUTATED FAM47C WILD-TYPE 
              20              105 
  FAM47C MUTATED FAM47C WILD-TYPE 
               8               54 
$`FAM47C MUTATED`
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-2J-AAB9 TCGA-2J-AABH TCGA-2L-AAQM TCGA-3A-A9IH 
       15.12        12.92        20.61        42.31        45.47        33.57 
TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAQ3 TCGA-HZ-A8P1 TCGA-IB-8126 TCGA-IB-A5SO 
       12.33        37.15         1.02         0.23        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-XD-AAUG 
        7.20        21.90         8.05        12.46        13.68        13.81 
TCGA-XN-A8T3 TCGA-YY-A8LH 
       31.27        66.28 

$`FAM47C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       22.72        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 
        4.70        22.49         3.39        12.95         9.60        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
       20.84         7.36        24.26        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26        10.85        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG 
       19.82        36.69        41.33        15.85        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
        6.02        11.11         7.40        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       16.80         0.39        18.67        12.99        12.03        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76        15.35 

  FAM47C MUTATED FAM47C WILD-TYPE 
            0.23             0.26 
  FAM47C MUTATED FAM47C WILD-TYPE 
           66.28            90.12 
  FAM47C MUTATED FAM47C WILD-TYPE 
          14.465           15.350 
[1] "0.2 - 66.3 (14.5)" "0.3 - 90.1 (15.3)"
[1] "hr=" "1.4"
D242V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM47C MUTATED         0        1        3         2        13         1
  FAM47C WILD-TYPE       1        2        9        17        69         3
                  vv
clus               STAGE IV
  FAM47C MUTATED          1
  FAM47C WILD-TYPE        2
D242V3, multiclass
           clus
vv          FAM47C MUTATED FAM47C WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               3                9
  STAGE IIA              2               17
  STAGE IIB             13               69
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  FAM47C MUTATED    1  3    17
  FAM47C WILD-TYPE  4 14    85
D242V4, multiclass
       clus
vv      FAM47C MUTATED FAM47C WILD-TYPE
  T1                 1                4
  T2                 3               14
  T3+T4             17               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V5, binary
                  cls
clus                0  1
  FAM47C MUTATED    6 15
  FAM47C WILD-TYPE 29 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      6   15
  FAM47C WILD-TYPE   29   74
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0              6               29
  1             15               74
[1] 2 2
[1] FALSE
D242V6, binary
                  cls
clus                0  1
  FAM47C MUTATED   10  1
  FAM47C WILD-TYPE 47  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     10    1
  FAM47C WILD-TYPE   47    2
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0             10               47
  1              1                2
[1] 2 2
[1] FALSE
D242V7, binary
                  cls
clus                0  1
  FAM47C MUTATED   11 10
  FAM47C WILD-TYPE 40 65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     11   10
  FAM47C WILD-TYPE   40   65
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE             11               40
  MALE               10               65
[1] 2 2
[1] FALSE
D242V8, binary
                  cls
clus                0  1
  FAM47C MUTATED   15  4
  FAM47C WILD-TYPE 73 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED     15    4
  FAM47C WILD-TYPE   73   26
     clus
vv    FAM47C MUTATED FAM47C WILD-TYPE
  NO              15               73
  YES              4               26
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM47C MUTATED                                    19
  FAM47C WILD-TYPE                                  86
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM47C MUTATED                                       2
  FAM47C WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM47C MUTATED                                                  0
  FAM47C WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM47C MUTATED                                     0
  FAM47C WILD-TYPE                                   1
D242V9, multiclass
                                                  clus
vv                                                 FAM47C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 FAM47C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            86
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V10, continuous
D242V11, continuous
                  vv
clus               R0 R1 R2 RX
  FAM47C MUTATED   16  5  0  0
  FAM47C WILD-TYPE 64 30  4  2
D242V12, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  R0             16               64
  R1              5               30
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       0                         2    19
  FAM47C WILD-TYPE     6                         3    95
D242V14, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                 19               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V15, binary
                  cls
clus                0  1
  FAM47C MUTATED    1 16
  FAM47C WILD-TYPE  4 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1   16
  FAM47C WILD-TYPE    4   75
                        clus
vv                       FAM47C MUTATED FAM47C WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO             16               75
[1] 2 2
[1] FALSE

Clustering(243) Variable = SEC62 MUTATION ANALYSIS
D243V1, survival
                 sevent
clus2              0  1
  SEC62 MUTATED    3  1
  SEC62 WILD-TYPE 60 61
  SEC62 MUTATED SEC62 WILD-TYPE 
              4             121 
  SEC62 MUTATED SEC62 WILD-TYPE 
              1              61 
$`SEC62 MUTATED`
TCGA-LB-A7SX TCGA-HZ-A77P TCGA-IB-A6UF TCGA-RB-AA9M 
       12.92        10.85        21.90         9.40 

$`SEC62 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SEC62 MUTATED SEC62 WILD-TYPE 
           9.40            0.23 
  SEC62 MUTATED SEC62 WILD-TYPE 
          21.90           90.12 
  SEC62 MUTATED SEC62 WILD-TYPE 
         11.885          15.320 
[1] "9.4 - 21.9 (11.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D243V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SEC62 MUTATED         0        0        0         0         5         0
  SEC62 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  SEC62 MUTATED          0
  SEC62 WILD-TYPE        3
D243V3, multiclass
           clus
vv          SEC62 MUTATED SEC62 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SEC62 MUTATED    1  0     4
  SEC62 WILD-TYPE  4 17    98
D243V4, multiclass
       clus
vv      SEC62 MUTATED SEC62 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V5, binary
                 cls
clus               0  1
  SEC62 MUTATED    0  5
  SEC62 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC62 MUTATED      0    5
  SEC62 WILD-TYPE   35   84
   clus
vv  SEC62 MUTATED SEC62 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D243V6, binary
                 cls
clus               0  1
  SEC62 MUTATED    1  0
  SEC62 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC62 MUTATED      1    0
  SEC62 WILD-TYPE   56    3
   clus
vv  SEC62 MUTATED SEC62 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D243V7, binary
                 cls
clus               0  1
  SEC62 MUTATED    1  4
  SEC62 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC62 MUTATED      1    4
  SEC62 WILD-TYPE   50   71
        clus
vv       SEC62 MUTATED SEC62 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D243V8, binary
                 cls
clus               0  1
  SEC62 MUTATED    3  1
  SEC62 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC62 MUTATED      3    1
  SEC62 WILD-TYPE   85   29
     clus
vv    SEC62 MUTATED SEC62 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEC62 MUTATED                                     4
  SEC62 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEC62 MUTATED                                       1
  SEC62 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEC62 MUTATED                                                  0
  SEC62 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SEC62 MUTATED                                     0
  SEC62 WILD-TYPE                                   1
D243V9, multiclass
                                                  clus
vv                                                 SEC62 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SEC62 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V10, continuous
D243V11, continuous
                 vv
clus              R0 R1 R2 RX
  SEC62 MUTATED    3  2  0  0
  SEC62 WILD-TYPE 77 33  4  2
D243V12, multiclass
    clus
vv   SEC62 MUTATED SEC62 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEC62 MUTATED       0                         1     4
  SEC62 WILD-TYPE     6                         4   110
D243V14, multiclass
                           clus
vv                          SEC62 MUTATED SEC62 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V15, binary
                 cls
clus               0  1
  SEC62 MUTATED    0  5
  SEC62 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC62 MUTATED      0    5
  SEC62 WILD-TYPE    5   86
                        clus
vv                       SEC62 MUTATED SEC62 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(244) Variable = CDC27 MUTATION ANALYSIS
D244V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    5  1
  CDC27 WILD-TYPE 58 61
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             119 
  CDC27 MUTATED CDC27 WILD-TYPE 
              1              61 
$`CDC27 MUTATED`
TCGA-2J-AABO TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IX TCGA-IB-AAUP TCGA-LB-A8F3 
       14.47        43.50        20.84        34.09        14.17        12.46 

$`CDC27 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       12.95         9.60        45.47         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        36.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28         7.56        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CDC27 MUTATED CDC27 WILD-TYPE 
          12.46            0.23 
  CDC27 MUTATED CDC27 WILD-TYPE 
          43.50           90.12 
  CDC27 MUTATED CDC27 WILD-TYPE 
         17.655          15.220 
[1] "12.5 - 43.5 (17.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3.9"
D244V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDC27 MUTATED         0        1        0         2         3         0
  CDC27 WILD-TYPE       1        2       12        17        79         4
                 vv
clus              STAGE IV
  CDC27 MUTATED          0
  CDC27 WILD-TYPE        3
D244V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CDC27 MUTATED    1  0     5
  CDC27 WILD-TYPE  4 17    97
D244V4, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V5, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  3
  CDC27 WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    3
  CDC27 WILD-TYPE   32   86
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D244V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  0
  CDC27 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    0
  CDC27 WILD-TYPE   55    3
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D244V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    1  5
  CDC27 WILD-TYPE 50 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    5
  CDC27 WILD-TYPE   50   70
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             1              50
  MALE               5              70
[1] 2 2
[1] FALSE
D244V8, binary
                 cls
clus               0  1
  CDC27 MUTATED    1  5
  CDC27 WILD-TYPE 87 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    5
  CDC27 WILD-TYPE   87   25
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              1              87
  YES             5              25
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC27 MUTATED                                     6
  CDC27 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC27 MUTATED                                       0
  CDC27 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC27 MUTATED                                                  0
  CDC27 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDC27 MUTATED                                     0
  CDC27 WILD-TYPE                                   1
D244V9, multiclass
                                                  clus
vv                                                 CDC27 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CDC27 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V10, continuous
D244V11, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-FB-A5VM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CDC27 MUTATED    5  1  0  0
  CDC27 WILD-TYPE 75 34  4  2
D244V12, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         2     4
  CDC27 WILD-TYPE     6                         3   110
D244V14, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V15, binary
                 cls
clus               0  1
  CDC27 MUTATED    0  5
  CDC27 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    5
  CDC27 WILD-TYPE    5   86
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(245) Variable = PLXNA3 MUTATION ANALYSIS
D245V1, survival
                  sevent
clus2               0  1
  PLXNA3 MUTATED    2  5
  PLXNA3 WILD-TYPE 61 57
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               7              118 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               5               57 
$`PLXNA3 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABK TCGA-F2-A7TX TCGA-FB-AAPP TCGA-FZ-5919 TCGA-IB-7651 
       20.61        15.91         3.12        15.95        24.36        19.82 
TCGA-IB-AAUM 
        0.26 

$`PLXNA3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        12.33        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 
       23.54        15.55         4.04         5.03         1.02         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22        15.88         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
            0.26             0.23 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
           24.36            90.12 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
          15.950           15.155 
[1] "0.3 - 24.4 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D245V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PLXNA3 MUTATED         0        0        0         0         7         0
  PLXNA3 WILD-TYPE       1        3       12        19        75         4
                  vv
clus               STAGE IV
  PLXNA3 MUTATED          0
  PLXNA3 WILD-TYPE        3
D245V3, multiclass
           clus
vv          PLXNA3 MUTATED PLXNA3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              7               75
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PLXNA3 MUTATED    0  1     6
  PLXNA3 WILD-TYPE  5 16    96
D245V4, multiclass
       clus
vv      PLXNA3 MUTATED PLXNA3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V5, binary
                  cls
clus                0  1
  PLXNA3 MUTATED    0  7
  PLXNA3 WILD-TYPE 35 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      0    7
  PLXNA3 WILD-TYPE   35   82
   clus
vv  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  0              0               35
  1              7               82
[1] 2 2
[1] FALSE
D245V6, binary
                  cls
clus                0  1
  PLXNA3 MUTATED    5  0
  PLXNA3 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      5    0
  PLXNA3 WILD-TYPE   52    3
   clus
vv  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D245V7, binary
                  cls
clus                0  1
  PLXNA3 MUTATED    3  4
  PLXNA3 WILD-TYPE 48 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      3    4
  PLXNA3 WILD-TYPE   48   71
        clus
vv       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  FEMALE              3               48
  MALE                4               71
[1] 2 2
[1] FALSE
D245V8, binary
                  cls
clus                0  1
  PLXNA3 MUTATED    4  3
  PLXNA3 WILD-TYPE 84 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      4    3
  PLXNA3 WILD-TYPE   84   27
     clus
vv    PLXNA3 MUTATED PLXNA3 WILD-TYPE
  NO               4               84
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLXNA3 MUTATED                                     7
  PLXNA3 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLXNA3 MUTATED                                       0
  PLXNA3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLXNA3 MUTATED                                                  0
  PLXNA3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PLXNA3 MUTATED                                     0
  PLXNA3 WILD-TYPE                                   1
D245V9, multiclass
                                                  clus
vv                                                 PLXNA3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PLXNA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V10, continuous
[1] "Remove cluster labels:" "PLXNA3 MUTATED"        
clus
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
D245V11, continuous
[1] "Remove cluster labels:" "PLXNA3 MUTATED"        
clus
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" "PLXNA3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PLXNA3 MUTATED    4  2  0  0
  PLXNA3 WILD-TYPE 76 33  4  2
D245V12, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  R0              4               76
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLXNA3 MUTATED       0                         0     7
  PLXNA3 WILD-TYPE     6                         5   107
D245V14, multiclass
                           clus
vv                          PLXNA3 MUTATED PLXNA3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V15, binary
                  cls
clus                0  1
  PLXNA3 MUTATED    0  4
  PLXNA3 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED      0    4
  PLXNA3 WILD-TYPE    5   87
                        clus
vv                       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(246) Variable = ACCN2 MUTATION ANALYSIS
D246V1, survival
                 sevent
clus2              0  1
  ACCN2 MUTATED    2  4
  ACCN2 WILD-TYPE 61 58
  ACCN2 MUTATED ACCN2 WILD-TYPE 
              6             119 
  ACCN2 MUTATED ACCN2 WILD-TYPE 
              4              58 
$`ACCN2 MUTATED`
TCGA-2L-AAQA TCGA-FZ-5923 TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-A5ST TCGA-US-A77G 
        4.70        20.35         0.23        19.82        20.88         0.39 

$`ACCN2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  ACCN2 MUTATED ACCN2 WILD-TYPE 
           0.23            0.26 
  ACCN2 MUTATED ACCN2 WILD-TYPE 
          20.88           90.12 
  ACCN2 MUTATED ACCN2 WILD-TYPE 
          12.26           15.22 
[1] "0.2 - 20.9 (12.3)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.9"
D246V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ACCN2 MUTATED         0        0        1         0         4         0
  ACCN2 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  ACCN2 MUTATED          1
  ACCN2 WILD-TYPE        2
D246V3, multiclass
           clus
vv          ACCN2 MUTATED ACCN2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ACCN2 MUTATED    0  1     5
  ACCN2 WILD-TYPE  5 16    97
D246V4, multiclass
       clus
vv      ACCN2 MUTATED ACCN2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V5, binary
                 cls
clus               0  1
  ACCN2 MUTATED    1  5
  ACCN2 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN2 MUTATED      1    5
  ACCN2 WILD-TYPE   34   84
   clus
vv  ACCN2 MUTATED ACCN2 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D246V6, binary
                 cls
clus               0  1
  ACCN2 MUTATED    2  1
  ACCN2 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN2 MUTATED      2    1
  ACCN2 WILD-TYPE   55    2
   clus
vv  ACCN2 MUTATED ACCN2 WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D246V7, binary
                 cls
clus               0  1
  ACCN2 MUTATED    2  4
  ACCN2 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN2 MUTATED      2    4
  ACCN2 WILD-TYPE   49   71
        clus
vv       ACCN2 MUTATED ACCN2 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D246V8, binary
                 cls
clus               0  1
  ACCN2 MUTATED    5  0
  ACCN2 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN2 MUTATED      5    0
  ACCN2 WILD-TYPE   83   30
     clus
vv    ACCN2 MUTATED ACCN2 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACCN2 MUTATED                                     6
  ACCN2 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACCN2 MUTATED                                       0
  ACCN2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACCN2 MUTATED                                                  0
  ACCN2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ACCN2 MUTATED                                     0
  ACCN2 WILD-TYPE                                   1
D246V9, multiclass
                                                  clus
vv                                                 ACCN2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ACCN2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V10, continuous
D246V11, continuous
[1] "Remove cluster labels:" "ACCN2 MUTATED"         
clus
  ACCN2 MUTATED ACCN2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-IB-7885      TCGA-IB-8126 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" "ACCN2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ACCN2 MUTATED    5  1  0  0
  ACCN2 WILD-TYPE 75 34  4  2
D246V12, multiclass
    clus
vv   ACCN2 MUTATED ACCN2 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACCN2 MUTATED       0                         0     6
  ACCN2 WILD-TYPE     6                         5   108
D246V14, multiclass
                           clus
vv                          ACCN2 MUTATED ACCN2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V15, binary
                 cls
clus               0  1
  ACCN2 MUTATED    0  5
  ACCN2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN2 MUTATED      0    5
  ACCN2 WILD-TYPE    5   86
                        clus
vv                       ACCN2 MUTATED ACCN2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(247) Variable = RGS22 MUTATION ANALYSIS
D247V1, survival
                 sevent
clus2              0  1
  RGS22 MUTATED    3  2
  RGS22 WILD-TYPE 60 60
  RGS22 MUTATED RGS22 WILD-TYPE 
              5             120 
  RGS22 MUTATED RGS22 WILD-TYPE 
              2              60 
$`RGS22 MUTATED`
TCGA-2J-AABP TCGA-F2-7273 TCGA-FB-AAQ2 TCGA-H8-A6C1 TCGA-YB-A89D 
       15.22        19.46         5.03        22.06        11.51 

$`RGS22 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         4.04         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  RGS22 MUTATED RGS22 WILD-TYPE 
           5.03            0.23 
  RGS22 MUTATED RGS22 WILD-TYPE 
          22.06           90.12 
  RGS22 MUTATED RGS22 WILD-TYPE 
         15.220          15.255 
[1] "5.0 - 22.1 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D247V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RGS22 MUTATED         0        0        0         1         4         0
  RGS22 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  RGS22 MUTATED          0
  RGS22 WILD-TYPE        3
D247V3, multiclass
           clus
vv          RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RGS22 MUTATED    0  0     5
  RGS22 WILD-TYPE  5 17    97
D247V4, multiclass
       clus
vv      RGS22 MUTATED RGS22 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V5, binary
                 cls
clus               0  1
  RGS22 MUTATED    1  4
  RGS22 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      1    4
  RGS22 WILD-TYPE   34   85
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D247V6, binary
                 cls
clus               0  1
  RGS22 MUTATED    2  0
  RGS22 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      2    0
  RGS22 WILD-TYPE   55    3
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D247V7, binary
                 cls
clus               0  1
  RGS22 MUTATED    2  3
  RGS22 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      2    3
  RGS22 WILD-TYPE   49   72
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D247V8, binary
                 cls
clus               0  1
  RGS22 MUTATED    3  2
  RGS22 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      3    2
  RGS22 WILD-TYPE   85   28
     clus
vv    RGS22 MUTATED RGS22 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RGS22 MUTATED                                     3
  RGS22 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RGS22 MUTATED                                       1
  RGS22 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RGS22 MUTATED                                                  0
  RGS22 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RGS22 MUTATED                                     1
  RGS22 WILD-TYPE                                   0
D247V9, multiclass
                                                  clus
vv                                                 RGS22 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 RGS22 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V10, continuous
[1] "Remove cluster labels:" "RGS22 MUTATED"         
clus
  RGS22 MUTATED RGS22 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
D247V11, continuous
[1] "Remove cluster labels:" "RGS22 MUTATED"         
clus
  RGS22 MUTATED RGS22 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" "RGS22 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RGS22 MUTATED    3  2  0  0
  RGS22 WILD-TYPE 77 33  4  2
D247V12, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGS22 MUTATED       0                         1     4
  RGS22 WILD-TYPE     6                         4   110
D247V14, multiclass
                           clus
vv                          RGS22 MUTATED RGS22 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V15, binary
                 cls
clus               0  1
  RGS22 MUTATED    0  4
  RGS22 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      0    4
  RGS22 WILD-TYPE    5   87
                        clus
vv                       RGS22 MUTATED RGS22 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(248) Variable = FRG1 MUTATION ANALYSIS
D248V1, survival
                sevent
clus2             0  1
  FRG1 MUTATED    3  4
  FRG1 WILD-TYPE 60 58
  FRG1 MUTATED FRG1 WILD-TYPE 
             7            118 
  FRG1 MUTATED FRG1 WILD-TYPE 
             4             58 
$`FRG1 MUTATED`
TCGA-S4-A8RO TCGA-3A-A9I7 TCGA-3A-A9IC TCGA-3A-A9IZ TCGA-FB-AAQ3 TCGA-HZ-A77P 
       17.26        43.50        24.26        10.13         1.02        10.85 
TCGA-IB-A5SO 
       12.00 

$`FRG1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
       12.95         9.60        45.47        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         5.03        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
       10.13         5.26         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  FRG1 MUTATED FRG1 WILD-TYPE 
          1.02           0.23 
  FRG1 MUTATED FRG1 WILD-TYPE 
         43.50          90.12 
  FRG1 MUTATED FRG1 WILD-TYPE 
         12.00          15.27 
[1] "1.0 - 43.5 (12.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D248V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FRG1 MUTATED         0        0        0         0         7         0
  FRG1 WILD-TYPE       1        3       12        19        75         4
                vv
clus             STAGE IV
  FRG1 MUTATED          0
  FRG1 WILD-TYPE        3
D248V3, multiclass
           clus
vv          FRG1 MUTATED FRG1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  FRG1 MUTATED    0  0     7
  FRG1 WILD-TYPE  5 17    95
D248V4, multiclass
       clus
vv      FRG1 MUTATED FRG1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V5, binary
                cls
clus              0  1
  FRG1 MUTATED    0  7
  FRG1 WILD-TYPE 35 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      0    7
  FRG1 WILD-TYPE   35   82
   clus
vv  FRG1 MUTATED FRG1 WILD-TYPE
  0            0             35
  1            7             82
[1] 2 2
[1] FALSE
D248V6, binary
                cls
clus              0  1
  FRG1 MUTATED    1  0
  FRG1 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      1    0
  FRG1 WILD-TYPE   56    3
   clus
vv  FRG1 MUTATED FRG1 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D248V7, binary
                cls
clus              0  1
  FRG1 MUTATED    3  4
  FRG1 WILD-TYPE 48 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      3    4
  FRG1 WILD-TYPE   48   71
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  FEMALE            3             48
  MALE              4             71
[1] 2 2
[1] FALSE
D248V8, binary
                cls
clus              0  1
  FRG1 MUTATED    4  3
  FRG1 WILD-TYPE 84 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      4    3
  FRG1 WILD-TYPE   84   27
     clus
vv    FRG1 MUTATED FRG1 WILD-TYPE
  NO             4             84
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FRG1 MUTATED                                     6
  FRG1 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FRG1 MUTATED                                       1
  FRG1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FRG1 MUTATED                                                  0
  FRG1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  FRG1 MUTATED                                     0
  FRG1 WILD-TYPE                                   1
D248V9, multiclass
                                                  clus
vv                                                 FRG1 MUTATED FRG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V10, continuous
D248V11, continuous
                vv
clus             R0 R1 R2 RX
  FRG1 MUTATED    5  2  0  0
  FRG1 WILD-TYPE 75 33  4  2
D248V12, multiclass
    clus
vv   FRG1 MUTATED FRG1 WILD-TYPE
  R0            5             75
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FRG1 MUTATED       0                         1     6
  FRG1 WILD-TYPE     6                         4   108
D248V14, multiclass
                           clus
vv                          FRG1 MUTATED FRG1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V15, binary
                cls
clus              0  1
  FRG1 MUTATED    1  5
  FRG1 WILD-TYPE  4 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      1    5
  FRG1 WILD-TYPE    4   86
                        clus
vv                       FRG1 MUTATED FRG1 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(249) Variable = CCDC88A MUTATION ANALYSIS
D249V1, survival
                   sevent
clus2                0  1
  CCDC88A MUTATED    5  1
  CCDC88A WILD-TYPE 58 61
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6               119 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                1                61 
$`CCDC88A MUTATED`
TCGA-2J-AABO TCGA-3A-A9IB TCGA-HV-A7OL TCGA-IB-7885 TCGA-IB-AAUU TCGA-YB-A89D 
       14.47         7.36         8.28        41.33         8.05        11.51 

$`CCDC88A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
             7.36              0.23 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            41.33             90.12 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            9.895            15.350 
[1] "7.4 - 41.3 (9.9)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.3"
D249V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC88A MUTATED         0        0        0         1         5         0
  CCDC88A WILD-TYPE       1        3       12        18        77         4
                   vv
clus                STAGE IV
  CCDC88A MUTATED          0
  CCDC88A WILD-TYPE        3
D249V3, multiclass
           clus
vv          CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC88A MUTATED    0  0     6
  CCDC88A WILD-TYPE  5 17    96
D249V4, multiclass
       clus
vv      CCDC88A MUTATED CCDC88A WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V5, binary
                   cls
clus                 0  1
  CCDC88A MUTATED    1  5
  CCDC88A WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      1    5
  CCDC88A WILD-TYPE   34   84
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D249V6, binary
                   cls
clus                 0  1
  CCDC88A MUTATED    3  0
  CCDC88A WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      3    0
  CCDC88A WILD-TYPE   54    3
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D249V7, binary
                   cls
clus                 0  1
  CCDC88A MUTATED    2  4
  CCDC88A WILD-TYPE 49 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      2    4
  CCDC88A WILD-TYPE   49   71
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE               2                49
  MALE                 4                71
[1] 2 2
[1] FALSE
D249V8, binary
                   cls
clus                 0  1
  CCDC88A MUTATED    4  2
  CCDC88A WILD-TYPE 84 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      4    2
  CCDC88A WILD-TYPE   84   28
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO                4                84
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC88A MUTATED                                     6
  CCDC88A WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC88A MUTATED                                       0
  CCDC88A WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC88A MUTATED                                                  0
  CCDC88A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC88A MUTATED                                     0
  CCDC88A WILD-TYPE                                   1
D249V9, multiclass
                                                  clus
vv                                                 CCDC88A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC88A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V10, continuous
D249V11, continuous
                   vv
clus                R0 R1 R2 RX
  CCDC88A MUTATED    5  0  1  0
  CCDC88A WILD-TYPE 75 35  3  2
D249V12, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0               5                75
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC88A MUTATED       1                         0     5
  CCDC88A WILD-TYPE     5                         5   109
D249V14, multiclass
                           clus
vv                          CCDC88A MUTATED CCDC88A WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V15, binary
                   cls
clus                 0  1
  CCDC88A MUTATED    0  4
  CCDC88A WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED      0    4
  CCDC88A WILD-TYPE    5   87
                        clus
vv                       CCDC88A MUTATED CCDC88A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(250) Variable = CR1L MUTATION ANALYSIS
D250V1, survival
                sevent
clus2             0  1
  CR1L MUTATED    2  3
  CR1L WILD-TYPE 61 59
  CR1L MUTATED CR1L WILD-TYPE 
             5            120 
  CR1L MUTATED CR1L WILD-TYPE 
             3             59 
$`CR1L MUTATED`
TCGA-HV-A7OP TCGA-HZ-8637 TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-A5SP 
       32.15        17.00        10.13        19.82        15.85 

$`CR1L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       17.49        31.86        20.19         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
       19.82        36.69        41.33        15.19        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CR1L MUTATED CR1L WILD-TYPE 
         10.13           0.23 
  CR1L MUTATED CR1L WILD-TYPE 
         32.15          90.12 
  CR1L MUTATED CR1L WILD-TYPE 
        17.000         15.155 
[1] "10.1 - 32.1 (17.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D250V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CR1L MUTATED         0        0        0         1         4         0
  CR1L WILD-TYPE       1        3       12        18        78         4
                vv
clus             STAGE IV
  CR1L MUTATED          0
  CR1L WILD-TYPE        3
D250V3, multiclass
           clus
vv          CR1L MUTATED CR1L WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CR1L MUTATED    0  0     5
  CR1L WILD-TYPE  5 17    97
D250V4, multiclass
       clus
vv      CR1L MUTATED CR1L WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V5, binary
                cls
clus              0  1
  CR1L MUTATED    1  4
  CR1L WILD-TYPE 34 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      1    4
  CR1L WILD-TYPE   34   85
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0            1             34
  1            4             85
[1] 2 2
[1] FALSE
D250V6, binary
                cls
clus              0  1
  CR1L MUTATED    3  0
  CR1L WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      3    0
  CR1L WILD-TYPE   54    3
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D250V7, binary
                cls
clus              0  1
  CR1L MUTATED    2  3
  CR1L WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      2    3
  CR1L WILD-TYPE   49   72
        clus
vv       CR1L MUTATED CR1L WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D250V8, binary
                cls
clus              0  1
  CR1L MUTATED    2  3
  CR1L WILD-TYPE 86 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      2    3
  CR1L WILD-TYPE   86   27
     clus
vv    CR1L MUTATED CR1L WILD-TYPE
  NO             2             86
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CR1L MUTATED                                     4
  CR1L WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CR1L MUTATED                                       1
  CR1L WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CR1L MUTATED                                                  0
  CR1L WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CR1L MUTATED                                     0
  CR1L WILD-TYPE                                   1
D250V9, multiclass
                                                  clus
vv                                                 CR1L MUTATED CR1L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V10, continuous
[1] "Remove cluster labels:" "CR1L MUTATED"          
clus
  CR1L MUTATED CR1L WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" 
D250V11, continuous
[1] "Remove cluster labels:" "CR1L MUTATED"          
clus
  CR1L MUTATED CR1L WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" "CR1L WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CR1L MUTATED    3  2  0  0
  CR1L WILD-TYPE 77 33  4  2
D250V12, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  R0            3             77
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR1L MUTATED       1                         0     4
  CR1L WILD-TYPE     5                         5   110
D250V14, multiclass
                           clus
vv                          CR1L MUTATED CR1L WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V15, binary
                cls
clus              0  1
  CR1L MUTATED    1  2
  CR1L WILD-TYPE  4 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      1    2
  CR1L WILD-TYPE    4   89
                        clus
vv                       CR1L MUTATED CR1L WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(251) Variable = HDLBP MUTATION ANALYSIS
D251V1, survival
                 sevent
clus2              0  1
  HDLBP MUTATED    4  4
  HDLBP WILD-TYPE 59 58
  HDLBP MUTATED HDLBP WILD-TYPE 
              8             117 
  HDLBP MUTATED HDLBP WILD-TYPE 
              4              58 
$`HDLBP MUTATED`
TCGA-F2-A7TX TCGA-FB-AAPU TCGA-HZ-A77O TCGA-IB-7651 TCGA-XN-A8T3 TCGA-YB-A89D 
        3.12        12.53         5.26        19.82        31.27        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

$`HDLBP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-Z5-AAPL 
       12.03        23.67        15.35 

  HDLBP MUTATED HDLBP WILD-TYPE 
           3.12            0.23 
  HDLBP MUTATED HDLBP WILD-TYPE 
          66.28           90.12 
  HDLBP MUTATED HDLBP WILD-TYPE 
         12.645          15.320 
[1] "3.1 - 66.3 (12.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D251V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HDLBP MUTATED         0        0        1         1         5         1
  HDLBP WILD-TYPE       1        3       11        18        77         3
                 vv
clus              STAGE IV
  HDLBP MUTATED          0
  HDLBP WILD-TYPE        3
D251V3, multiclass
           clus
vv          HDLBP MUTATED HDLBP WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HDLBP MUTATED    0  2     6
  HDLBP WILD-TYPE  5 15    96
D251V4, multiclass
       clus
vv      HDLBP MUTATED HDLBP WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V5, binary
                 cls
clus               0  1
  HDLBP MUTATED    2  6
  HDLBP WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      2    6
  HDLBP WILD-TYPE   33   83
   clus
vv  HDLBP MUTATED HDLBP WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D251V6, binary
                 cls
clus               0  1
  HDLBP MUTATED    3  0
  HDLBP WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      3    0
  HDLBP WILD-TYPE   54    3
   clus
vv  HDLBP MUTATED HDLBP WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D251V7, binary
                 cls
clus               0  1
  HDLBP MUTATED    5  3
  HDLBP WILD-TYPE 46 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      5    3
  HDLBP WILD-TYPE   46   72
        clus
vv       HDLBP MUTATED HDLBP WILD-TYPE
  FEMALE             5              46
  MALE               3              72
[1] 2 2
[1] FALSE
D251V8, binary
                 cls
clus               0  1
  HDLBP MUTATED    4  4
  HDLBP WILD-TYPE 84 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      4    4
  HDLBP WILD-TYPE   84   26
     clus
vv    HDLBP MUTATED HDLBP WILD-TYPE
  NO              4              84
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HDLBP MUTATED                                     7
  HDLBP WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HDLBP MUTATED                                       0
  HDLBP WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HDLBP MUTATED                                                  0
  HDLBP WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HDLBP MUTATED                                     0
  HDLBP WILD-TYPE                                   1
D251V9, multiclass
                                                  clus
vv                                                 HDLBP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HDLBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V10, continuous
[1] "Remove cluster labels:" "HDLBP MUTATED"         
clus
  HDLBP MUTATED HDLBP WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-XN-A8T5 
"HDLBP WILD-TYPE" 
D251V11, continuous
[1] "Remove cluster labels:" "HDLBP MUTATED"         
clus
  HDLBP MUTATED HDLBP WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"HDLBP WILD-TYPE" "HDLBP WILD-TYPE" "HDLBP WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HDLBP MUTATED    4  3  0  0
  HDLBP WILD-TYPE 76 32  4  2
D251V12, multiclass
    clus
vv   HDLBP MUTATED HDLBP WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HDLBP MUTATED       1                         0     7
  HDLBP WILD-TYPE     5                         5   107
D251V14, multiclass
                           clus
vv                          HDLBP MUTATED HDLBP WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V15, binary
                 cls
clus               0  1
  HDLBP MUTATED    1  6
  HDLBP WILD-TYPE  4 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDLBP MUTATED      1    6
  HDLBP WILD-TYPE    4   85
                        clus
vv                       HDLBP MUTATED HDLBP WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(252) Variable = KBTBD4 MUTATION ANALYSIS
D252V1, survival
                  sevent
clus2               0  1
  KBTBD4 MUTATED    3  1
  KBTBD4 WILD-TYPE 60 61
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               4              121 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               1               61 
$`KBTBD4 MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB1 TCGA-HV-A7OL TCGA-HZ-A77P 
       17.26         2.17         8.28        10.85 

$`KBTBD4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
            2.17             0.23 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
           17.26            90.12 
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
           9.565           15.320 
[1] "2.2 - 17.3 (9.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D252V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KBTBD4 MUTATED         0        0        0         1         3         0
  KBTBD4 WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  KBTBD4 MUTATED          0
  KBTBD4 WILD-TYPE        3
D252V3, multiclass
           clus
vv          KBTBD4 MUTATED KBTBD4 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  KBTBD4 MUTATED    0  0     4
  KBTBD4 WILD-TYPE  5 17    98
D252V4, multiclass
       clus
vv      KBTBD4 MUTATED KBTBD4 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V5, binary
                  cls
clus                0  1
  KBTBD4 MUTATED    1  3
  KBTBD4 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      1    3
  KBTBD4 WILD-TYPE   34   86
   clus
vv  KBTBD4 MUTATED KBTBD4 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D252V6, binary
                  cls
clus                0  1
  KBTBD4 MUTATED    1  0
  KBTBD4 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      1    0
  KBTBD4 WILD-TYPE   56    3
   clus
vv  KBTBD4 MUTATED KBTBD4 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D252V7, binary
                  cls
clus                0  1
  KBTBD4 MUTATED    1  3
  KBTBD4 WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      1    3
  KBTBD4 WILD-TYPE   50   72
        clus
vv       KBTBD4 MUTATED KBTBD4 WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D252V8, binary
                  cls
clus                0  1
  KBTBD4 MUTATED    3  1
  KBTBD4 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      3    1
  KBTBD4 WILD-TYPE   85   29
     clus
vv    KBTBD4 MUTATED KBTBD4 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KBTBD4 MUTATED                                     2
  KBTBD4 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KBTBD4 MUTATED                                       2
  KBTBD4 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KBTBD4 MUTATED                                                  0
  KBTBD4 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  KBTBD4 MUTATED                                     0
  KBTBD4 WILD-TYPE                                   1
D252V9, multiclass
                                                  clus
vv                                                 KBTBD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 KBTBD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V10, continuous
[1] "Remove cluster labels:" "KBTBD4 MUTATED"        
clus
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AABA       TCGA-2J-AABE 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
D252V11, continuous
[1] "Remove cluster labels:" "KBTBD4 MUTATED"        
clus
  KBTBD4 MUTATED KBTBD4 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AABE       TCGA-2J-AABF 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" "KBTBD4 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  KBTBD4 MUTATED    2  1  1  0
  KBTBD4 WILD-TYPE 78 34  3  2
D252V12, multiclass
    clus
vv   KBTBD4 MUTATED KBTBD4 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KBTBD4 MUTATED       1                         0     3
  KBTBD4 WILD-TYPE     5                         5   111
D252V14, multiclass
                           clus
vv                          KBTBD4 MUTATED KBTBD4 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V15, binary
                  cls
clus                0  1
  KBTBD4 MUTATED    0  2
  KBTBD4 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD4 MUTATED      0    2
  KBTBD4 WILD-TYPE    5   89
                        clus
vv                       KBTBD4 MUTATED KBTBD4 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(253) Variable = SBSN MUTATION ANALYSIS
D253V1, survival
                sevent
clus2             0  1
  SBSN MUTATED    2  3
  SBSN WILD-TYPE 61 59
  SBSN MUTATED SBSN WILD-TYPE 
             5            120 
  SBSN MUTATED SBSN WILD-TYPE 
             3             59 
$`SBSN MUTATED`
TCGA-2J-AAB1 TCGA-FB-AAPP TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-RL-AAAS 
        2.17        15.95        19.82        19.82         0.30 

$`SBSN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
        8.78        13.68         3.12        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SBSN MUTATED SBSN WILD-TYPE 
          0.30           0.23 
  SBSN MUTATED SBSN WILD-TYPE 
         19.82          90.12 
  SBSN MUTATED SBSN WILD-TYPE 
        15.950         15.205 
[1] "0.3 - 19.8 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D253V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SBSN MUTATED         0        0        1         0         3         0
  SBSN WILD-TYPE       1        3       11        19        79         4
                vv
clus             STAGE IV
  SBSN MUTATED          1
  SBSN WILD-TYPE        2
D253V3, multiclass
           clus
vv          SBSN MUTATED SBSN WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  SBSN MUTATED    0  1     4
  SBSN WILD-TYPE  5 16    98
D253V4, multiclass
       clus
vv      SBSN MUTATED SBSN WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V5, binary
                cls
clus              0  1
  SBSN MUTATED    2  3
  SBSN WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      2    3
  SBSN WILD-TYPE   33   86
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D253V6, binary
                cls
clus              0  1
  SBSN MUTATED    3  1
  SBSN WILD-TYPE 54  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      3    1
  SBSN WILD-TYPE   54    2
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            3             54
  1            1              2
[1] 2 2
[1] FALSE
D253V7, binary
                cls
clus              0  1
  SBSN MUTATED    2  3
  SBSN WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      2    3
  SBSN WILD-TYPE   49   72
        clus
vv       SBSN MUTATED SBSN WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D253V8, binary
                cls
clus              0  1
  SBSN MUTATED    4  1
  SBSN WILD-TYPE 84 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      4    1
  SBSN WILD-TYPE   84   29
     clus
vv    SBSN MUTATED SBSN WILD-TYPE
  NO             4             84
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SBSN MUTATED                                     3
  SBSN WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SBSN MUTATED                                       2
  SBSN WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SBSN MUTATED                                                  0
  SBSN WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  SBSN MUTATED                                     0
  SBSN WILD-TYPE                                   1
D253V9, multiclass
                                                  clus
vv                                                 SBSN MUTATED SBSN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V10, continuous
[1] "Remove cluster labels:" "SBSN MUTATED"          
clus
  SBSN MUTATED SBSN WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABA     TCGA-2J-AABE 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-YY-A8LH 
"SBSN WILD-TYPE" 
D253V11, continuous
[1] "Remove cluster labels:" "SBSN MUTATED"          
clus
  SBSN MUTATED SBSN WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"SBSN WILD-TYPE" "SBSN WILD-TYPE" "SBSN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  SBSN MUTATED    5  0  0  0
  SBSN WILD-TYPE 75 35  4  2
D253V12, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  R0            5             75
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SBSN MUTATED       0                         0     5
  SBSN WILD-TYPE     6                         5   109
D253V14, multiclass
                           clus
vv                          SBSN MUTATED SBSN WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V15, binary
                cls
clus              0  1
  SBSN MUTATED    0  4
  SBSN WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      0    4
  SBSN WILD-TYPE    5   87
                        clus
vv                       SBSN MUTATED SBSN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(254) Variable = KCTD3 MUTATION ANALYSIS
D254V1, survival
                 sevent
clus2              0  1
  KCTD3 MUTATED    2  2
  KCTD3 WILD-TYPE 61 60
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              4             121 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              2              60 
$`KCTD3 MUTATED`
TCGA-2J-AABO TCGA-FB-AAQ1 TCGA-IB-7651 TCGA-YY-A8LH 
       14.47         4.04        19.82        66.28 

$`KCTD3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
           4.04            0.23 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          66.28           90.12 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         17.145          15.220 
[1] "4.0 - 66.3 (17.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D254V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KCTD3 MUTATED         0        0        0         0         4         0
  KCTD3 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  KCTD3 MUTATED          0
  KCTD3 WILD-TYPE        3
D254V3, multiclass
           clus
vv          KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KCTD3 MUTATED    0  0     4
  KCTD3 WILD-TYPE  5 17    98
D254V4, multiclass
       clus
vv      KCTD3 MUTATED KCTD3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V5, binary
                 cls
clus               0  1
  KCTD3 MUTATED    0  4
  KCTD3 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0    4
  KCTD3 WILD-TYPE   35   85
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D254V6, binary
                 cls
clus               0  1
  KCTD3 MUTATED    2  0
  KCTD3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      2    0
  KCTD3 WILD-TYPE   55    3
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D254V7, binary
                 cls
clus               0  1
  KCTD3 MUTATED    2  2
  KCTD3 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      2    2
  KCTD3 WILD-TYPE   49   73
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D254V8, binary
                 cls
clus               0  1
  KCTD3 MUTATED    2  2
  KCTD3 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      2    2
  KCTD3 WILD-TYPE   86   28
     clus
vv    KCTD3 MUTATED KCTD3 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCTD3 MUTATED                                     4
  KCTD3 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCTD3 MUTATED                                       0
  KCTD3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCTD3 MUTATED                                                  0
  KCTD3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KCTD3 MUTATED                                     0
  KCTD3 WILD-TYPE                                   1
D254V9, multiclass
                                                  clus
vv                                                 KCTD3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KCTD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V10, continuous
D254V11, continuous
                 vv
clus              R0 R1 R2 RX
  KCTD3 MUTATED    3  1  0  0
  KCTD3 WILD-TYPE 77 34  4  2
D254V12, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCTD3 MUTATED       0                         0     4
  KCTD3 WILD-TYPE     6                         5   110
D254V14, multiclass
                           clus
vv                          KCTD3 MUTATED KCTD3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V15, binary
                 cls
clus               0  1
  KCTD3 MUTATED    0  3
  KCTD3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0    3
  KCTD3 WILD-TYPE    5   88
                        clus
vv                       KCTD3 MUTATED KCTD3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(255) Variable = GUCY2F MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2               0  1
  GUCY2F MUTATED    4  3
  GUCY2F WILD-TYPE 59 59
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               7              118 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               3               59 
$`GUCY2F MUTATED`
TCGA-3A-A9IJ TCGA-S4-A8RO TCGA-3A-A9IB TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SQ 
       60.95        17.26         7.36        19.82        41.33         7.20 
TCGA-YY-A8LH 
       66.28 

$`GUCY2F WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST 
       19.82        36.69        15.19        12.00        15.85        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
            7.20             0.23 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
           66.28            90.12 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
          19.820           15.155 
[1] "7.2 - 66.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D255V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GUCY2F MUTATED         0        0        2         0         5         0
  GUCY2F WILD-TYPE       1        3       10        19        77         4
                  vv
clus               STAGE IV
  GUCY2F MUTATED          0
  GUCY2F WILD-TYPE        3
D255V3, multiclass
           clus
vv          GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GUCY2F MUTATED    0  2     5
  GUCY2F WILD-TYPE  5 15    97
D255V4, multiclass
       clus
vv      GUCY2F MUTATED GUCY2F WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V5, binary
                  cls
clus                0  1
  GUCY2F MUTATED    2  5
  GUCY2F WILD-TYPE 33 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      2    5
  GUCY2F WILD-TYPE   33   84
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0              2               33
  1              5               84
[1] 2 2
[1] FALSE
D255V6, binary
                  cls
clus                0  1
  GUCY2F MUTATED    3  0
  GUCY2F WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      3    0
  GUCY2F WILD-TYPE   54    3
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D255V7, binary
                  cls
clus                0  1
  GUCY2F MUTATED    6  1
  GUCY2F WILD-TYPE 45 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      6    1
  GUCY2F WILD-TYPE   45   74
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  FEMALE              6               45
  MALE                1               74
[1] 2 2
[1] FALSE
D255V8, binary
                  cls
clus                0  1
  GUCY2F MUTATED    5  2
  GUCY2F WILD-TYPE 83 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      5    2
  GUCY2F WILD-TYPE   83   28
     clus
vv    GUCY2F MUTATED GUCY2F WILD-TYPE
  NO               5               83
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GUCY2F MUTATED                                     6
  GUCY2F WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GUCY2F MUTATED                                       1
  GUCY2F WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GUCY2F MUTATED                                                  0
  GUCY2F WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GUCY2F MUTATED                                     0
  GUCY2F WILD-TYPE                                   1
D255V9, multiclass
                                                  clus
vv                                                 GUCY2F MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GUCY2F WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V10, continuous
D255V11, continuous
                  vv
clus               R0 R1 R2 RX
  GUCY2F MUTATED    6  1  0  0
  GUCY2F WILD-TYPE 74 34  4  2
D255V12, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUCY2F MUTATED       0                         0     7
  GUCY2F WILD-TYPE     6                         5   107
D255V14, multiclass
                           clus
vv                          GUCY2F MUTATED GUCY2F WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V15, binary
                  cls
clus                0  1
  GUCY2F MUTATED    0  7
  GUCY2F WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      0    7
  GUCY2F WILD-TYPE    5   84
                        clus
vv                       GUCY2F MUTATED GUCY2F WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(256) Variable = PHIP MUTATION ANALYSIS
D256V1, survival
                sevent
clus2             0  1
  PHIP MUTATED    4  3
  PHIP WILD-TYPE 59 59
  PHIP MUTATED PHIP WILD-TYPE 
             7            118 
  PHIP MUTATED PHIP WILD-TYPE 
             3             59 
$`PHIP MUTATED`
TCGA-2J-AABE TCGA-3A-A9IH TCGA-FB-AAPP TCGA-FB-AAQ3 TCGA-IB-7651 TCGA-IB-7885 
       22.22        33.57        15.95         1.02        19.82        41.33 
TCGA-YY-A8LH 
       66.28 

$`PHIP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         5.03        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  PHIP MUTATED PHIP WILD-TYPE 
          1.02           0.23 
  PHIP MUTATED PHIP WILD-TYPE 
         66.28          90.12 
  PHIP MUTATED PHIP WILD-TYPE 
         22.22          15.09 
[1] "1.0 - 66.3 (22.2)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.7"
D256V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHIP MUTATED         0        1        0         1         5         0
  PHIP WILD-TYPE       1        2       12        18        77         4
                vv
clus             STAGE IV
  PHIP MUTATED          0
  PHIP WILD-TYPE        3
D256V3, multiclass
           clus
vv          PHIP MUTATED PHIP WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PHIP MUTATED    1  0     6
  PHIP WILD-TYPE  4 17    96
D256V4, multiclass
       clus
vv      PHIP MUTATED PHIP WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V5, binary
                cls
clus              0  1
  PHIP MUTATED    2  5
  PHIP WILD-TYPE 33 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHIP MUTATED      2    5
  PHIP WILD-TYPE   33   84
   clus
vv  PHIP MUTATED PHIP WILD-TYPE
  0            2             33
  1            5             84
[1] 2 2
[1] FALSE
D256V6, binary
                cls
clus              0  1
  PHIP MUTATED    3  0
  PHIP WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHIP MUTATED      3    0
  PHIP WILD-TYPE   54    3
   clus
vv  PHIP MUTATED PHIP WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D256V7, binary
                cls
clus              0  1
  PHIP MUTATED    5  2
  PHIP WILD-TYPE 46 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHIP MUTATED      5    2
  PHIP WILD-TYPE   46   73
        clus
vv       PHIP MUTATED PHIP WILD-TYPE
  FEMALE            5             46
  MALE              2             73
[1] 2 2
[1] FALSE
D256V8, binary
                cls
clus              0  1
  PHIP MUTATED    4  3
  PHIP WILD-TYPE 84 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHIP MUTATED      4    3
  PHIP WILD-TYPE   84   27
     clus
vv    PHIP MUTATED PHIP WILD-TYPE
  NO             4             84
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHIP MUTATED                                     7
  PHIP WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHIP MUTATED                                       0
  PHIP WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHIP MUTATED                                                  0
  PHIP WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHIP MUTATED                                     0
  PHIP WILD-TYPE                                   1
D256V9, multiclass
                                                  clus
vv                                                 PHIP MUTATED PHIP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V10, continuous
D256V11, continuous
                vv
clus             R0 R1 R2 RX
  PHIP MUTATED    7  0  0  0
  PHIP WILD-TYPE 73 35  4  2
D256V12, multiclass
    clus
vv   PHIP MUTATED PHIP WILD-TYPE
  R0            7             73
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHIP MUTATED       0                         0     7
  PHIP WILD-TYPE     6                         5   107
D256V14, multiclass
                           clus
vv                          PHIP MUTATED PHIP WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V15, binary
                cls
clus              0  1
  PHIP MUTATED    0  6
  PHIP WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHIP MUTATED      0    6
  PHIP WILD-TYPE    5   85
                        clus
vv                       PHIP MUTATED PHIP WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(257) Variable = FOXJ2 MUTATION ANALYSIS
D257V1, survival
                 sevent
clus2              0  1
  FOXJ2 MUTATED    3  2
  FOXJ2 WILD-TYPE 60 60
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              5             120 
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              2              60 
$`FOXJ2 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A7LX TCGA-Q3-AA2A TCGA-RL-AAAS 
       19.82        41.33         8.22         3.12         0.30 

$`FOXJ2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 
        5.26        10.85         0.23        19.82        36.69        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
       10.29         8.78        13.68        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
           0.30            0.23 
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
          41.33           90.12 
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
           8.22           15.27 
[1] "0.3 - 41.3 (8.2)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D257V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FOXJ2 MUTATED         0        0        2         0         3         0
  FOXJ2 WILD-TYPE       1        3       10        19        79         4
                 vv
clus              STAGE IV
  FOXJ2 MUTATED          0
  FOXJ2 WILD-TYPE        3
D257V3, multiclass
           clus
vv          FOXJ2 MUTATED FOXJ2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FOXJ2 MUTATED    0  1     4
  FOXJ2 WILD-TYPE  5 16    98
D257V4, multiclass
       clus
vv      FOXJ2 MUTATED FOXJ2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V5, binary
                 cls
clus               0  1
  FOXJ2 MUTATED    1  4
  FOXJ2 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ2 MUTATED      1    4
  FOXJ2 WILD-TYPE   34   85
   clus
vv  FOXJ2 MUTATED FOXJ2 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D257V6, binary
                 cls
clus               0  1
  FOXJ2 MUTATED    3  0
  FOXJ2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ2 MUTATED      3    0
  FOXJ2 WILD-TYPE   54    3
   clus
vv  FOXJ2 MUTATED FOXJ2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D257V7, binary
                 cls
clus               0  1
  FOXJ2 MUTATED    4  1
  FOXJ2 WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ2 MUTATED      4    1
  FOXJ2 WILD-TYPE   47   74
        clus
vv       FOXJ2 MUTATED FOXJ2 WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D257V8, binary
                 cls
clus               0  1
  FOXJ2 MUTATED    5  0
  FOXJ2 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ2 MUTATED      5    0
  FOXJ2 WILD-TYPE   83   30
     clus
vv    FOXJ2 MUTATED FOXJ2 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FOXJ2 MUTATED                                     5
  FOXJ2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FOXJ2 MUTATED                                       0
  FOXJ2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FOXJ2 MUTATED                                                  0
  FOXJ2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FOXJ2 MUTATED                                     0
  FOXJ2 WILD-TYPE                                   1
D257V9, multiclass
                                                  clus
vv                                                 FOXJ2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FOXJ2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V10, continuous
[1] "Remove cluster labels:" "FOXJ2 MUTATED"         
clus
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-YY-A8LH 
"FOXJ2 WILD-TYPE" 
D257V11, continuous
[1] "Remove cluster labels:" "FOXJ2 MUTATED"         
clus
  FOXJ2 MUTATED FOXJ2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-8126 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" "FOXJ2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  FOXJ2 MUTATED    4  0  0  1
  FOXJ2 WILD-TYPE 76 35  4  1
D257V12, multiclass
    clus
vv   FOXJ2 MUTATED FOXJ2 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXJ2 MUTATED       0                         0     5
  FOXJ2 WILD-TYPE     6                         5   109
D257V14, multiclass
                           clus
vv                          FOXJ2 MUTATED FOXJ2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V15, binary
                 cls
clus               0  1
  FOXJ2 MUTATED    0  5
  FOXJ2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXJ2 MUTATED      0    5
  FOXJ2 WILD-TYPE    5   86
                        clus
vv                       FOXJ2 MUTATED FOXJ2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(258) Variable = KIF3C MUTATION ANALYSIS
D258V1, survival
                 sevent
clus2              0  1
  KIF3C MUTATED    2  2
  KIF3C WILD-TYPE 61 60
  KIF3C MUTATED KIF3C WILD-TYPE 
              4             121 
  KIF3C MUTATED KIF3C WILD-TYPE 
              2              60 
$`KIF3C MUTATED`
TCGA-F2-A8YN TCGA-FB-AAPS TCGA-FZ-5922 TCGA-IB-7651 
       17.00         7.50        36.20        19.82 

$`KIF3C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KIF3C MUTATED KIF3C WILD-TYPE 
           7.50            0.23 
  KIF3C MUTATED KIF3C WILD-TYPE 
          36.20           90.12 
  KIF3C MUTATED KIF3C WILD-TYPE 
          18.41           15.19 
[1] "7.5 - 36.2 (18.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D258V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIF3C MUTATED         0        0        0         2         2         0
  KIF3C WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  KIF3C MUTATED          0
  KIF3C WILD-TYPE        3
D258V3, multiclass
           clus
vv          KIF3C MUTATED KIF3C WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KIF3C MUTATED    0  1     3
  KIF3C WILD-TYPE  5 16    99
D258V4, multiclass
       clus
vv      KIF3C MUTATED KIF3C WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V5, binary
                 cls
clus               0  1
  KIF3C MUTATED    2  2
  KIF3C WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF3C MUTATED      2    2
  KIF3C WILD-TYPE   33   87
   clus
vv  KIF3C MUTATED KIF3C WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D258V6, binary
                 cls
clus               0  1
  KIF3C MUTATED    3  0
  KIF3C WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF3C MUTATED      3    0
  KIF3C WILD-TYPE   54    3
   clus
vv  KIF3C MUTATED KIF3C WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D258V7, binary
                 cls
clus               0  1
  KIF3C MUTATED    2  2
  KIF3C WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF3C MUTATED      2    2
  KIF3C WILD-TYPE   49   73
        clus
vv       KIF3C MUTATED KIF3C WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D258V8, binary
                 cls
clus               0  1
  KIF3C MUTATED    3  1
  KIF3C WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF3C MUTATED      3    1
  KIF3C WILD-TYPE   85   29
     clus
vv    KIF3C MUTATED KIF3C WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIF3C MUTATED                                     4
  KIF3C WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIF3C MUTATED                                       0
  KIF3C WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIF3C MUTATED                                                  0
  KIF3C WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIF3C MUTATED                                     0
  KIF3C WILD-TYPE                                   1
D258V9, multiclass
                                                  clus
vv                                                 KIF3C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KIF3C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V10, continuous
D258V11, continuous
[1] "Remove cluster labels:" "KIF3C MUTATED"         
clus
  KIF3C MUTATED KIF3C WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KIF3C WILD-TYPE" "KIF3C WILD-TYPE" "KIF3C WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KIF3C MUTATED    3  1  0  0
  KIF3C WILD-TYPE 77 34  4  2
D258V12, multiclass
    clus
vv   KIF3C MUTATED KIF3C WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF3C MUTATED       0                         0     4
  KIF3C WILD-TYPE     6                         5   110
D258V14, multiclass
                           clus
vv                          KIF3C MUTATED KIF3C WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V15, binary
                 cls
clus               0  1
  KIF3C MUTATED    0  4
  KIF3C WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF3C MUTATED      0    4
  KIF3C WILD-TYPE    5   87
                        clus
vv                       KIF3C MUTATED KIF3C WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(259) Variable = ZC3H13 MUTATION ANALYSIS
D259V1, survival
                  sevent
clus2               0  1
  ZC3H13 MUTATED    3  6
  ZC3H13 WILD-TYPE 60 56
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               9              116 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               6               56 
$`ZC3H13 MUTATED`
TCGA-US-A77E TCGA-2L-AAQE TCGA-3A-A9IS TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-A6UG 
       14.14        22.49        32.81        71.74        19.82         1.35 
TCGA-LB-A9Q5 TCGA-XN-A8T5 TCGA-YB-A89D 
       10.29        23.67        11.51 

$`ZC3H13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        75.12        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY 
       18.67        13.81        12.99        12.03        31.27        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
            1.35             0.23 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
           71.74            90.12 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
          19.820           15.205 
[1] "1.4 - 71.7 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D259V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZC3H13 MUTATED         0        0        2         1         6         0
  ZC3H13 WILD-TYPE       1        3       10        18        76         4
                  vv
clus               STAGE IV
  ZC3H13 MUTATED          0
  ZC3H13 WILD-TYPE        3
D259V3, multiclass
           clus
vv          ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZC3H13 MUTATED    0  2     7
  ZC3H13 WILD-TYPE  5 15    95
D259V4, multiclass
       clus
vv      ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V5, binary
                  cls
clus                0  1
  ZC3H13 MUTATED    3  6
  ZC3H13 WILD-TYPE 32 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      3    6
  ZC3H13 WILD-TYPE   32   83
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0              3               32
  1              6               83
[1] 2 2
[1] FALSE
D259V6, binary
                  cls
clus                0  1
  ZC3H13 MUTATED    4  0
  ZC3H13 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      4    0
  ZC3H13 WILD-TYPE   53    3
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D259V7, binary
                  cls
clus                0  1
  ZC3H13 MUTATED    3  6
  ZC3H13 WILD-TYPE 48 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      3    6
  ZC3H13 WILD-TYPE   48   69
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE              3               48
  MALE                6               69
[1] 2 2
[1] FALSE
D259V8, binary
                  cls
clus                0  1
  ZC3H13 MUTATED    5  3
  ZC3H13 WILD-TYPE 83 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      5    3
  ZC3H13 WILD-TYPE   83   27
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO               5               83
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZC3H13 MUTATED                                     6
  ZC3H13 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZC3H13 MUTATED                                       3
  ZC3H13 WILD-TYPE                                    15
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZC3H13 MUTATED                                                  0
  ZC3H13 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZC3H13 MUTATED                                     0
  ZC3H13 WILD-TYPE                                   1
D259V9, multiclass
                                                  clus
vv                                                 ZC3H13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZC3H13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V10, continuous
D259V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZC3H13 MUTATED    5  3  0  0
  ZC3H13 WILD-TYPE 75 32  4  2
D259V12, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0              5               75
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H13 MUTATED       0                         0     9
  ZC3H13 WILD-TYPE     6                         5   105
D259V14, multiclass
                           clus
vv                          ZC3H13 MUTATED ZC3H13 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V15, binary
                  cls
clus                0  1
  ZC3H13 MUTATED    2  6
  ZC3H13 WILD-TYPE  3 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED      2    6
  ZC3H13 WILD-TYPE    3   85
                        clus
vv                       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  HISPANIC OR LATINO                  2                3
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(260) Variable = NAGPA MUTATION ANALYSIS
D260V1, survival
                 sevent
clus2              0  1
  NAGPA MUTATED    2  3
  NAGPA WILD-TYPE 61 59
  NAGPA MUTATED NAGPA WILD-TYPE 
              5             120 
  NAGPA MUTATED NAGPA WILD-TYPE 
              3              59 
$`NAGPA MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQI TCGA-FB-AAPS TCGA-HV-A7OL TCGA-IB-7651 
       12.92         3.39         7.50         8.28        19.82 

$`NAGPA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  NAGPA MUTATED NAGPA WILD-TYPE 
           3.39            0.23 
  NAGPA MUTATED NAGPA WILD-TYPE 
          19.82           90.12 
  NAGPA MUTATED NAGPA WILD-TYPE 
          8.280          15.335 
[1] "3.4 - 19.8 (8.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.3"
D260V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NAGPA MUTATED         0        0        0         1         4         0
  NAGPA WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  NAGPA MUTATED          0
  NAGPA WILD-TYPE        3
D260V3, multiclass
           clus
vv          NAGPA MUTATED NAGPA WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NAGPA MUTATED    0  1     4
  NAGPA WILD-TYPE  5 16    98
D260V4, multiclass
       clus
vv      NAGPA MUTATED NAGPA WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V5, binary
                 cls
clus               0  1
  NAGPA MUTATED    1  4
  NAGPA WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      1    4
  NAGPA WILD-TYPE   34   85
   clus
vv  NAGPA MUTATED NAGPA WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D260V6, binary
                 cls
clus               0  1
  NAGPA MUTATED    1  0
  NAGPA WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      1    0
  NAGPA WILD-TYPE   56    3
   clus
vv  NAGPA MUTATED NAGPA WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D260V7, binary
                 cls
clus               0  1
  NAGPA MUTATED    3  2
  NAGPA WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      3    2
  NAGPA WILD-TYPE   48   73
        clus
vv       NAGPA MUTATED NAGPA WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D260V8, binary
                 cls
clus               0  1
  NAGPA MUTATED    4  1
  NAGPA WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      4    1
  NAGPA WILD-TYPE   84   29
     clus
vv    NAGPA MUTATED NAGPA WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAGPA MUTATED                                     5
  NAGPA WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAGPA MUTATED                                       0
  NAGPA WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAGPA MUTATED                                                  0
  NAGPA WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NAGPA MUTATED                                     0
  NAGPA WILD-TYPE                                   1
D260V9, multiclass
                                                  clus
vv                                                 NAGPA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NAGPA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V10, continuous
D260V11, continuous
                 vv
clus              R0 R1 R2 RX
  NAGPA MUTATED    2  2  1  0
  NAGPA WILD-TYPE 78 33  3  2
D260V12, multiclass
    clus
vv   NAGPA MUTATED NAGPA WILD-TYPE
  R0             2              78
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAGPA MUTATED       1                         1     3
  NAGPA WILD-TYPE     5                         4   111
D260V14, multiclass
                           clus
vv                          NAGPA MUTATED NAGPA WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V15, binary
                 cls
clus               0  1
  NAGPA MUTATED    0  3
  NAGPA WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAGPA MUTATED      0    3
  NAGPA WILD-TYPE    5   88
                        clus
vv                       NAGPA MUTATED NAGPA WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(261) Variable = CLIP1 MUTATION ANALYSIS
D261V1, survival
                 sevent
clus2              0  1
  CLIP1 MUTATED    3  3
  CLIP1 WILD-TYPE 60 59
  CLIP1 MUTATED CLIP1 WILD-TYPE 
              6             119 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
              3              59 
$`CLIP1 MUTATED`
TCGA-3A-A9J0 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A6UG TCGA-OE-A75W 
       24.43        19.82        19.82        41.33         1.35         8.78 

$`CLIP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        10.13        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       10.85         0.23        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CLIP1 MUTATED CLIP1 WILD-TYPE 
           1.35            0.23 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
          41.33           90.12 
  CLIP1 MUTATED CLIP1 WILD-TYPE 
          19.82           15.19 
[1] "1.4 - 41.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D261V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CLIP1 MUTATED         0        0        0         1         4         0
  CLIP1 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  CLIP1 MUTATED          1
  CLIP1 WILD-TYPE        2
D261V3, multiclass
           clus
vv          CLIP1 MUTATED CLIP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CLIP1 MUTATED    0  0     6
  CLIP1 WILD-TYPE  5 17    96
D261V4, multiclass
       clus
vv      CLIP1 MUTATED CLIP1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V5, binary
                 cls
clus               0  1
  CLIP1 MUTATED    2  4
  CLIP1 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      2    4
  CLIP1 WILD-TYPE   33   85
   clus
vv  CLIP1 MUTATED CLIP1 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D261V6, binary
                 cls
clus               0  1
  CLIP1 MUTATED    4  1
  CLIP1 WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      4    1
  CLIP1 WILD-TYPE   53    2
   clus
vv  CLIP1 MUTATED CLIP1 WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D261V7, binary
                 cls
clus               0  1
  CLIP1 MUTATED    2  4
  CLIP1 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      2    4
  CLIP1 WILD-TYPE   49   71
        clus
vv       CLIP1 MUTATED CLIP1 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D261V8, binary
                 cls
clus               0  1
  CLIP1 MUTATED    5  1
  CLIP1 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      5    1
  CLIP1 WILD-TYPE   83   29
     clus
vv    CLIP1 MUTATED CLIP1 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CLIP1 MUTATED                                     5
  CLIP1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CLIP1 MUTATED                                       1
  CLIP1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CLIP1 MUTATED                                                  0
  CLIP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CLIP1 MUTATED                                     0
  CLIP1 WILD-TYPE                                   1
D261V9, multiclass
                                                  clus
vv                                                 CLIP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CLIP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V10, continuous
D261V11, continuous
                 vv
clus              R0 R1 R2 RX
  CLIP1 MUTATED    5  1  0  0
  CLIP1 WILD-TYPE 75 34  4  2
D261V12, multiclass
    clus
vv   CLIP1 MUTATED CLIP1 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLIP1 MUTATED       0                         0     6
  CLIP1 WILD-TYPE     6                         5   108
D261V14, multiclass
                           clus
vv                          CLIP1 MUTATED CLIP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V15, binary
                 cls
clus               0  1
  CLIP1 MUTATED    0  6
  CLIP1 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP1 MUTATED      0    6
  CLIP1 WILD-TYPE    5   85
                        clus
vv                       CLIP1 MUTATED CLIP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(262) Variable = FNDC7 MUTATION ANALYSIS
D262V1, survival
                 sevent
clus2              0  1
  FNDC7 MUTATED    4  0
  FNDC7 WILD-TYPE 59 62
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              4             121 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              0              62 
$`FNDC7 MUTATED`
TCGA-S4-A8RO TCGA-F2-A8YN TCGA-XN-A8T3 TCGA-Z5-AAPL 
       17.26        17.00        31.27        15.35 

$`FNDC7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  FNDC7 MUTATED FNDC7 WILD-TYPE 
          15.35            0.23 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          31.27           90.12 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          17.13           15.12 
[1] "15.3 - 31.3 (17.1)" "0.2 - 90.1 (15.1)" 
[1] "hr="     "2.6e+07"
D262V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FNDC7 MUTATED         0        0        1         2         1         0
  FNDC7 WILD-TYPE       1        3       11        17        81         4
                 vv
clus              STAGE IV
  FNDC7 MUTATED          0
  FNDC7 WILD-TYPE        3
D262V3, multiclass
           clus
vv          FNDC7 MUTATED FNDC7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FNDC7 MUTATED    0  1     3
  FNDC7 WILD-TYPE  5 16    99
D262V4, multiclass
       clus
vv      FNDC7 MUTATED FNDC7 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V5, binary
                 cls
clus               0  1
  FNDC7 MUTATED    3  1
  FNDC7 WILD-TYPE 32 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      3    1
  FNDC7 WILD-TYPE   32   88
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             3              32
  1             1              88
[1] 2 2
[1] FALSE
D262V6, binary
                 cls
clus               0  1
  FNDC7 MUTATED    3  0
  FNDC7 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      3    0
  FNDC7 WILD-TYPE   54    3
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D262V7, binary
                 cls
clus               0  1
  FNDC7 MUTATED    2  2
  FNDC7 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      2    2
  FNDC7 WILD-TYPE   49   73
        clus
vv       FNDC7 MUTATED FNDC7 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D262V8, binary
                 cls
clus               0  1
  FNDC7 MUTATED    2  2
  FNDC7 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      2    2
  FNDC7 WILD-TYPE   86   28
     clus
vv    FNDC7 MUTATED FNDC7 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FNDC7 MUTATED                                     4
  FNDC7 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FNDC7 MUTATED                                       0
  FNDC7 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FNDC7 MUTATED                                                  0
  FNDC7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FNDC7 MUTATED                                     0
  FNDC7 WILD-TYPE                                   1
D262V9, multiclass
                                                  clus
vv                                                 FNDC7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FNDC7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V10, continuous
[1] "Remove cluster labels:" "FNDC7 MUTATED"         
clus
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"FNDC7 WILD-TYPE" "FNDC7 WILD-TYPE" 
D262V11, continuous
                 vv
clus              R0 R1 R2 RX
  FNDC7 MUTATED    1  3  0  0
  FNDC7 WILD-TYPE 79 32  4  2
D262V12, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  R0             1              79
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FNDC7 MUTATED       0                         0     4
  FNDC7 WILD-TYPE     6                         5   110
D262V14, multiclass
                           clus
vv                          FNDC7 MUTATED FNDC7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V15, binary
                 cls
clus               0  1
  FNDC7 MUTATED    1  3
  FNDC7 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      1    3
  FNDC7 WILD-TYPE    4   88
                        clus
vv                       FNDC7 MUTATED FNDC7 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(263) Variable = MOGS MUTATION ANALYSIS
D263V1, survival
                sevent
clus2             0  1
  MOGS MUTATED    1  4
  MOGS WILD-TYPE 62 58
  MOGS MUTATED MOGS WILD-TYPE 
             5            120 
  MOGS MUTATED MOGS WILD-TYPE 
             4             58 
$`MOGS MUTATED`
TCGA-2J-AABA TCGA-2L-AAQE TCGA-3A-A9IU TCGA-IB-7651 TCGA-IB-7885 
       19.96        22.49        15.06        19.82        41.33 

$`MOGS WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  MOGS MUTATED MOGS WILD-TYPE 
         15.06           0.23 
  MOGS MUTATED MOGS WILD-TYPE 
         41.33          90.12 
  MOGS MUTATED MOGS WILD-TYPE 
        19.960         15.155 
[1] "15.1 - 41.3 (20.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D263V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MOGS MUTATED         0        0        0         0         5         0
  MOGS WILD-TYPE       1        3       12        19        77         4
                vv
clus             STAGE IV
  MOGS MUTATED          0
  MOGS WILD-TYPE        3
D263V3, multiclass
           clus
vv          MOGS MUTATED MOGS WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  MOGS MUTATED    0  0     5
  MOGS WILD-TYPE  5 17    97
D263V4, multiclass
       clus
vv      MOGS MUTATED MOGS WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V5, binary
                cls
clus              0  1
  MOGS MUTATED    0  5
  MOGS WILD-TYPE 35 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  MOGS MUTATED      0    5
  MOGS WILD-TYPE   35   84
   clus
vv  MOGS MUTATED MOGS WILD-TYPE
  0            0             35
  1            5             84
[1] 2 2
[1] FALSE
D263V6, binary
                cls
clus              0  1
  MOGS MUTATED    4  0
  MOGS WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MOGS MUTATED      4    0
  MOGS WILD-TYPE   53    3
   clus
vv  MOGS MUTATED MOGS WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D263V7, binary
                cls
clus              0  1
  MOGS MUTATED    2  3
  MOGS WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  MOGS MUTATED      2    3
  MOGS WILD-TYPE   49   72
        clus
vv       MOGS MUTATED MOGS WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D263V8, binary
                cls
clus              0  1
  MOGS MUTATED    5  0
  MOGS WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  MOGS MUTATED      5    0
  MOGS WILD-TYPE   83   30
     clus
vv    MOGS MUTATED MOGS WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MOGS MUTATED                                     5
  MOGS WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MOGS MUTATED                                       0
  MOGS WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MOGS MUTATED                                                  0
  MOGS WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MOGS MUTATED                                     0
  MOGS WILD-TYPE                                   1
D263V9, multiclass
                                                  clus
vv                                                 MOGS MUTATED MOGS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V10, continuous
D263V11, continuous
[1] "Remove cluster labels:" "MOGS MUTATED"          
clus
  MOGS MUTATED MOGS WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-8126 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"MOGS WILD-TYPE" "MOGS WILD-TYPE" "MOGS WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MOGS MUTATED    4  1  0  0
  MOGS WILD-TYPE 76 34  4  2
D263V12, multiclass
    clus
vv   MOGS MUTATED MOGS WILD-TYPE
  R0            4             76
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MOGS MUTATED       0                         0     5
  MOGS WILD-TYPE     6                         5   109
D263V14, multiclass
                           clus
vv                          MOGS MUTATED MOGS WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V15, binary
                cls
clus              0  1
  MOGS MUTATED    0  3
  MOGS WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  MOGS MUTATED      0    3
  MOGS WILD-TYPE    5   88
                        clus
vv                       MOGS MUTATED MOGS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(264) Variable = BCL3 MUTATION ANALYSIS
D264V1, survival
                sevent
clus2             0  1
  BCL3 MUTATED    3  2
  BCL3 WILD-TYPE 60 60
  BCL3 MUTATED BCL3 WILD-TYPE 
             5            120 
  BCL3 MUTATED BCL3 WILD-TYPE 
             2             60 
$`BCL3 MUTATED`
TCGA-XD-AAUL TCGA-2J-AAB6 TCGA-IB-7651 TCGA-IB-A6UF TCGA-IB-AAUP 
       16.37         9.63        19.82        21.90        14.17 

$`BCL3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14         2.17        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  BCL3 MUTATED BCL3 WILD-TYPE 
          9.63           0.23 
  BCL3 MUTATED BCL3 WILD-TYPE 
         21.90          90.12 
  BCL3 MUTATED BCL3 WILD-TYPE 
        16.370         15.205 
[1] "9.6 - 21.9 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D264V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BCL3 MUTATED         0        0        0         2         3         0
  BCL3 WILD-TYPE       1        3       12        17        79         4
                vv
clus             STAGE IV
  BCL3 MUTATED          0
  BCL3 WILD-TYPE        3
D264V3, multiclass
           clus
vv          BCL3 MUTATED BCL3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  BCL3 MUTATED    0  0     5
  BCL3 WILD-TYPE  5 17    97
D264V4, multiclass
       clus
vv      BCL3 MUTATED BCL3 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V5, binary
                cls
clus              0  1
  BCL3 MUTATED    2  3
  BCL3 WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL3 MUTATED      2    3
  BCL3 WILD-TYPE   33   86
   clus
vv  BCL3 MUTATED BCL3 WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D264V6, binary
                cls
clus              0  1
  BCL3 MUTATED    4  0
  BCL3 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL3 MUTATED      4    0
  BCL3 WILD-TYPE   53    3
   clus
vv  BCL3 MUTATED BCL3 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D264V7, binary
                cls
clus              0  1
  BCL3 MUTATED    1  4
  BCL3 WILD-TYPE 50 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL3 MUTATED      1    4
  BCL3 WILD-TYPE   50   71
        clus
vv       BCL3 MUTATED BCL3 WILD-TYPE
  FEMALE            1             50
  MALE              4             71
[1] 2 2
[1] FALSE
D264V8, binary
                cls
clus              0  1
  BCL3 MUTATED    5  0
  BCL3 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL3 MUTATED      5    0
  BCL3 WILD-TYPE   83   30
     clus
vv    BCL3 MUTATED BCL3 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCL3 MUTATED                                     5
  BCL3 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCL3 MUTATED                                       0
  BCL3 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCL3 MUTATED                                                  0
  BCL3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  BCL3 MUTATED                                     0
  BCL3 WILD-TYPE                                   1
D264V9, multiclass
                                                  clus
vv                                                 BCL3 MUTATED BCL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V10, continuous
D264V11, continuous
                vv
clus             R0 R1 R2 RX
  BCL3 MUTATED    3  2  0  0
  BCL3 WILD-TYPE 77 33  4  2
D264V12, multiclass
    clus
vv   BCL3 MUTATED BCL3 WILD-TYPE
  R0            3             77
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL3 MUTATED       0                         0     5
  BCL3 WILD-TYPE     6                         5   109
D264V14, multiclass
                           clus
vv                          BCL3 MUTATED BCL3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V15, binary
                cls
clus              0  1
  BCL3 MUTATED    0  4
  BCL3 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL3 MUTATED      0    4
  BCL3 WILD-TYPE    5   87
                        clus
vv                       BCL3 MUTATED BCL3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(265) Variable = MED12L MUTATION ANALYSIS
D265V1, survival
                  sevent
clus2               0  1
  MED12L MUTATED    7  6
  MED12L WILD-TYPE 56 56
  MED12L MUTATED MED12L WILD-TYPE 
              13              112 
  MED12L MUTATED MED12L WILD-TYPE 
               6               56 
$`MED12L MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB9 TCGA-2J-AABU TCGA-2L-AAQI TCGA-3A-A9IU TCGA-3A-A9IX 
       17.26        20.61         9.11         3.39        15.06        34.09 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-AAUS 
       23.54        15.55        22.06        32.15        19.82         7.40 
TCGA-XD-AAUH 
       12.99 

$`MED12L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       50.70        32.81        36.26        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       15.95        37.15         7.50        12.53         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       17.79         8.28        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU 
        4.73         7.86        14.17         6.02        11.11         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        13.81        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MED12L MUTATED MED12L WILD-TYPE 
            3.39             0.23 
  MED12L MUTATED MED12L WILD-TYPE 
           34.09            90.12 
  MED12L MUTATED MED12L WILD-TYPE 
          17.260           15.155 
[1] "3.4 - 34.1 (17.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D265V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MED12L MUTATED         0        1        0         2        10         0
  MED12L WILD-TYPE       1        2       12        17        72         4
                  vv
clus               STAGE IV
  MED12L MUTATED          0
  MED12L WILD-TYPE        3
D265V3, multiclass
           clus
vv          MED12L MUTATED MED12L WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB             10               72
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MED12L MUTATED    1  1    11
  MED12L WILD-TYPE  4 16    91
D265V4, multiclass
       clus
vv      MED12L MUTATED MED12L WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4             11               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V5, binary
                  cls
clus                0  1
  MED12L MUTATED    3 10
  MED12L WILD-TYPE 32 79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED      3   10
  MED12L WILD-TYPE   32   79
   clus
vv  MED12L MUTATED MED12L WILD-TYPE
  0              3               32
  1             10               79
[1] 2 2
[1] FALSE
D265V6, binary
                  cls
clus                0  1
  MED12L MUTATED    6  0
  MED12L WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED      6    0
  MED12L WILD-TYPE   51    3
   clus
vv  MED12L MUTATED MED12L WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D265V7, binary
                  cls
clus                0  1
  MED12L MUTATED    5  8
  MED12L WILD-TYPE 46 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED      5    8
  MED12L WILD-TYPE   46   67
        clus
vv       MED12L MUTATED MED12L WILD-TYPE
  FEMALE              5               46
  MALE                8               67
[1] 2 2
[1] FALSE
D265V8, binary
                  cls
clus                0  1
  MED12L MUTATED    8  5
  MED12L WILD-TYPE 80 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED      8    5
  MED12L WILD-TYPE   80   25
     clus
vv    MED12L MUTATED MED12L WILD-TYPE
  NO               8               80
  YES              5               25
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED12L MUTATED                                    11
  MED12L WILD-TYPE                                  94
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED12L MUTATED                                       2
  MED12L WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED12L MUTATED                                                  0
  MED12L WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MED12L MUTATED                                     0
  MED12L WILD-TYPE                                   1
D265V9, multiclass
                                                  clus
vv                                                 MED12L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MED12L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V10, continuous
D265V11, continuous
                  vv
clus               R0 R1 R2 RX
  MED12L MUTATED    9  3  1  0
  MED12L WILD-TYPE 71 32  3  2
D265V12, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  R0              9               71
  R1              3               32
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12L MUTATED       1                         0    12
  MED12L WILD-TYPE     5                         5   102
D265V14, multiclass
                           clus
vv                          MED12L MUTATED MED12L WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                 12              102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V15, binary
                  cls
clus                0  1
  MED12L MUTATED    0  9
  MED12L WILD-TYPE  5 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED      0    9
  MED12L WILD-TYPE    5   82
                        clus
vv                       MED12L MUTATED MED12L WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              9               82
[1] 2 2
[1] FALSE

Clustering(266) Variable = EXOC4 MUTATION ANALYSIS
D266V1, survival
                 sevent
clus2              0  1
  EXOC4 MUTATED    3  4
  EXOC4 WILD-TYPE 60 58
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              7             118 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              4              58 
$`EXOC4 MUTATED`
TCGA-3A-A9I9 TCGA-FB-A5VM TCGA-HZ-A77P TCGA-IB-7651 TCGA-US-A779 TCGA-YB-A89D 
       20.84        16.37        10.85        19.82        16.80        11.51 
TCGA-YY-A8LH 
       66.28 

$`EXOC4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        12.76        15.35 

  EXOC4 MUTATED EXOC4 WILD-TYPE 
          10.85            0.23 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
          66.28           90.12 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         16.800          15.155 
[1] "10.8 - 66.3 (16.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1"  
D266V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EXOC4 MUTATED         0        0        1         1         5         0
  EXOC4 WILD-TYPE       1        3       11        18        77         4
                 vv
clus              STAGE IV
  EXOC4 MUTATED          0
  EXOC4 WILD-TYPE        3
D266V3, multiclass
           clus
vv          EXOC4 MUTATED EXOC4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  EXOC4 MUTATED    0  1     6
  EXOC4 WILD-TYPE  5 16    96
D266V4, multiclass
       clus
vv      EXOC4 MUTATED EXOC4 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V5, binary
                 cls
clus               0  1
  EXOC4 MUTATED    2  5
  EXOC4 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      2    5
  EXOC4 WILD-TYPE   33   84
   clus
vv  EXOC4 MUTATED EXOC4 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D266V6, binary
                 cls
clus               0  1
  EXOC4 MUTATED    2  0
  EXOC4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      2    0
  EXOC4 WILD-TYPE   55    3
   clus
vv  EXOC4 MUTATED EXOC4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D266V7, binary
                 cls
clus               0  1
  EXOC4 MUTATED    3  4
  EXOC4 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      3    4
  EXOC4 WILD-TYPE   48   71
        clus
vv       EXOC4 MUTATED EXOC4 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D266V8, binary
                 cls
clus               0  1
  EXOC4 MUTATED    3  3
  EXOC4 WILD-TYPE 85 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      3    3
  EXOC4 WILD-TYPE   85   27
     clus
vv    EXOC4 MUTATED EXOC4 WILD-TYPE
  NO              3              85
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EXOC4 MUTATED                                     6
  EXOC4 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EXOC4 MUTATED                                       1
  EXOC4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EXOC4 MUTATED                                                  0
  EXOC4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EXOC4 MUTATED                                     0
  EXOC4 WILD-TYPE                                   1
D266V9, multiclass
                                                  clus
vv                                                 EXOC4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 EXOC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V10, continuous
D266V11, continuous
                 vv
clus              R0 R1 R2 RX
  EXOC4 MUTATED    7  0  0  0
  EXOC4 WILD-TYPE 73 35  4  2
D266V12, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  R0             7              73
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EXOC4 MUTATED       0                         0     7
  EXOC4 WILD-TYPE     6                         5   107
D266V14, multiclass
                           clus
vv                          EXOC4 MUTATED EXOC4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V15, binary
                 cls
clus               0  1
  EXOC4 MUTATED    0  7
  EXOC4 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      0    7
  EXOC4 WILD-TYPE    5   84
                        clus
vv                       EXOC4 MUTATED EXOC4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(267) Variable = MARCH7 MUTATION ANALYSIS
D267V1, survival
                  sevent
clus2               0  1
  MARCH7 MUTATED    2  2
  MARCH7 WILD-TYPE 61 60
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               4              121 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               2               60 
$`MARCH7 MUTATED`
TCGA-F2-A44G TCGA-LB-A7SX TCGA-Q3-AA2A TCGA-YH-A8SY 
        7.66        12.92         3.12        12.76 

$`MARCH7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  MARCH7 MUTATED MARCH7 WILD-TYPE 
            3.12             0.23 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
           12.92            90.12 
  MARCH7 MUTATED MARCH7 WILD-TYPE 
           10.21            15.35 
[1] "3.1 - 12.9 (10.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D267V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MARCH7 MUTATED         0        0        1         0         2         1
  MARCH7 WILD-TYPE       1        3       11        19        80         3
                  vv
clus               STAGE IV
  MARCH7 MUTATED          0
  MARCH7 WILD-TYPE        3
D267V3, multiclass
           clus
vv          MARCH7 MUTATED MARCH7 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MARCH7 MUTATED    0  0     4
  MARCH7 WILD-TYPE  5 17    98
D267V4, multiclass
       clus
vv      MARCH7 MUTATED MARCH7 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V5, binary
                  cls
clus                0  1
  MARCH7 MUTATED    0  4
  MARCH7 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      0    4
  MARCH7 WILD-TYPE   35   85
   clus
vv  MARCH7 MUTATED MARCH7 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D267V6, binary
                  cls
clus                0  1
  MARCH7 MUTATED    1  0
  MARCH7 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      1    0
  MARCH7 WILD-TYPE   56    3
   clus
vv  MARCH7 MUTATED MARCH7 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D267V7, binary
                  cls
clus                0  1
  MARCH7 MUTATED    4  0
  MARCH7 WILD-TYPE 47 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      4    0
  MARCH7 WILD-TYPE   47   75
        clus
vv       MARCH7 MUTATED MARCH7 WILD-TYPE
  FEMALE              4               47
  MALE                0               75
[1] 2 2
[1] FALSE
D267V8, binary
                  cls
clus                0  1
  MARCH7 MUTATED    2  2
  MARCH7 WILD-TYPE 86 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      2    2
  MARCH7 WILD-TYPE   86   28
     clus
vv    MARCH7 MUTATED MARCH7 WILD-TYPE
  NO               2               86
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MARCH7 MUTATED                                     3
  MARCH7 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MARCH7 MUTATED                                       0
  MARCH7 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MARCH7 MUTATED                                                  0
  MARCH7 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MARCH7 MUTATED                                     0
  MARCH7 WILD-TYPE                                   1
D267V9, multiclass
                                                  clus
vv                                                 MARCH7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MARCH7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V10, continuous
[1] "Remove cluster labels:" "MARCH7 MUTATED"        
clus
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
D267V11, continuous
[1] "Remove cluster labels:" "MARCH7 MUTATED"        
clus
  MARCH7 MUTATED MARCH7 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" "MARCH7 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  MARCH7 MUTATED    0  2  0  1
  MARCH7 WILD-TYPE 80 33  4  1
D267V12, multiclass
    clus
vv   MARCH7 MUTATED MARCH7 WILD-TYPE
  R0              0               80
  R1              2               33
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MARCH7 MUTATED       0                         1     3
  MARCH7 WILD-TYPE     6                         4   111
D267V14, multiclass
                           clus
vv                          MARCH7 MUTATED MARCH7 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V15, binary
                  cls
clus                0  1
  MARCH7 MUTATED    0  4
  MARCH7 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MARCH7 MUTATED      0    4
  MARCH7 WILD-TYPE    5   87
                        clus
vv                       MARCH7 MUTATED MARCH7 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(268) Variable = TMCC1 MUTATION ANALYSIS
D268V1, survival
                 sevent
clus2              0  1
  TMCC1 MUTATED    2  4
  TMCC1 WILD-TYPE 61 58
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              6             119 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              4              58 
$`TMCC1 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABV TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-HZ-A77O TCGA-IB-7651 
        1.08        21.44        43.50         7.36         5.26        19.82 

$`TMCC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
        9.60        45.47        20.84        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TMCC1 MUTATED TMCC1 WILD-TYPE 
           1.08            0.23 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          43.50           90.12 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          13.59           15.22 
[1] "1.1 - 43.5 (13.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D268V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMCC1 MUTATED         0        0        0         0         6         0
  TMCC1 WILD-TYPE       1        3       12        19        76         4
                 vv
clus              STAGE IV
  TMCC1 MUTATED          0
  TMCC1 WILD-TYPE        3
D268V3, multiclass
           clus
vv          TMCC1 MUTATED TMCC1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TMCC1 MUTATED    0  1     5
  TMCC1 WILD-TYPE  5 16    97
D268V4, multiclass
       clus
vv      TMCC1 MUTATED TMCC1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V5, binary
                 cls
clus               0  1
  TMCC1 MUTATED    0  6
  TMCC1 WILD-TYPE 35 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      0    6
  TMCC1 WILD-TYPE   35   83
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             0              35
  1             6              83
[1] 2 2
[1] FALSE
D268V6, binary
                 cls
clus               0  1
  TMCC1 MUTATED    2  0
  TMCC1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    0
  TMCC1 WILD-TYPE   55    3
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D268V7, binary
                 cls
clus               0  1
  TMCC1 MUTATED    4  2
  TMCC1 WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      4    2
  TMCC1 WILD-TYPE   47   73
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D268V8, binary
                 cls
clus               0  1
  TMCC1 MUTATED    4  1
  TMCC1 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      4    1
  TMCC1 WILD-TYPE   84   29
     clus
vv    TMCC1 MUTATED TMCC1 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMCC1 MUTATED                                     5
  TMCC1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMCC1 MUTATED                                       1
  TMCC1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMCC1 MUTATED                                                  0
  TMCC1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMCC1 MUTATED                                     0
  TMCC1 WILD-TYPE                                   1
D268V9, multiclass
                                                  clus
vv                                                 TMCC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TMCC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V10, continuous
D268V11, continuous
                 vv
clus              R0 R1 R2 RX
  TMCC1 MUTATED    5  1  0  0
  TMCC1 WILD-TYPE 75 34  4  2
D268V12, multiclass
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCC1 MUTATED       0                         1     5
  TMCC1 WILD-TYPE     6                         4   109
D268V14, multiclass
                           clus
vv                          TMCC1 MUTATED TMCC1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V15, binary
                 cls
clus               0  1
  TMCC1 MUTATED    0  5
  TMCC1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      0    5
  TMCC1 WILD-TYPE    5   86
                        clus
vv                       TMCC1 MUTATED TMCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(269) Variable = NBPF10 MUTATION ANALYSIS
D269V1, survival
                  sevent
clus2               0  1
  NBPF10 MUTATED    6  3
  NBPF10 WILD-TYPE 57 59
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              116 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               3               59 
$`NBPF10 MUTATED`
TCGA-2J-AABO TCGA-2L-AAQA TCGA-3A-A9J0 TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FZ-5921 
       14.47         4.70        24.43        23.54        15.55         5.10 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-IB-8126 
        8.28        32.15        15.19 

$`NBPF10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       12.53         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-AA8V TCGA-HV-AA8X 
       36.20        20.35        17.79        22.06        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
        0.23        19.82        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            4.70             0.23 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           32.15            90.12 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           15.19            15.27 
[1] "4.7 - 32.1 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D269V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NBPF10 MUTATED         0        0        0         2         6         1
  NBPF10 WILD-TYPE       1        3       12        17        76         3
                  vv
clus               STAGE IV
  NBPF10 MUTATED          0
  NBPF10 WILD-TYPE        3
D269V3, multiclass
           clus
vv          NBPF10 MUTATED NBPF10 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              6               76
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NBPF10 MUTATED    0  1     8
  NBPF10 WILD-TYPE  5 16    94
D269V4, multiclass
       clus
vv      NBPF10 MUTATED NBPF10 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              8               94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V5, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  7
  NBPF10 WILD-TYPE 33 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    7
  NBPF10 WILD-TYPE   33   82
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              2               33
  1              7               82
[1] 2 2
[1] FALSE
D269V6, binary
                  cls
clus                0  1
  NBPF10 MUTATED    4  0
  NBPF10 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      4    0
  NBPF10 WILD-TYPE   53    3
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D269V7, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  7
  NBPF10 WILD-TYPE 49 68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    7
  NBPF10 WILD-TYPE   49   68
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  FEMALE              2               49
  MALE                7               68
[1] 2 2
[1] FALSE
D269V8, binary
                  cls
clus                0  1
  NBPF10 MUTATED    6  3
  NBPF10 WILD-TYPE 82 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      6    3
  NBPF10 WILD-TYPE   82   27
     clus
vv    NBPF10 MUTATED NBPF10 WILD-TYPE
  NO               6               82
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF10 MUTATED                                     8
  NBPF10 WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF10 MUTATED                                       1
  NBPF10 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF10 MUTATED                                                  0
  NBPF10 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NBPF10 MUTATED                                     0
  NBPF10 WILD-TYPE                                   1
D269V9, multiclass
                                                  clus
vv                                                 NBPF10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NBPF10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V10, continuous
D269V11, continuous
[1] "Remove cluster labels:" "NBPF10 MUTATED"        
clus
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" "NBPF10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NBPF10 MUTATED    5  2  1  0
  NBPF10 WILD-TYPE 75 33  3  2
D269V12, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  R0              5               75
  R1              2               33
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED       2                         0     6
  NBPF10 WILD-TYPE     4                         5   108
D269V14, multiclass
                           clus
vv                          NBPF10 MUTATED NBPF10 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V15, binary
                  cls
clus                0  1
  NBPF10 MUTATED    0  4
  NBPF10 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      0    4
  NBPF10 WILD-TYPE    5   87
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(270) Variable = IFFO1 MUTATION ANALYSIS
D270V1, survival
                 sevent
clus2              0  1
  IFFO1 MUTATED    3  2
  IFFO1 WILD-TYPE 60 60
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              5             120 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              2              60 
$`IFFO1 MUTATED`
TCGA-3A-A9IS TCGA-H8-A6C1 TCGA-IB-7651 TCGA-US-A776 TCGA-US-A779 
       32.81        22.06        19.82        39.98        16.80 

$`IFFO1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
        0.30         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  IFFO1 MUTATED IFFO1 WILD-TYPE 
          16.80            0.23 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
          39.98           90.12 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
          22.06           15.09 
[1] "16.8 - 40.0 (22.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "2"  
D270V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IFFO1 MUTATED         0        0        1         2         2         0
  IFFO1 WILD-TYPE       1        3       11        17        80         4
                 vv
clus              STAGE IV
  IFFO1 MUTATED          0
  IFFO1 WILD-TYPE        3
D270V3, multiclass
           clus
vv          IFFO1 MUTATED IFFO1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  IFFO1 MUTATED    0  1     4
  IFFO1 WILD-TYPE  5 16    98
D270V4, multiclass
       clus
vv      IFFO1 MUTATED IFFO1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V5, binary
                 cls
clus               0  1
  IFFO1 MUTATED    3  2
  IFFO1 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      3    2
  IFFO1 WILD-TYPE   32   87
   clus
vv  IFFO1 MUTATED IFFO1 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D270V6, binary
                 cls
clus               0  1
  IFFO1 MUTATED    1  0
  IFFO1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      1    0
  IFFO1 WILD-TYPE   56    3
   clus
vv  IFFO1 MUTATED IFFO1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D270V7, binary
                 cls
clus               0  1
  IFFO1 MUTATED    2  3
  IFFO1 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      2    3
  IFFO1 WILD-TYPE   49   72
        clus
vv       IFFO1 MUTATED IFFO1 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D270V8, binary
                 cls
clus               0  1
  IFFO1 MUTATED    4  0
  IFFO1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      4    0
  IFFO1 WILD-TYPE   84   30
     clus
vv    IFFO1 MUTATED IFFO1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IFFO1 MUTATED                                     2
  IFFO1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IFFO1 MUTATED                                       2
  IFFO1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IFFO1 MUTATED                                                  1
  IFFO1 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  IFFO1 MUTATED                                     0
  IFFO1 WILD-TYPE                                   1
D270V9, multiclass
                                                  clus
vv                                                 IFFO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 IFFO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V10, continuous
[1] "Remove cluster labels:" "IFFO1 MUTATED"         
clus
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-YY-A8LH 
"IFFO1 WILD-TYPE" 
D270V11, continuous
[1] "Remove cluster labels:" "IFFO1 MUTATED"         
clus
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  IFFO1 MUTATED    5  0  0  0
  IFFO1 WILD-TYPE 75 35  4  2
D270V12, multiclass
    clus
vv   IFFO1 MUTATED IFFO1 WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFFO1 MUTATED       0                         0     5
  IFFO1 WILD-TYPE     6                         5   109
D270V14, multiclass
                           clus
vv                          IFFO1 MUTATED IFFO1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V15, binary
                 cls
clus               0  1
  IFFO1 MUTATED    0  5
  IFFO1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      0    5
  IFFO1 WILD-TYPE    5   86
                        clus
vv                       IFFO1 MUTATED IFFO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(271) Variable = ARHGEF7 MUTATION ANALYSIS
D271V1, survival
                   sevent
clus2                0  1
  ARHGEF7 MUTATED    3  3
  ARHGEF7 WILD-TYPE 60 59
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
                6               119 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
                3                59 
$`ARHGEF7 MUTATED`
TCGA-LB-A7SX TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-AAUP TCGA-XN-A8T5 
       12.92         5.26        10.85        19.82        14.17        23.67 

$`ARHGEF7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A8P1 
       17.49        31.86        20.19        17.00        10.13         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        11.51        12.76        66.28        15.35 

  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
             5.26              0.23 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
            23.67             90.12 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
           13.545            15.320 
[1] "5.3 - 23.7 (13.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D271V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ARHGEF7 MUTATED         0        0        1         0         5         0
  ARHGEF7 WILD-TYPE       1        3       11        19        77         4
                   vv
clus                STAGE IV
  ARHGEF7 MUTATED          0
  ARHGEF7 WILD-TYPE        3
D271V3, multiclass
           clus
vv          ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ARHGEF7 MUTATED    0  2     4
  ARHGEF7 WILD-TYPE  5 15    98
D271V4, multiclass
       clus
vv      ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V5, binary
                   cls
clus                 0  1
  ARHGEF7 MUTATED    1  5
  ARHGEF7 WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED      1    5
  ARHGEF7 WILD-TYPE   34   84
   clus
vv  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D271V6, binary
                   cls
clus                 0  1
  ARHGEF7 MUTATED    3  0
  ARHGEF7 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED      3    0
  ARHGEF7 WILD-TYPE   54    3
   clus
vv  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D271V7, binary
                   cls
clus                 0  1
  ARHGEF7 MUTATED    4  2
  ARHGEF7 WILD-TYPE 47 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED      4    2
  ARHGEF7 WILD-TYPE   47   73
        clus
vv       ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  FEMALE               4                47
  MALE                 2                73
[1] 2 2
[1] FALSE
D271V8, binary
                   cls
clus                 0  1
  ARHGEF7 MUTATED    5  1
  ARHGEF7 WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED      5    1
  ARHGEF7 WILD-TYPE   83   29
     clus
vv    ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARHGEF7 MUTATED                                     4
  ARHGEF7 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARHGEF7 MUTATED                                       2
  ARHGEF7 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARHGEF7 MUTATED                                                  0
  ARHGEF7 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ARHGEF7 MUTATED                                     0
  ARHGEF7 WILD-TYPE                                   1
D271V9, multiclass
                                                  clus
vv                                                 ARHGEF7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ARHGEF7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V10, continuous
D271V11, continuous
                   vv
clus                R0 R1 R2 RX
  ARHGEF7 MUTATED    3  3  0  0
  ARHGEF7 WILD-TYPE 77 32  4  2
D271V12, multiclass
    clus
vv   ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  R0               3                77
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF7 MUTATED       0                         1     5
  ARHGEF7 WILD-TYPE     6                         4   109
D271V14, multiclass
                           clus
vv                          ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V15, binary
                   cls
clus                 0  1
  ARHGEF7 MUTATED    1  5
  ARHGEF7 WILD-TYPE  4 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED      1    5
  ARHGEF7 WILD-TYPE    4   86
                        clus
vv                       ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(272) Variable = ZNF878 MUTATION ANALYSIS
D272V1, survival
                  sevent
clus2               0  1
  ZNF878 MUTATED    3  5
  ZNF878 WILD-TYPE 60 57
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               8              117 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
               5               57 
$`ZNF878 MUTATED`
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-2J-AAB4 TCGA-FB-A5VM TCGA-IB-7651 TCGA-LB-A9Q5 
        1.08        15.12        23.97        16.37        19.82        10.29 
TCGA-US-A77G TCGA-XD-AAUG 
        0.39        13.81 

$`ZNF878 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZNF878 MUTATED ZNF878 WILD-TYPE 
            0.39             0.23 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
           23.97            90.12 
  ZNF878 MUTATED ZNF878 WILD-TYPE 
          14.465           15.320 
[1] "0.4 - 24.0 (14.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.7"
D272V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF878 MUTATED         0        0        1         0         6         0
  ZNF878 WILD-TYPE       1        3       11        19        76         4
                  vv
clus               STAGE IV
  ZNF878 MUTATED          1
  ZNF878 WILD-TYPE        2
D272V3, multiclass
           clus
vv          ZNF878 MUTATED ZNF878 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF878 MUTATED    0  2     6
  ZNF878 WILD-TYPE  5 15    96
D272V4, multiclass
       clus
vv      ZNF878 MUTATED ZNF878 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V5, binary
                  cls
clus                0  1
  ZNF878 MUTATED    1  7
  ZNF878 WILD-TYPE 34 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      1    7
  ZNF878 WILD-TYPE   34   82
   clus
vv  ZNF878 MUTATED ZNF878 WILD-TYPE
  0              1               34
  1              7               82
[1] 2 2
[1] FALSE
D272V6, binary
                  cls
clus                0  1
  ZNF878 MUTATED    4  1
  ZNF878 WILD-TYPE 53  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      4    1
  ZNF878 WILD-TYPE   53    2
   clus
vv  ZNF878 MUTATED ZNF878 WILD-TYPE
  0              4               53
  1              1                2
[1] 2 2
[1] FALSE
D272V7, binary
                  cls
clus                0  1
  ZNF878 MUTATED    5  3
  ZNF878 WILD-TYPE 46 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      5    3
  ZNF878 WILD-TYPE   46   72
        clus
vv       ZNF878 MUTATED ZNF878 WILD-TYPE
  FEMALE              5               46
  MALE                3               72
[1] 2 2
[1] FALSE
D272V8, binary
                  cls
clus                0  1
  ZNF878 MUTATED    6  1
  ZNF878 WILD-TYPE 82 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      6    1
  ZNF878 WILD-TYPE   82   29
     clus
vv    ZNF878 MUTATED ZNF878 WILD-TYPE
  NO               6               82
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF878 MUTATED                                     6
  ZNF878 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF878 MUTATED                                       2
  ZNF878 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF878 MUTATED                                                  0
  ZNF878 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF878 MUTATED                                     0
  ZNF878 WILD-TYPE                                   1
D272V9, multiclass
                                                  clus
vv                                                 ZNF878 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF878 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V10, continuous
D272V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF878 MUTATED    8  0  0  0
  ZNF878 WILD-TYPE 72 35  4  2
D272V12, multiclass
    clus
vv   ZNF878 MUTATED ZNF878 WILD-TYPE
  R0              8               72
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF878 MUTATED       0                         0     8
  ZNF878 WILD-TYPE     6                         5   106
D272V14, multiclass
                           clus
vv                          ZNF878 MUTATED ZNF878 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V15, binary
                  cls
clus                0  1
  ZNF878 MUTATED    0  7
  ZNF878 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF878 MUTATED      0    7
  ZNF878 WILD-TYPE    5   84
                        clus
vv                       ZNF878 MUTATED ZNF878 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(273) Variable = AFF4 MUTATION ANALYSIS
D273V1, survival
                sevent
clus2             0  1
  AFF4 MUTATED    0  4
  AFF4 WILD-TYPE 63 58
  AFF4 MUTATED AFF4 WILD-TYPE 
             4            121 
  AFF4 MUTATED AFF4 WILD-TYPE 
             4             58 
$`AFF4 MUTATED`
TCGA-3A-A9IU TCGA-IB-AAUW TCGA-RB-A7B8 TCGA-US-A77G 
       15.06         7.56        15.32         0.39 

$`AFF4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  AFF4 MUTATED AFF4 WILD-TYPE 
          0.39           0.23 
  AFF4 MUTATED AFF4 WILD-TYPE 
         15.32          90.12 
  AFF4 MUTATED AFF4 WILD-TYPE 
         11.31          15.35 
[1] "0.4 - 15.3 (11.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "4.6"
D273V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AFF4 MUTATED         0        0        0         0         4         0
  AFF4 WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  AFF4 MUTATED          0
  AFF4 WILD-TYPE        3
D273V3, multiclass
           clus
vv          AFF4 MUTATED AFF4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  AFF4 MUTATED    0  0     4
  AFF4 WILD-TYPE  5 17    98
D273V4, multiclass
       clus
vv      AFF4 MUTATED AFF4 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V5, binary
                cls
clus              0  1
  AFF4 MUTATED    0  4
  AFF4 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF4 MUTATED      0    4
  AFF4 WILD-TYPE   35   85
   clus
vv  AFF4 MUTATED AFF4 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D273V6, binary
                cls
clus              0  1
  AFF4 MUTATED    1  0
  AFF4 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF4 MUTATED      1    0
  AFF4 WILD-TYPE   56    3
   clus
vv  AFF4 MUTATED AFF4 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D273V7, binary
                cls
clus              0  1
  AFF4 MUTATED    2  2
  AFF4 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF4 MUTATED      2    2
  AFF4 WILD-TYPE   49   73
        clus
vv       AFF4 MUTATED AFF4 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D273V8, binary
                cls
clus              0  1
  AFF4 MUTATED    4  0
  AFF4 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF4 MUTATED      4    0
  AFF4 WILD-TYPE   84   30
     clus
vv    AFF4 MUTATED AFF4 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AFF4 MUTATED                                     3
  AFF4 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AFF4 MUTATED                                       1
  AFF4 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AFF4 MUTATED                                                  0
  AFF4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  AFF4 MUTATED                                     0
  AFF4 WILD-TYPE                                   1
D273V9, multiclass
                                                  clus
vv                                                 AFF4 MUTATED AFF4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V10, continuous
D273V11, continuous
                vv
clus             R0 R1 R2 RX
  AFF4 MUTATED    4  0  0  0
  AFF4 WILD-TYPE 76 35  4  2
D273V12, multiclass
    clus
vv   AFF4 MUTATED AFF4 WILD-TYPE
  R0            4             76
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AFF4 MUTATED       0                         0     4
  AFF4 WILD-TYPE     6                         5   110
D273V14, multiclass
                           clus
vv                          AFF4 MUTATED AFF4 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V15, binary
                cls
clus              0  1
  AFF4 MUTATED    0  4
  AFF4 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF4 MUTATED      0    4
  AFF4 WILD-TYPE    5   87
                        clus
vv                       AFF4 MUTATED AFF4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(274) Variable = ZNF493 MUTATION ANALYSIS
D274V1, survival
                  sevent
clus2               0  1
  ZNF493 MUTATED    7  2
  ZNF493 WILD-TYPE 56 60
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               9              116 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               2               60 
$`ZNF493 MUTATED`
TCGA-2J-AABA TCGA-2J-AABH TCGA-3A-A9IV TCGA-3E-AAAY TCGA-HZ-A8P1 TCGA-IB-7651 
       19.96        42.31        36.26        75.12         0.23        19.82 
TCGA-IB-AAUM TCGA-XD-AAUG TCGA-YH-A8SY 
        0.26        13.81        12.76 

$`ZNF493 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       20.61        22.22        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13         5.26        10.85        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         8.22        15.88         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF493 MUTATED ZNF493 WILD-TYPE 
            0.23             0.30 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
           75.12            90.12 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
          19.820           15.205 
[1] "0.2 - 75.1 (19.8)" "0.3 - 90.1 (15.2)"
[1] "hr=" "2.9"
D274V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF493 MUTATED         0        0        2         1         4         1
  ZNF493 WILD-TYPE       1        3       10        18        78         3
                  vv
clus               STAGE IV
  ZNF493 MUTATED          1
  ZNF493 WILD-TYPE        2
D274V3, multiclass
           clus
vv          ZNF493 MUTATED ZNF493 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF493 MUTATED    0  3     6
  ZNF493 WILD-TYPE  5 14    96
D274V4, multiclass
       clus
vv      ZNF493 MUTATED ZNF493 WILD-TYPE
  T1                 0                5
  T2                 3               14
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V5, binary
                  cls
clus                0  1
  ZNF493 MUTATED    3  6
  ZNF493 WILD-TYPE 32 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      3    6
  ZNF493 WILD-TYPE   32   83
   clus
vv  ZNF493 MUTATED ZNF493 WILD-TYPE
  0              3               32
  1              6               83
[1] 2 2
[1] FALSE
D274V6, binary
                  cls
clus                0  1
  ZNF493 MUTATED    4  1
  ZNF493 WILD-TYPE 53  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      4    1
  ZNF493 WILD-TYPE   53    2
   clus
vv  ZNF493 MUTATED ZNF493 WILD-TYPE
  0              4               53
  1              1                2
[1] 2 2
[1] FALSE
D274V7, binary
                  cls
clus                0  1
  ZNF493 MUTATED    4  5
  ZNF493 WILD-TYPE 47 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      4    5
  ZNF493 WILD-TYPE   47   70
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  FEMALE              4               47
  MALE                5               70
[1] 2 2
[1] FALSE
D274V8, binary
                  cls
clus                0  1
  ZNF493 MUTATED    7  1
  ZNF493 WILD-TYPE 81 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      7    1
  ZNF493 WILD-TYPE   81   29
     clus
vv    ZNF493 MUTATED ZNF493 WILD-TYPE
  NO               7               81
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF493 MUTATED                                     6
  ZNF493 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF493 MUTATED                                       2
  ZNF493 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF493 MUTATED                                                  0
  ZNF493 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF493 MUTATED                                     0
  ZNF493 WILD-TYPE                                   1
D274V9, multiclass
                                                  clus
vv                                                 ZNF493 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF493 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V10, continuous
D274V11, continuous
[1] "Remove cluster labels:" "ZNF493 MUTATED"        
clus
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-IB-7885       TCGA-IB-8126 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" "ZNF493 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF493 MUTATED    6  1  0  0
  ZNF493 WILD-TYPE 74 34  4  2
D274V12, multiclass
    clus
vv   ZNF493 MUTATED ZNF493 WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF493 MUTATED       0                         0     9
  ZNF493 WILD-TYPE     6                         5   105
D274V14, multiclass
                           clus
vv                          ZNF493 MUTATED ZNF493 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V15, binary
                  cls
clus                0  1
  ZNF493 MUTATED    0  7
  ZNF493 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      0    7
  ZNF493 WILD-TYPE    5   84
                        clus
vv                       ZNF493 MUTATED ZNF493 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(275) Variable = HMGB1 MUTATION ANALYSIS
D275V1, survival
                 sevent
clus2              0  1
  HMGB1 MUTATED    5  0
  HMGB1 WILD-TYPE 58 62
  HMGB1 MUTATED HMGB1 WILD-TYPE 
              5             120 
  HMGB1 MUTATED HMGB1 WILD-TYPE 
              0              62 
$`HMGB1 MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9IX TCGA-H8-A6C1 TCGA-RB-AA9M TCGA-XD-AAUH 
       60.95        34.09        22.06         9.40        12.99 

$`HMGB1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI 
       39.98        16.80         0.39        18.67        13.81        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  HMGB1 MUTATED HMGB1 WILD-TYPE 
           9.40            0.23 
  HMGB1 MUTATED HMGB1 WILD-TYPE 
          60.95           90.12 
  HMGB1 MUTATED HMGB1 WILD-TYPE 
         22.060          15.205 
[1] "9.4 - 61.0 (22.1)" "0.2 - 90.1 (15.2)"
[1] "hr="     "2.6e+07"
D275V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HMGB1 MUTATED         0        1        1         1         2         0
  HMGB1 WILD-TYPE       1        2       11        18        80         4
                 vv
clus              STAGE IV
  HMGB1 MUTATED          0
  HMGB1 WILD-TYPE        3
D275V3, multiclass
           clus
vv          HMGB1 MUTATED HMGB1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  HMGB1 MUTATED     2   1     2
  HMGB1 WILD-TYPE   3  16   100
D275V4, multiclass
       clus
vv      HMGB1 MUTATED HMGB1 WILD-TYPE
  T1                2               3
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V5, binary
                 cls
clus               0  1
  HMGB1 MUTATED    3  2
  HMGB1 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGB1 MUTATED      3    2
  HMGB1 WILD-TYPE   32   87
   clus
vv  HMGB1 MUTATED HMGB1 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D275V6, binary
                 cls
clus               0  1
  HMGB1 MUTATED    1  0
  HMGB1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGB1 MUTATED      1    0
  HMGB1 WILD-TYPE   56    3
   clus
vv  HMGB1 MUTATED HMGB1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D275V7, binary
                 cls
clus               0  1
  HMGB1 MUTATED    1  4
  HMGB1 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGB1 MUTATED      1    4
  HMGB1 WILD-TYPE   50   71
        clus
vv       HMGB1 MUTATED HMGB1 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D275V8, binary
                 cls
clus               0  1
  HMGB1 MUTATED    2  3
  HMGB1 WILD-TYPE 86 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGB1 MUTATED      2    3
  HMGB1 WILD-TYPE   86   27
     clus
vv    HMGB1 MUTATED HMGB1 WILD-TYPE
  NO              2              86
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HMGB1 MUTATED                                     3
  HMGB1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HMGB1 MUTATED                                       2
  HMGB1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HMGB1 MUTATED                                                  0
  HMGB1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HMGB1 MUTATED                                     0
  HMGB1 WILD-TYPE                                   1
D275V9, multiclass
                                                  clus
vv                                                 HMGB1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HMGB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V10, continuous
D275V11, continuous
                 vv
clus              R0 R1 R2 RX
  HMGB1 MUTATED    4  0  1  0
  HMGB1 WILD-TYPE 76 35  3  2
D275V12, multiclass
    clus
vv   HMGB1 MUTATED HMGB1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMGB1 MUTATED       0                         0     5
  HMGB1 WILD-TYPE     6                         5   109
D275V14, multiclass
                           clus
vv                          HMGB1 MUTATED HMGB1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V15, binary
                 cls
clus               0  1
  HMGB1 MUTATED    0  5
  HMGB1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGB1 MUTATED      0    5
  HMGB1 WILD-TYPE    5   86
                        clus
vv                       HMGB1 MUTATED HMGB1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(276) Variable = NKAP MUTATION ANALYSIS
D276V1, survival
                sevent
clus2             0  1
  NKAP MUTATED    2  2
  NKAP WILD-TYPE 61 60
  NKAP MUTATED NKAP WILD-TYPE 
             4            121 
  NKAP MUTATED NKAP WILD-TYPE 
             2             60 
$`NKAP MUTATED`
TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-XN-A8T5 TCGA-YH-A8SY 
        5.03        19.82        23.67        12.76 

$`NKAP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        12.03        31.27        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  NKAP MUTATED NKAP WILD-TYPE 
          5.03           0.23 
  NKAP MUTATED NKAP WILD-TYPE 
         23.67          90.12 
  NKAP MUTATED NKAP WILD-TYPE 
         16.29          15.22 
[1] "5.0 - 23.7 (16.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D276V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NKAP MUTATED         0        0        1         0         2         1
  NKAP WILD-TYPE       1        3       11        19        80         3
                vv
clus             STAGE IV
  NKAP MUTATED          0
  NKAP WILD-TYPE        3
D276V3, multiclass
           clus
vv          NKAP MUTATED NKAP WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NKAP MUTATED    0  1     3
  NKAP WILD-TYPE  5 16    99
D276V4, multiclass
       clus
vv      NKAP MUTATED NKAP WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V5, binary
                cls
clus              0  1
  NKAP MUTATED    1  3
  NKAP WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKAP MUTATED      1    3
  NKAP WILD-TYPE   34   86
   clus
vv  NKAP MUTATED NKAP WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D276V6, binary
                cls
clus              0  1
  NKAP MUTATED    2  0
  NKAP WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKAP MUTATED      2    0
  NKAP WILD-TYPE   55    3
   clus
vv  NKAP MUTATED NKAP WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D276V7, binary
                cls
clus              0  1
  NKAP MUTATED    4  0
  NKAP WILD-TYPE 47 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKAP MUTATED      4    0
  NKAP WILD-TYPE   47   75
        clus
vv       NKAP MUTATED NKAP WILD-TYPE
  FEMALE            4             47
  MALE              0             75
[1] 2 2
[1] FALSE
D276V8, binary
                cls
clus              0  1
  NKAP MUTATED    2  2
  NKAP WILD-TYPE 86 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKAP MUTATED      2    2
  NKAP WILD-TYPE   86   28
     clus
vv    NKAP MUTATED NKAP WILD-TYPE
  NO             2             86
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NKAP MUTATED                                     2
  NKAP WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NKAP MUTATED                                       1
  NKAP WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NKAP MUTATED                                                  0
  NKAP WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NKAP MUTATED                                     0
  NKAP WILD-TYPE                                   1
D276V9, multiclass
                                                  clus
vv                                                 NKAP MUTATED NKAP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V10, continuous
[1] "Remove cluster labels:" "NKAP MUTATED"          
clus
  NKAP MUTATED NKAP WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-YY-A8LH 
"NKAP WILD-TYPE" 
D276V11, continuous
[1] "Remove cluster labels:" "NKAP MUTATED"          
clus
  NKAP MUTATED NKAP WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-YY-A8LH 
"NKAP WILD-TYPE" "NKAP WILD-TYPE" "NKAP WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  NKAP MUTATED    1  2  0  0
  NKAP WILD-TYPE 79 33  4  2
D276V12, multiclass
    clus
vv   NKAP MUTATED NKAP WILD-TYPE
  R0            1             79
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NKAP MUTATED       0                         0     4
  NKAP WILD-TYPE     6                         5   110
D276V14, multiclass
                           clus
vv                          NKAP MUTATED NKAP WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V15, binary
                cls
clus              0  1
  NKAP MUTATED    1  3
  NKAP WILD-TYPE  4 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKAP MUTATED      1    3
  NKAP WILD-TYPE    4   88
                        clus
vv                       NKAP MUTATED NKAP WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(277) Variable = ZFP36 MUTATION ANALYSIS
D277V1, survival
                 sevent
clus2              0  1
  ZFP36 MUTATED    4  0
  ZFP36 WILD-TYPE 59 62
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              4             121 
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              0              62 
$`ZFP36 MUTATED`
TCGA-HZ-A9TJ TCGA-IB-8126 TCGA-US-A776 TCGA-XD-AAUH 
       19.82        15.19        39.98        12.99 

$`ZFP36 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZFP36 MUTATED ZFP36 WILD-TYPE 
          12.99            0.23 
  ZFP36 MUTATED ZFP36 WILD-TYPE 
          39.98           90.12 
  ZFP36 MUTATED ZFP36 WILD-TYPE 
         17.505          15.220 
[1] "13.0 - 40.0 (17.5)" "0.2 - 90.1 (15.2)" 
[1] "hr="     "2.6e+07"
D277V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZFP36 MUTATED         0        0        0         1         1         1
  ZFP36 WILD-TYPE       1        3       12        18        81         3
                 vv
clus              STAGE IV
  ZFP36 MUTATED          1
  ZFP36 WILD-TYPE        2
D277V3, multiclass
           clus
vv          ZFP36 MUTATED ZFP36 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZFP36 MUTATED    0  0     4
  ZFP36 WILD-TYPE  5 17    98
D277V4, multiclass
       clus
vv      ZFP36 MUTATED ZFP36 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V5, binary
                 cls
clus               0  1
  ZFP36 MUTATED    2  2
  ZFP36 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP36 MUTATED      2    2
  ZFP36 WILD-TYPE   33   87
   clus
vv  ZFP36 MUTATED ZFP36 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D277V6, binary
                 cls
clus               0  1
  ZFP36 MUTATED    2  1
  ZFP36 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP36 MUTATED      2    1
  ZFP36 WILD-TYPE   55    2
   clus
vv  ZFP36 MUTATED ZFP36 WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D277V7, binary
                 cls
clus               0  1
  ZFP36 MUTATED    2  2
  ZFP36 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP36 MUTATED      2    2
  ZFP36 WILD-TYPE   49   73
        clus
vv       ZFP36 MUTATED ZFP36 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D277V8, binary
                 cls
clus               0  1
  ZFP36 MUTATED    3  1
  ZFP36 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP36 MUTATED      3    1
  ZFP36 WILD-TYPE   85   29
     clus
vv    ZFP36 MUTATED ZFP36 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZFP36 MUTATED                                     2
  ZFP36 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZFP36 MUTATED                                       1
  ZFP36 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZFP36 MUTATED                                                  1
  ZFP36 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZFP36 MUTATED                                     0
  ZFP36 WILD-TYPE                                   1
D277V9, multiclass
                                                  clus
vv                                                 ZFP36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZFP36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V10, continuous
[1] "Remove cluster labels:" "ZFP36 MUTATED"         
clus
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-A6UF 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
D277V11, continuous
[1] "Remove cluster labels:" "ZFP36 MUTATED"         
clus
  ZFP36 MUTATED ZFP36 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" "ZFP36 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZFP36 MUTATED    2  1  1  0
  ZFP36 WILD-TYPE 78 34  3  2
D277V12, multiclass
    clus
vv   ZFP36 MUTATED ZFP36 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36 MUTATED       0                         0     4
  ZFP36 WILD-TYPE     6                         5   110
D277V14, multiclass
                           clus
vv                          ZFP36 MUTATED ZFP36 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V15, binary
                 cls
clus               0  1
  ZFP36 MUTATED    0  4
  ZFP36 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP36 MUTATED      0    4
  ZFP36 WILD-TYPE    5   87
                        clus
vv                       ZFP36 MUTATED ZFP36 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(278) Variable = GIT1 MUTATION ANALYSIS
D278V1, survival
                sevent
clus2             0  1
  GIT1 MUTATED    2  3
  GIT1 WILD-TYPE 61 59
  GIT1 MUTATED GIT1 WILD-TYPE 
             5            120 
  GIT1 MUTATED GIT1 WILD-TYPE 
             3             59 
$`GIT1 MUTATED`
TCGA-LB-A7SX TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A6UG TCGA-XD-AAUG 
       12.92        19.82        15.19         1.35        13.81 

$`GIT1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        18.67        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  GIT1 MUTATED GIT1 WILD-TYPE 
          1.35           0.23 
  GIT1 MUTATED GIT1 WILD-TYPE 
         19.82          90.12 
  GIT1 MUTATED GIT1 WILD-TYPE 
        13.810         15.335 
[1] "1.4 - 19.8 (13.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D278V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GIT1 MUTATED         0        0        0         0         3         1
  GIT1 WILD-TYPE       1        3       12        19        79         3
                vv
clus             STAGE IV
  GIT1 MUTATED          1
  GIT1 WILD-TYPE        2
D278V3, multiclass
           clus
vv          GIT1 MUTATED GIT1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            1              3
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  GIT1 MUTATED    0  0     5
  GIT1 WILD-TYPE  5 17    97
D278V4, multiclass
       clus
vv      GIT1 MUTATED GIT1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V5, binary
                cls
clus              0  1
  GIT1 MUTATED    0  5
  GIT1 WILD-TYPE 35 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      0    5
  GIT1 WILD-TYPE   35   84
   clus
vv  GIT1 MUTATED GIT1 WILD-TYPE
  0            0             35
  1            5             84
[1] 2 2
[1] FALSE
D278V6, binary
                cls
clus              0  1
  GIT1 MUTATED    3  1
  GIT1 WILD-TYPE 54  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      3    1
  GIT1 WILD-TYPE   54    2
   clus
vv  GIT1 MUTATED GIT1 WILD-TYPE
  0            3             54
  1            1              2
[1] 2 2
[1] FALSE
D278V7, binary
                cls
clus              0  1
  GIT1 MUTATED    4  1
  GIT1 WILD-TYPE 47 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      4    1
  GIT1 WILD-TYPE   47   74
        clus
vv       GIT1 MUTATED GIT1 WILD-TYPE
  FEMALE            4             47
  MALE              1             74
[1] 2 2
[1] FALSE
D278V8, binary
                cls
clus              0  1
  GIT1 MUTATED    5  0
  GIT1 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      5    0
  GIT1 WILD-TYPE   83   30
     clus
vv    GIT1 MUTATED GIT1 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GIT1 MUTATED                                     5
  GIT1 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GIT1 MUTATED                                       0
  GIT1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GIT1 MUTATED                                                  0
  GIT1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  GIT1 MUTATED                                     0
  GIT1 WILD-TYPE                                   1
D278V9, multiclass
                                                  clus
vv                                                 GIT1 MUTATED GIT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V10, continuous
D278V11, continuous
                vv
clus             R0 R1 R2 RX
  GIT1 MUTATED    2  3  0  0
  GIT1 WILD-TYPE 78 32  4  2
D278V12, multiclass
    clus
vv   GIT1 MUTATED GIT1 WILD-TYPE
  R0            2             78
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GIT1 MUTATED       0                         1     4
  GIT1 WILD-TYPE     6                         4   110
D278V14, multiclass
                           clus
vv                          GIT1 MUTATED GIT1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V15, binary
                cls
clus              0  1
  GIT1 MUTATED    0  5
  GIT1 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      0    5
  GIT1 WILD-TYPE    5   86
                        clus
vv                       GIT1 MUTATED GIT1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(279) Variable = RUNX1T1 MUTATION ANALYSIS
D279V1, survival
                   sevent
clus2                0  1
  RUNX1T1 MUTATED    3  2
  RUNX1T1 WILD-TYPE 60 60
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
                5               120 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
                2                60 
$`RUNX1T1 MUTATED`
TCGA-US-A77E TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A7M4 TCGA-IB-AAUU 
       14.14        32.15        19.82        15.88         8.05 

$`RUNX1T1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
             8.05              0.23 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
            32.15             90.12 
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
           15.880            15.205 
[1] "8.1 - 32.1 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D279V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RUNX1T1 MUTATED         0        0        0         0         5         0
  RUNX1T1 WILD-TYPE       1        3       12        19        77         4
                   vv
clus                STAGE IV
  RUNX1T1 MUTATED          0
  RUNX1T1 WILD-TYPE        3
D279V3, multiclass
           clus
vv          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  RUNX1T1 MUTATED    0  0     5
  RUNX1T1 WILD-TYPE  5 17    97
D279V4, multiclass
       clus
vv      RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V5, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED    0  5
  RUNX1T1 WILD-TYPE 35 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      0    5
  RUNX1T1 WILD-TYPE   35   84
   clus
vv  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  0               0                35
  1               5                84
[1] 2 2
[1] FALSE
D279V6, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED    3  0
  RUNX1T1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      3    0
  RUNX1T1 WILD-TYPE   54    3
   clus
vv  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D279V7, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED    1  4
  RUNX1T1 WILD-TYPE 50 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      1    4
  RUNX1T1 WILD-TYPE   50   71
        clus
vv       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  FEMALE               1                50
  MALE                 4                71
[1] 2 2
[1] FALSE
D279V8, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED    4  1
  RUNX1T1 WILD-TYPE 84 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      4    1
  RUNX1T1 WILD-TYPE   84   29
     clus
vv    RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  NO                4                84
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RUNX1T1 MUTATED                                     3
  RUNX1T1 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RUNX1T1 MUTATED                                       2
  RUNX1T1 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RUNX1T1 MUTATED                                                  0
  RUNX1T1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  RUNX1T1 MUTATED                                     0
  RUNX1T1 WILD-TYPE                                   1
D279V9, multiclass
                                                  clus
vv                                                 RUNX1T1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 RUNX1T1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V10, continuous
D279V11, continuous
[1] "Remove cluster labels:" "RUNX1T1 MUTATED"       
clus
  RUNX1T1 MUTATED RUNX1T1 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-AAUQ 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" "RUNX1T1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  RUNX1T1 MUTATED    4  1  0  0
  RUNX1T1 WILD-TYPE 76 34  4  2
D279V12, multiclass
    clus
vv   RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  R0               4                76
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1T1 MUTATED       1                         0     4
  RUNX1T1 WILD-TYPE     5                         5   110
D279V14, multiclass
                           clus
vv                          RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V15, binary
                   cls
clus                 0  1
  RUNX1T1 MUTATED    0  4
  RUNX1T1 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNX1T1 MUTATED      0    4
  RUNX1T1 WILD-TYPE    5   87
                        clus
vv                       RUNX1T1 MUTATED RUNX1T1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(280) Variable = RP1L1 MUTATION ANALYSIS
D280V1, survival
                 sevent
clus2              0  1
  RP1L1 MUTATED    4 10
  RP1L1 WILD-TYPE 59 52
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             14             111 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             10              52 
$`RP1L1 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQI TCGA-3E-AAAZ TCGA-FB-AAQ1 TCGA-HZ-A49I TCGA-HZ-A77P 
        4.70         3.39        71.74         4.04        10.13        10.85 
TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A7LX TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-OE-A75W 
       19.82        15.19         8.22        14.17         6.02         8.78 
TCGA-US-A77G TCGA-XN-A8T3 
        0.39        31.27 

$`RP1L1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQJ 
       14.47        15.22         9.11        21.44        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       17.00         5.26         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         0.26         4.73         7.86        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RP1L1 MUTATED RP1L1 WILD-TYPE 
           0.39            0.23 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          71.74           90.12 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          9.455          15.780 
[1] "0.4 - 71.7 (9.5)"  "0.2 - 90.1 (15.8)"
[1] "hr=" "2.3"
D280V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RP1L1 MUTATED         0        0        1         2        10         1
  RP1L1 WILD-TYPE       1        3       11        17        72         3
                 vv
clus              STAGE IV
  RP1L1 MUTATED          0
  RP1L1 WILD-TYPE        3
D280V3, multiclass
           clus
vv          RP1L1 MUTATED RP1L1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB            10              72
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RP1L1 MUTATED    0  1    13
  RP1L1 WILD-TYPE  5 16    89
D280V4, multiclass
       clus
vv      RP1L1 MUTATED RP1L1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            13              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V5, binary
                 cls
clus               0  1
  RP1L1 MUTATED    3 11
  RP1L1 WILD-TYPE 32 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      3   11
  RP1L1 WILD-TYPE   32   78
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0             3              32
  1            11              78
[1] 2 2
[1] FALSE
D280V6, binary
                 cls
clus               0  1
  RP1L1 MUTATED    6  0
  RP1L1 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      6    0
  RP1L1 WILD-TYPE   51    3
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D280V7, binary
                 cls
clus               0  1
  RP1L1 MUTATED    2 12
  RP1L1 WILD-TYPE 49 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      2   12
  RP1L1 WILD-TYPE   49   63
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  FEMALE             2              49
  MALE              12              63
[1] 2 2
[1] FALSE
D280V8, binary
                 cls
clus               0  1
  RP1L1 MUTATED   10  3
  RP1L1 WILD-TYPE 78 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     10    3
  RP1L1 WILD-TYPE   78   27
     clus
vv    RP1L1 MUTATED RP1L1 WILD-TYPE
  NO             10              78
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RP1L1 MUTATED                                    13
  RP1L1 WILD-TYPE                                  92
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RP1L1 MUTATED                                       1
  RP1L1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RP1L1 MUTATED                                                  0
  RP1L1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RP1L1 MUTATED                                     0
  RP1L1 WILD-TYPE                                   1
D280V9, multiclass
                                                  clus
vv                                                 RP1L1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RP1L1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           92
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V10, continuous
D280V11, continuous
                 vv
clus              R0 R1 R2 RX
  RP1L1 MUTATED    5  8  0  0
  RP1L1 WILD-TYPE 75 27  4  2
D280V12, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  R0             5              75
  R1             8              27
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RP1L1 MUTATED       0                         0    14
  RP1L1 WILD-TYPE     6                         5   100
D280V14, multiclass
                           clus
vv                          RP1L1 MUTATED RP1L1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                14             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V15, binary
                 cls
clus               0  1
  RP1L1 MUTATED    2 10
  RP1L1 WILD-TYPE  3 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      2   10
  RP1L1 WILD-TYPE    3   81
                        clus
vv                       RP1L1 MUTATED RP1L1 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO            10              81
[1] 2 2
[1] FALSE

Clustering(281) Variable = AP2A2 MUTATION ANALYSIS
D281V1, survival
                 sevent
clus2              0  1
  AP2A2 MUTATED    3  2
  AP2A2 WILD-TYPE 60 60
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              5             120 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              2              60 
$`AP2A2 MUTATED`
TCGA-3A-A9IJ TCGA-IB-7651 TCGA-US-A776 TCGA-US-A77J TCGA-YH-A8SY 
       60.95        19.82        39.98        18.67        12.76 

$`AP2A2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        9.40         0.30        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  AP2A2 MUTATED AP2A2 WILD-TYPE 
          12.76            0.23 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
          60.95           90.12 
  AP2A2 MUTATED AP2A2 WILD-TYPE 
         19.820          15.155 
[1] "12.8 - 61.0 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.9"
D281V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AP2A2 MUTATED         0        0        1         1         2         1
  AP2A2 WILD-TYPE       1        3       11        18        80         3
                 vv
clus              STAGE IV
  AP2A2 MUTATED          0
  AP2A2 WILD-TYPE        3
D281V3, multiclass
           clus
vv          AP2A2 MUTATED AP2A2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AP2A2 MUTATED    0  1     4
  AP2A2 WILD-TYPE  5 16    98
D281V4, multiclass
       clus
vv      AP2A2 MUTATED AP2A2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V5, binary
                 cls
clus               0  1
  AP2A2 MUTATED    2  3
  AP2A2 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      2    3
  AP2A2 WILD-TYPE   33   86
   clus
vv  AP2A2 MUTATED AP2A2 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D281V6, binary
                 cls
clus               0  1
  AP2A2 MUTATED    1  0
  AP2A2 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      1    0
  AP2A2 WILD-TYPE   56    3
   clus
vv  AP2A2 MUTATED AP2A2 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D281V7, binary
                 cls
clus               0  1
  AP2A2 MUTATED    3  2
  AP2A2 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      3    2
  AP2A2 WILD-TYPE   48   73
        clus
vv       AP2A2 MUTATED AP2A2 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D281V8, binary
                 cls
clus               0  1
  AP2A2 MUTATED    3  1
  AP2A2 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      3    1
  AP2A2 WILD-TYPE   85   29
     clus
vv    AP2A2 MUTATED AP2A2 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AP2A2 MUTATED                                     2
  AP2A2 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AP2A2 MUTATED                                       1
  AP2A2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AP2A2 MUTATED                                                  1
  AP2A2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AP2A2 MUTATED                                     0
  AP2A2 WILD-TYPE                                   1
D281V9, multiclass
                                                  clus
vv                                                 AP2A2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 AP2A2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V10, continuous
[1] "Remove cluster labels:" "AP2A2 MUTATED"         
clus
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              2              37 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-YY-A8LH 
"AP2A2 WILD-TYPE" 
D281V11, continuous
[1] "Remove cluster labels:" "AP2A2 MUTATED"         
clus
  AP2A2 MUTATED AP2A2 WILD-TYPE 
              2              31 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" "AP2A2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  AP2A2 MUTATED    4  0  0  0
  AP2A2 WILD-TYPE 76 35  4  2
D281V12, multiclass
    clus
vv   AP2A2 MUTATED AP2A2 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AP2A2 MUTATED       0                         0     5
  AP2A2 WILD-TYPE     6                         5   109
D281V14, multiclass
                           clus
vv                          AP2A2 MUTATED AP2A2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V15, binary
                 cls
clus               0  1
  AP2A2 MUTATED    0  5
  AP2A2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP2A2 MUTATED      0    5
  AP2A2 WILD-TYPE    5   86
                        clus
vv                       AP2A2 MUTATED AP2A2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(282) Variable = EIF5B MUTATION ANALYSIS
D282V1, survival
                 sevent
clus2              0  1
  EIF5B MUTATED    2  3
  EIF5B WILD-TYPE 61 59
  EIF5B MUTATED EIF5B WILD-TYPE 
              5             120 
  EIF5B MUTATED EIF5B WILD-TYPE 
              3              59 
$`EIF5B MUTATED`
TCGA-XD-AAUL TCGA-3A-A9IH TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-A6UG 
       16.37        33.57        10.13        19.82         1.35 

$`EIF5B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  EIF5B MUTATED EIF5B WILD-TYPE 
           1.35            0.23 
  EIF5B MUTATED EIF5B WILD-TYPE 
          33.57           90.12 
  EIF5B MUTATED EIF5B WILD-TYPE 
         16.370          15.205 
[1] "1.4 - 33.6 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D282V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EIF5B MUTATED         0        1        0         1         3         0
  EIF5B WILD-TYPE       1        2       12        18        79         4
                 vv
clus              STAGE IV
  EIF5B MUTATED          0
  EIF5B WILD-TYPE        3
D282V3, multiclass
           clus
vv          EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  EIF5B MUTATED    1  0     4
  EIF5B WILD-TYPE  4 17    98
D282V4, multiclass
       clus
vv      EIF5B MUTATED EIF5B WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V5, binary
                 cls
clus               0  1
  EIF5B MUTATED    2  3
  EIF5B WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      2    3
  EIF5B WILD-TYPE   33   86
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D282V6, binary
                 cls
clus               0  1
  EIF5B MUTATED    2  0
  EIF5B WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      2    0
  EIF5B WILD-TYPE   55    3
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D282V7, binary
                 cls
clus               0  1
  EIF5B MUTATED    2  3
  EIF5B WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      2    3
  EIF5B WILD-TYPE   49   72
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D282V8, binary
                 cls
clus               0  1
  EIF5B MUTATED    4  1
  EIF5B WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      4    1
  EIF5B WILD-TYPE   84   29
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EIF5B MUTATED                                     5
  EIF5B WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EIF5B MUTATED                                       0
  EIF5B WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EIF5B MUTATED                                                  0
  EIF5B WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EIF5B MUTATED                                     0
  EIF5B WILD-TYPE                                   1
D282V9, multiclass
                                                  clus
vv                                                 EIF5B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 EIF5B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V10, continuous
D282V11, continuous
                 vv
clus              R0 R1 R2 RX
  EIF5B MUTATED    3  2  0  0
  EIF5B WILD-TYPE 77 33  4  2
D282V12, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF5B MUTATED       0                         0     5
  EIF5B WILD-TYPE     6                         5   109
D282V14, multiclass
                           clus
vv                          EIF5B MUTATED EIF5B WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V15, binary
                 cls
clus               0  1
  EIF5B MUTATED    0  5
  EIF5B WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      0    5
  EIF5B WILD-TYPE    5   86
                        clus
vv                       EIF5B MUTATED EIF5B WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(283) Variable = WHSC1L1 MUTATION ANALYSIS
D283V1, survival
                   sevent
clus2                0  1
  WHSC1L1 MUTATED    4  2
  WHSC1L1 WILD-TYPE 59 60
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                6               119 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                60 
$`WHSC1L1 MUTATED`
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-HZ-A49I TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-AAUU 
       24.26        63.85        10.13        36.69        15.19         8.05 

$`WHSC1L1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
        7.36        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        19.82        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
             8.05              0.23 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
            63.85             90.12 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
           19.725            15.220 
[1] "8.1 - 63.9 (19.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D283V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WHSC1L1 MUTATED         0        0        0         0         4         1
  WHSC1L1 WILD-TYPE       1        3       12        19        78         3
                   vv
clus                STAGE IV
  WHSC1L1 MUTATED          0
  WHSC1L1 WILD-TYPE        3
D283V3, multiclass
           clus
vv          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  WHSC1L1 MUTATED    0  0     5
  WHSC1L1 WILD-TYPE  5 17    97
D283V4, multiclass
       clus
vv      WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V5, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    0  5
  WHSC1L1 WILD-TYPE 35 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0    5
  WHSC1L1 WILD-TYPE   35   84
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0               0                35
  1               5                84
[1] 2 2
[1] FALSE
D283V6, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    3  0
  WHSC1L1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      3    0
  WHSC1L1 WILD-TYPE   54    3
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D283V7, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    3  3
  WHSC1L1 WILD-TYPE 48 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      3    3
  WHSC1L1 WILD-TYPE   48   72
        clus
vv       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  FEMALE               3                48
  MALE                 3                72
[1] 2 2
[1] FALSE
D283V8, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    4  2
  WHSC1L1 WILD-TYPE 84 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      4    2
  WHSC1L1 WILD-TYPE   84   28
     clus
vv    WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  NO                4                84
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WHSC1L1 MUTATED                                     5
  WHSC1L1 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WHSC1L1 MUTATED                                       1
  WHSC1L1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WHSC1L1 MUTATED                                                  0
  WHSC1L1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  WHSC1L1 MUTATED                                     0
  WHSC1L1 WILD-TYPE                                   1
D283V9, multiclass
                                                  clus
vv                                                 WHSC1L1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 WHSC1L1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V10, continuous
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
clus
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-A6UF 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-YY-A8LH 
"WHSC1L1 WILD-TYPE" 
D283V11, continuous
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
clus
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  WHSC1L1 MUTATED    3  3  0  0
  WHSC1L1 WILD-TYPE 77 32  4  2
D283V12, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  R0               3                77
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WHSC1L1 MUTATED       1                         0     5
  WHSC1L1 WILD-TYPE     5                         5   109
D283V14, multiclass
                           clus
vv                          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V15, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    0  6
  WHSC1L1 WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0    6
  WHSC1L1 WILD-TYPE    5   85
                        clus
vv                       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(284) Variable = BRCA2 MUTATION ANALYSIS
D284V1, survival
                 sevent
clus2              0  1
  BRCA2 MUTATED    3  4
  BRCA2 WILD-TYPE 60 58
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              7             118 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              4              58 
$`BRCA2 MUTATED`
TCGA-3A-A9IO TCGA-FB-AAPU TCGA-HZ-A49I TCGA-IB-7651 TCGA-IB-A6UF TCGA-US-A776 
       63.85        12.53        10.13        19.82        21.90        39.98 
TCGA-US-A77J 
       18.67 

$`BRCA2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
       13.68         3.12        15.32         9.40         0.30        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
          10.13            0.23 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
          63.85           90.12 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         19.820          15.155 
[1] "10.1 - 63.9 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D284V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BRCA2 MUTATED         0        0        0         2         4         0
  BRCA2 WILD-TYPE       1        3       12        17        78         4
                 vv
clus              STAGE IV
  BRCA2 MUTATED          0
  BRCA2 WILD-TYPE        3
D284V3, multiclass
           clus
vv          BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  BRCA2 MUTATED    0  0     6
  BRCA2 WILD-TYPE  5 17    96
D284V4, multiclass
       clus
vv      BRCA2 MUTATED BRCA2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V5, binary
                 cls
clus               0  1
  BRCA2 MUTATED    2  4
  BRCA2 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      2    4
  BRCA2 WILD-TYPE   33   85
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D284V6, binary
                 cls
clus               0  1
  BRCA2 MUTATED    2  0
  BRCA2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      2    0
  BRCA2 WILD-TYPE   55    3
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D284V7, binary
                 cls
clus               0  1
  BRCA2 MUTATED    3  4
  BRCA2 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      3    4
  BRCA2 WILD-TYPE   48   71
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D284V8, binary
                 cls
clus               0  1
  BRCA2 MUTATED    5  1
  BRCA2 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      5    1
  BRCA2 WILD-TYPE   83   29
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRCA2 MUTATED                                     5
  BRCA2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRCA2 MUTATED                                       1
  BRCA2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRCA2 MUTATED                                                  1
  BRCA2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  BRCA2 MUTATED                                     0
  BRCA2 WILD-TYPE                                   1
D284V9, multiclass
                                                  clus
vv                                                 BRCA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 BRCA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V10, continuous
[1] "Remove cluster labels:" "BRCA2 MUTATED"         
clus
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-YY-A8LH 
"BRCA2 WILD-TYPE" 
D284V11, continuous
[1] "Remove cluster labels:" "BRCA2 MUTATED"         
clus
  BRCA2 MUTATED BRCA2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" "BRCA2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  BRCA2 MUTATED    4  3  0  0
  BRCA2 WILD-TYPE 76 32  4  2
D284V12, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  R0             4              76
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRCA2 MUTATED       1                         0     6
  BRCA2 WILD-TYPE     5                         5   108
D284V14, multiclass
                           clus
vv                          BRCA2 MUTATED BRCA2 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V15, binary
                 cls
clus               0  1
  BRCA2 MUTATED    0  7
  BRCA2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED      0    7
  BRCA2 WILD-TYPE    5   84
                        clus
vv                       BRCA2 MUTATED BRCA2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(285) Variable = E2F8 MUTATION ANALYSIS
D285V1, survival
                sevent
clus2             0  1
  E2F8 MUTATED    0  4
  E2F8 WILD-TYPE 63 58
  E2F8 MUTATED E2F8 WILD-TYPE 
             4            121 
  E2F8 MUTATED E2F8 WILD-TYPE 
             4             58 
$`E2F8 MUTATED`
TCGA-2J-AABF TCGA-2L-AAQA TCGA-2L-AAQL TCGA-IB-7651 
       22.72         4.70         9.60        19.82 

$`E2F8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  E2F8 MUTATED E2F8 WILD-TYPE 
          4.70           0.23 
  E2F8 MUTATED E2F8 WILD-TYPE 
         22.72          90.12 
  E2F8 MUTATED E2F8 WILD-TYPE 
         14.71          15.22 
[1] "4.7 - 22.7 (14.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.4"
D285V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  E2F8 MUTATED         0        0        0         0         4         0
  E2F8 WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  E2F8 MUTATED          0
  E2F8 WILD-TYPE        3
D285V3, multiclass
           clus
vv          E2F8 MUTATED E2F8 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  E2F8 MUTATED    0  0     4
  E2F8 WILD-TYPE  5 17    98
D285V4, multiclass
       clus
vv      E2F8 MUTATED E2F8 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V5, binary
                cls
clus              0  1
  E2F8 MUTATED    0  4
  E2F8 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F8 MUTATED      0    4
  E2F8 WILD-TYPE   35   85
   clus
vv  E2F8 MUTATED E2F8 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D285V6, binary
                cls
clus              0  1
  E2F8 MUTATED    2  0
  E2F8 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F8 MUTATED      2    0
  E2F8 WILD-TYPE   55    3
   clus
vv  E2F8 MUTATED E2F8 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D285V7, binary
                cls
clus              0  1
  E2F8 MUTATED    1  3
  E2F8 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F8 MUTATED      1    3
  E2F8 WILD-TYPE   50   72
        clus
vv       E2F8 MUTATED E2F8 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D285V8, binary
                cls
clus              0  1
  E2F8 MUTATED    3  1
  E2F8 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F8 MUTATED      3    1
  E2F8 WILD-TYPE   85   29
     clus
vv    E2F8 MUTATED E2F8 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  E2F8 MUTATED                                     4
  E2F8 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  E2F8 MUTATED                                       0
  E2F8 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  E2F8 MUTATED                                                  0
  E2F8 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  E2F8 MUTATED                                     0
  E2F8 WILD-TYPE                                   1
D285V9, multiclass
                                                  clus
vv                                                 E2F8 MUTATED E2F8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V10, continuous
D285V11, continuous
[1] "Remove cluster labels:" "E2F8 MUTATED"          
clus
  E2F8 MUTATED E2F8 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"E2F8 WILD-TYPE" "E2F8 WILD-TYPE" "E2F8 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  E2F8 MUTATED    1  2  0  1
  E2F8 WILD-TYPE 79 33  4  1
D285V12, multiclass
    clus
vv   E2F8 MUTATED E2F8 WILD-TYPE
  R0            1             79
  R1            2             33
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  E2F8 MUTATED       0                         0     4
  E2F8 WILD-TYPE     6                         5   110
D285V14, multiclass
                           clus
vv                          E2F8 MUTATED E2F8 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V15, binary
                cls
clus              0  1
  E2F8 MUTATED    0  1
  E2F8 WILD-TYPE  5 90
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F8 MUTATED      0    1
  E2F8 WILD-TYPE    5   90
                        clus
vv                       E2F8 MUTATED E2F8 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            1             90
[1] 2 2
[1] FALSE

Clustering(286) Variable = SPRR4 MUTATION ANALYSIS
D286V1, survival
                 sevent
clus2              0  1
  SPRR4 MUTATED    4  0
  SPRR4 WILD-TYPE 59 62
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              4             121 
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              0              62 
$`SPRR4 MUTATED`
TCGA-2J-AABT TCGA-H8-A6C1 TCGA-LB-A8F3 TCGA-YY-A8LH 
       10.49        22.06        12.46        66.28 

$`SPRR4 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  SPRR4 MUTATED SPRR4 WILD-TYPE 
          10.49            0.23 
  SPRR4 MUTATED SPRR4 WILD-TYPE 
          66.28           90.12 
  SPRR4 MUTATED SPRR4 WILD-TYPE 
          17.26           15.22 
[1] "10.5 - 66.3 (17.3)" "0.2 - 90.1 (15.2)" 
[1] "hr="     "2.6e+07"
D286V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SPRR4 MUTATED         0        0        0         2         2         0
  SPRR4 WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  SPRR4 MUTATED          0
  SPRR4 WILD-TYPE        3
D286V3, multiclass
           clus
vv          SPRR4 MUTATED SPRR4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SPRR4 MUTATED    0  0     4
  SPRR4 WILD-TYPE  5 17    98
D286V4, multiclass
       clus
vv      SPRR4 MUTATED SPRR4 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V5, binary
                 cls
clus               0  1
  SPRR4 MUTATED    2  2
  SPRR4 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPRR4 MUTATED      2    2
  SPRR4 WILD-TYPE   33   87
   clus
vv  SPRR4 MUTATED SPRR4 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D286V6, binary
                 cls
clus               0  1
  SPRR4 MUTATED    1  0
  SPRR4 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPRR4 MUTATED      1    0
  SPRR4 WILD-TYPE   56    3
   clus
vv  SPRR4 MUTATED SPRR4 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D286V7, binary
                 cls
clus               0  1
  SPRR4 MUTATED    3  1
  SPRR4 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPRR4 MUTATED      3    1
  SPRR4 WILD-TYPE   48   74
        clus
vv       SPRR4 MUTATED SPRR4 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D286V8, binary
                 cls
clus               0  1
  SPRR4 MUTATED    1  2
  SPRR4 WILD-TYPE 87 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPRR4 MUTATED      1    2
  SPRR4 WILD-TYPE   87   28
     clus
vv    SPRR4 MUTATED SPRR4 WILD-TYPE
  NO              1              87
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPRR4 MUTATED                                     3
  SPRR4 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPRR4 MUTATED                                       1
  SPRR4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPRR4 MUTATED                                                  0
  SPRR4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SPRR4 MUTATED                                     0
  SPRR4 WILD-TYPE                                   1
D286V9, multiclass
                                                  clus
vv                                                 SPRR4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SPRR4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V10, continuous
[1] "Remove cluster labels:" "SPRR4 MUTATED"         
clus
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-XN-A8T5 
"SPRR4 WILD-TYPE" 
D286V11, continuous
[1] "Remove cluster labels:" "SPRR4 MUTATED"         
clus
  SPRR4 MUTATED SPRR4 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" "SPRR4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SPRR4 MUTATED    4  0  0  0
  SPRR4 WILD-TYPE 76 35  4  2
D286V12, multiclass
    clus
vv   SPRR4 MUTATED SPRR4 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPRR4 MUTATED       0                         1     3
  SPRR4 WILD-TYPE     6                         4   111
D286V14, multiclass
                           clus
vv                          SPRR4 MUTATED SPRR4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V15, binary
                 cls
clus               0  1
  SPRR4 MUTATED    0  3
  SPRR4 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPRR4 MUTATED      0    3
  SPRR4 WILD-TYPE    5   88
                        clus
vv                       SPRR4 MUTATED SPRR4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(287) Variable = ZMIZ2 MUTATION ANALYSIS
D287V1, survival
                 sevent
clus2              0  1
  ZMIZ2 MUTATED    3  3
  ZMIZ2 WILD-TYPE 60 59
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              6             119 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              3              59 
$`ZMIZ2 MUTATED`
TCGA-S4-A8RO TCGA-F2-A8YN TCGA-FZ-5921 TCGA-IB-7651 TCGA-IB-AAUU TCGA-US-A77G 
       17.26        17.00         5.10        19.82         8.05         0.39 

$`ZMIZ2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
           0.39            0.23 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
          19.82           90.12 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
         12.525          15.220 
[1] "0.4 - 19.8 (12.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D287V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZMIZ2 MUTATED         0        0        0         1         5         0
  ZMIZ2 WILD-TYPE       1        3       12        18        77         4
                 vv
clus              STAGE IV
  ZMIZ2 MUTATED          0
  ZMIZ2 WILD-TYPE        3
D287V3, multiclass
           clus
vv          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZMIZ2 MUTATED    0  0     6
  ZMIZ2 WILD-TYPE  5 17    96
D287V4, multiclass
       clus
vv      ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V5, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    1  5
  ZMIZ2 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      1    5
  ZMIZ2 WILD-TYPE   34   84
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D287V6, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    4  0
  ZMIZ2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      4    0
  ZMIZ2 WILD-TYPE   53    3
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D287V7, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    3  3
  ZMIZ2 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      3    3
  ZMIZ2 WILD-TYPE   48   72
        clus
vv       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D287V8, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    4  2
  ZMIZ2 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      4    2
  ZMIZ2 WILD-TYPE   84   28
     clus
vv    ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMIZ2 MUTATED                                     6
  ZMIZ2 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMIZ2 MUTATED                                       0
  ZMIZ2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMIZ2 MUTATED                                                  0
  ZMIZ2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZMIZ2 MUTATED                                     0
  ZMIZ2 WILD-TYPE                                   1
D287V9, multiclass
                                                  clus
vv                                                 ZMIZ2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZMIZ2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V10, continuous
D287V11, continuous
[1] "Remove cluster labels:" "ZMIZ2 MUTATED"         
clus
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" "ZMIZ2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZMIZ2 MUTATED    3  2  0  0
  ZMIZ2 WILD-TYPE 77 33  4  2
D287V12, multiclass
    clus
vv   ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ2 MUTATED       0                         0     5
  ZMIZ2 WILD-TYPE     6                         5   109
D287V14, multiclass
                           clus
vv                          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V15, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    0  5
  ZMIZ2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      0    5
  ZMIZ2 WILD-TYPE    5   86
                        clus
vv                       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(288) Variable = OR5H1 MUTATION ANALYSIS
D288V1, survival
                 sevent
clus2              0  1
  OR5H1 MUTATED    3  4
  OR5H1 WILD-TYPE 60 58
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              7             118 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              4              58 
$`OR5H1 MUTATED`
TCGA-S4-A8RO TCGA-US-A77E TCGA-3E-AAAZ TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-A6UG 
       17.26        14.14        71.74        17.00        19.82         1.35 
TCGA-IB-AAUM 
        0.26 

$`OR5H1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-XD-AAUL 
        8.02        15.78         1.08        15.12        12.92        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90         8.22        15.88         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  OR5H1 MUTATED OR5H1 WILD-TYPE 
           0.26            0.23 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          71.74           90.12 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
         17.000          15.205 
[1] "0.3 - 71.7 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D288V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR5H1 MUTATED         0        0        0         2         5         0
  OR5H1 WILD-TYPE       1        3       12        17        77         4
                 vv
clus              STAGE IV
  OR5H1 MUTATED          0
  OR5H1 WILD-TYPE        3
D288V3, multiclass
           clus
vv          OR5H1 MUTATED OR5H1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OR5H1 MUTATED    0  1     6
  OR5H1 WILD-TYPE  5 16    96
D288V4, multiclass
       clus
vv      OR5H1 MUTATED OR5H1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V5, binary
                 cls
clus               0  1
  OR5H1 MUTATED    2  5
  OR5H1 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      2    5
  OR5H1 WILD-TYPE   33   84
   clus
vv  OR5H1 MUTATED OR5H1 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D288V6, binary
                 cls
clus               0  1
  OR5H1 MUTATED    4  0
  OR5H1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      4    0
  OR5H1 WILD-TYPE   53    3
   clus
vv  OR5H1 MUTATED OR5H1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D288V7, binary
                 cls
clus               0  1
  OR5H1 MUTATED    2  5
  OR5H1 WILD-TYPE 49 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      2    5
  OR5H1 WILD-TYPE   49   70
        clus
vv       OR5H1 MUTATED OR5H1 WILD-TYPE
  FEMALE             2              49
  MALE               5              70
[1] 2 2
[1] FALSE
D288V8, binary
                 cls
clus               0  1
  OR5H1 MUTATED    5  1
  OR5H1 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      5    1
  OR5H1 WILD-TYPE   83   29
     clus
vv    OR5H1 MUTATED OR5H1 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR5H1 MUTATED                                     6
  OR5H1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR5H1 MUTATED                                       1
  OR5H1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR5H1 MUTATED                                                  0
  OR5H1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR5H1 MUTATED                                     0
  OR5H1 WILD-TYPE                                   1
D288V9, multiclass
                                                  clus
vv                                                 OR5H1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 OR5H1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V10, continuous
D288V11, continuous
[1] "Remove cluster labels:" "OR5H1 MUTATED"         
clus
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" "OR5H1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR5H1 MUTATED    2  4  0  0
  OR5H1 WILD-TYPE 78 31  4  2
D288V12, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  R0             2              78
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR5H1 MUTATED       0                         0     7
  OR5H1 WILD-TYPE     6                         5   107
D288V14, multiclass
                           clus
vv                          OR5H1 MUTATED OR5H1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V15, binary
                 cls
clus               0  1
  OR5H1 MUTATED    1  6
  OR5H1 WILD-TYPE  4 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      1    6
  OR5H1 WILD-TYPE    4   85
                        clus
vv                       OR5H1 MUTATED OR5H1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(289) Variable = SMYD5 MUTATION ANALYSIS
D289V1, survival
                 sevent
clus2              0  1
  SMYD5 MUTATED    1  4
  SMYD5 WILD-TYPE 62 58
  SMYD5 MUTATED SMYD5 WILD-TYPE 
              5             120 
  SMYD5 MUTATED SMYD5 WILD-TYPE 
              4              58 
$`SMYD5 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABE TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-IB-7651 
       12.92        22.22         4.70        12.95        19.82 

$`SMYD5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM 
        9.11        21.44        22.49         3.39         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SMYD5 MUTATED SMYD5 WILD-TYPE 
           4.70            0.23 
  SMYD5 MUTATED SMYD5 WILD-TYPE 
          22.22           90.12 
  SMYD5 MUTATED SMYD5 WILD-TYPE 
          12.95           15.27 
[1] "4.7 - 22.2 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D289V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMYD5 MUTATED         0        0        0         1         3         1
  SMYD5 WILD-TYPE       1        3       12        18        79         3
                 vv
clus              STAGE IV
  SMYD5 MUTATED          0
  SMYD5 WILD-TYPE        3
D289V3, multiclass
           clus
vv          SMYD5 MUTATED SMYD5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SMYD5 MUTATED    0  0     5
  SMYD5 WILD-TYPE  5 17    97
D289V4, multiclass
       clus
vv      SMYD5 MUTATED SMYD5 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V5, binary
                 cls
clus               0  1
  SMYD5 MUTATED    2  3
  SMYD5 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMYD5 MUTATED      2    3
  SMYD5 WILD-TYPE   33   86
   clus
vv  SMYD5 MUTATED SMYD5 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D289V6, binary
                 cls
clus               0  1
  SMYD5 MUTATED    2  0
  SMYD5 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMYD5 MUTATED      2    0
  SMYD5 WILD-TYPE   55    3
   clus
vv  SMYD5 MUTATED SMYD5 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D289V7, binary
                 cls
clus               0  1
  SMYD5 MUTATED    3  2
  SMYD5 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMYD5 MUTATED      3    2
  SMYD5 WILD-TYPE   48   73
        clus
vv       SMYD5 MUTATED SMYD5 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D289V8, binary
                 cls
clus               0  1
  SMYD5 MUTATED    4  1
  SMYD5 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMYD5 MUTATED      4    1
  SMYD5 WILD-TYPE   84   29
     clus
vv    SMYD5 MUTATED SMYD5 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMYD5 MUTATED                                     5
  SMYD5 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMYD5 MUTATED                                       0
  SMYD5 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMYD5 MUTATED                                                  0
  SMYD5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMYD5 MUTATED                                     0
  SMYD5 WILD-TYPE                                   1
D289V9, multiclass
                                                  clus
vv                                                 SMYD5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SMYD5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V10, continuous
D289V11, continuous
                 vv
clus              R0 R1 R2 RX
  SMYD5 MUTATED    2  3  0  0
  SMYD5 WILD-TYPE 78 32  4  2
D289V12, multiclass
    clus
vv   SMYD5 MUTATED SMYD5 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMYD5 MUTATED       0                         1     4
  SMYD5 WILD-TYPE     6                         4   110
D289V14, multiclass
                           clus
vv                          SMYD5 MUTATED SMYD5 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V15, binary
                 cls
clus               0  1
  SMYD5 MUTATED    0  2
  SMYD5 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMYD5 MUTATED      0    2
  SMYD5 WILD-TYPE    5   89
                        clus
vv                       SMYD5 MUTATED SMYD5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(290) Variable = NIPA2 MUTATION ANALYSIS
D290V1, survival
                 sevent
clus2              0  1
  NIPA2 MUTATED    1  2
  NIPA2 WILD-TYPE 62 60
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              3             122 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              2              60 
$`NIPA2 MUTATED`
TCGA-LB-A7SX TCGA-F2-A8YN TCGA-OE-A75W 
       12.92        17.00         8.78 

$`NIPA2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           8.78            0.23 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          17.00           90.12 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
          12.92           15.27 
[1] "8.8 - 17.0 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D290V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NIPA2 MUTATED         0        0        0         2         1         0
  NIPA2 WILD-TYPE       1        3       12        17        81         4
                 vv
clus              STAGE IV
  NIPA2 MUTATED          0
  NIPA2 WILD-TYPE        3
D290V3, multiclass
           clus
vv          NIPA2 MUTATED NIPA2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NIPA2 MUTATED    0  0     3
  NIPA2 WILD-TYPE  5 17    99
D290V4, multiclass
       clus
vv      NIPA2 MUTATED NIPA2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V5, binary
                 cls
clus               0  1
  NIPA2 MUTATED    2  1
  NIPA2 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      2    1
  NIPA2 WILD-TYPE   33   88
   clus
vv  NIPA2 MUTATED NIPA2 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D290V6, binary
                 cls
clus               0  1
  NIPA2 MUTATED    2  0
  NIPA2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      2    0
  NIPA2 WILD-TYPE   55    3
   clus
vv  NIPA2 MUTATED NIPA2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D290V7, binary
                 cls
clus               0  1
  NIPA2 MUTATED    1  2
  NIPA2 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      1    2
  NIPA2 WILD-TYPE   50   73
        clus
vv       NIPA2 MUTATED NIPA2 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D290V8, binary
                 cls
clus               0  1
  NIPA2 MUTATED    2  1
  NIPA2 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      2    1
  NIPA2 WILD-TYPE   86   29
     clus
vv    NIPA2 MUTATED NIPA2 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NIPA2 MUTATED                                     3
  NIPA2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NIPA2 MUTATED                                       0
  NIPA2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NIPA2 MUTATED                                                  0
  NIPA2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NIPA2 MUTATED                                     0
  NIPA2 WILD-TYPE                                   1
D290V9, multiclass
                                                  clus
vv                                                 NIPA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NIPA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V10, continuous
D290V11, continuous
[1] "Remove cluster labels:" "NIPA2 MUTATED"         
clus
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NIPA2 MUTATED    1  2  0  0
  NIPA2 WILD-TYPE 79 33  4  2
D290V12, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             1              79
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NIPA2 MUTATED       0                         1     2
  NIPA2 WILD-TYPE     6                         4   112
D290V14, multiclass
                           clus
vv                          NIPA2 MUTATED NIPA2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V15, binary
                 cls
clus               0  1
  NIPA2 MUTATED    0  3
  NIPA2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      0    3
  NIPA2 WILD-TYPE    5   88
                        clus
vv                       NIPA2 MUTATED NIPA2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(291) Variable = C7ORF16 MUTATION ANALYSIS
D291V1, survival
                   sevent
clus2                0  1
  C7ORF16 MUTATED    3  1
  C7ORF16 WILD-TYPE 60 61
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
                4               121 
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
                1                61 
$`C7ORF16 MUTATED`
TCGA-3A-A9IV TCGA-FZ-5922 TCGA-HZ-A9TJ TCGA-XD-AAUH 
       36.26        36.20        19.82        12.99 

$`C7ORF16 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
            12.99              0.23 
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
            36.26             90.12 
  C7ORF16 MUTATED C7ORF16 WILD-TYPE 
            28.01             15.19 
[1] "13.0 - 36.3 (28.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3"  
D291V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C7ORF16 MUTATED         0        0        1         1         1         0
  C7ORF16 WILD-TYPE       1        3       11        18        81         4
                   vv
clus                STAGE IV
  C7ORF16 MUTATED          1
  C7ORF16 WILD-TYPE        2
D291V3, multiclass
           clus
vv          C7ORF16 MUTATED C7ORF16 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               1                81
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  C7ORF16 MUTATED    0  1     3
  C7ORF16 WILD-TYPE  5 16    99
D291V4, multiclass
       clus
vv      C7ORF16 MUTATED C7ORF16 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V5, binary
                   cls
clus                 0  1
  C7ORF16 MUTATED    3  1
  C7ORF16 WILD-TYPE 32 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF16 MUTATED      3    1
  C7ORF16 WILD-TYPE   32   88
   clus
vv  C7ORF16 MUTATED C7ORF16 WILD-TYPE
  0               3                32
  1               1                88
[1] 2 2
[1] FALSE
D291V6, binary
                   cls
clus                 0  1
  C7ORF16 MUTATED    2  1
  C7ORF16 WILD-TYPE 55  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF16 MUTATED      2    1
  C7ORF16 WILD-TYPE   55    2
   clus
vv  C7ORF16 MUTATED C7ORF16 WILD-TYPE
  0               2                55
  1               1                 2
[1] 2 2
[1] FALSE
D291V7, binary
                   cls
clus                 0  1
  C7ORF16 MUTATED    2  2
  C7ORF16 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF16 MUTATED      2    2
  C7ORF16 WILD-TYPE   49   73
        clus
vv       C7ORF16 MUTATED C7ORF16 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D291V8, binary
                   cls
clus                 0  1
  C7ORF16 MUTATED    3  1
  C7ORF16 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF16 MUTATED      3    1
  C7ORF16 WILD-TYPE   85   29
     clus
vv    C7ORF16 MUTATED C7ORF16 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C7ORF16 MUTATED                                     2
  C7ORF16 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C7ORF16 MUTATED                                       2
  C7ORF16 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C7ORF16 MUTATED                                                  0
  C7ORF16 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  C7ORF16 MUTATED                                     0
  C7ORF16 WILD-TYPE                                   1
D291V9, multiclass
                                                  clus
vv                                                 C7ORF16 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 C7ORF16 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V10, continuous
D291V11, continuous
                   vv
clus                R0 R1 R2 RX
  C7ORF16 MUTATED    3  0  1  0
  C7ORF16 WILD-TYPE 77 35  3  2
D291V12, multiclass
    clus
vv   C7ORF16 MUTATED C7ORF16 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C7ORF16 MUTATED       0                         0     4
  C7ORF16 WILD-TYPE     6                         5   110
D291V14, multiclass
                           clus
vv                          C7ORF16 MUTATED C7ORF16 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V15, binary
                   cls
clus                 0  1
  C7ORF16 MUTATED    0  4
  C7ORF16 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF16 MUTATED      0    4
  C7ORF16 WILD-TYPE    5   87
                        clus
vv                       C7ORF16 MUTATED C7ORF16 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(292) Variable = DOCK6 MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2              0  1
  DOCK6 MUTATED    3  2
  DOCK6 WILD-TYPE 60 60
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              5             120 
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              2              60 
$`DOCK6 MUTATED`
TCGA-2L-AAQA TCGA-3A-A9I7 TCGA-IB-7651 TCGA-IB-AAUP TCGA-YB-A89D 
        4.70        43.50        19.82        14.17        11.51 

$`DOCK6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  DOCK6 MUTATED DOCK6 WILD-TYPE 
           4.70            0.23 
  DOCK6 MUTATED DOCK6 WILD-TYPE 
          43.50           90.12 
  DOCK6 MUTATED DOCK6 WILD-TYPE 
          14.17           15.27 
[1] "4.7 - 43.5 (14.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D292V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DOCK6 MUTATED         0        0        0         0         5         0
  DOCK6 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  DOCK6 MUTATED          0
  DOCK6 WILD-TYPE        3
D292V3, multiclass
           clus
vv          DOCK6 MUTATED DOCK6 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DOCK6 MUTATED    0  0     5
  DOCK6 WILD-TYPE  5 17    97
D292V4, multiclass
       clus
vv      DOCK6 MUTATED DOCK6 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V5, binary
                 cls
clus               0  1
  DOCK6 MUTATED    0  5
  DOCK6 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK6 MUTATED      0    5
  DOCK6 WILD-TYPE   35   84
   clus
vv  DOCK6 MUTATED DOCK6 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D292V6, binary
                 cls
clus               0  1
  DOCK6 MUTATED    2  0
  DOCK6 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK6 MUTATED      2    0
  DOCK6 WILD-TYPE   55    3
   clus
vv  DOCK6 MUTATED DOCK6 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D292V7, binary
                 cls
clus               0  1
  DOCK6 MUTATED    1  4
  DOCK6 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK6 MUTATED      1    4
  DOCK6 WILD-TYPE   50   71
        clus
vv       DOCK6 MUTATED DOCK6 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D292V8, binary
                 cls
clus               0  1
  DOCK6 MUTATED    3  2
  DOCK6 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK6 MUTATED      3    2
  DOCK6 WILD-TYPE   85   28
     clus
vv    DOCK6 MUTATED DOCK6 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DOCK6 MUTATED                                     5
  DOCK6 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DOCK6 MUTATED                                       0
  DOCK6 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DOCK6 MUTATED                                                  0
  DOCK6 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DOCK6 MUTATED                                     0
  DOCK6 WILD-TYPE                                   1
D292V9, multiclass
                                                  clus
vv                                                 DOCK6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DOCK6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V10, continuous
[1] "Remove cluster labels:" "DOCK6 MUTATED"         
clus
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-YY-A8LH 
"DOCK6 WILD-TYPE" 
D292V11, continuous
[1] "Remove cluster labels:" "DOCK6 MUTATED"         
clus
  DOCK6 MUTATED DOCK6 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" "DOCK6 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DOCK6 MUTATED    3  2  0  0
  DOCK6 WILD-TYPE 77 33  4  2
D292V12, multiclass
    clus
vv   DOCK6 MUTATED DOCK6 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOCK6 MUTATED       0                         1     4
  DOCK6 WILD-TYPE     6                         4   110
D292V14, multiclass
                           clus
vv                          DOCK6 MUTATED DOCK6 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V15, binary
                 cls
clus               0  1
  DOCK6 MUTATED    0  4
  DOCK6 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK6 MUTATED      0    4
  DOCK6 WILD-TYPE    5   87
                        clus
vv                       DOCK6 MUTATED DOCK6 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(293) Variable = OR10A2 MUTATION ANALYSIS
D293V1, survival
                  sevent
clus2               0  1
  OR10A2 MUTATED    3  1
  OR10A2 WILD-TYPE 60 61
  OR10A2 MUTATED OR10A2 WILD-TYPE 
               4              121 
  OR10A2 MUTATED OR10A2 WILD-TYPE 
               1               61 
$`OR10A2 MUTATED`
TCGA-3E-AAAZ TCGA-HV-A7OP TCGA-IB-A5ST TCGA-US-A776 
       71.74        32.15        20.88        39.98 

$`OR10A2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OR10A2 MUTATED OR10A2 WILD-TYPE 
           20.88             0.23 
  OR10A2 MUTATED OR10A2 WILD-TYPE 
           71.74            90.12 
  OR10A2 MUTATED OR10A2 WILD-TYPE 
          36.065           15.120 
[1] "20.9 - 71.7 (36.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "4.4"
D293V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR10A2 MUTATED         0        0        0         2         2         0
  OR10A2 WILD-TYPE       1        3       12        17        80         4
                  vv
clus               STAGE IV
  OR10A2 MUTATED          0
  OR10A2 WILD-TYPE        3
D293V3, multiclass
           clus
vv          OR10A2 MUTATED OR10A2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  OR10A2 MUTATED    0  0     4
  OR10A2 WILD-TYPE  5 17    98
D293V4, multiclass
       clus
vv      OR10A2 MUTATED OR10A2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V5, binary
                  cls
clus                0  1
  OR10A2 MUTATED    2  2
  OR10A2 WILD-TYPE 33 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A2 MUTATED      2    2
  OR10A2 WILD-TYPE   33   87
   clus
vv  OR10A2 MUTATED OR10A2 WILD-TYPE
  0              2               33
  1              2               87
[1] 2 2
[1] FALSE
D293V6, binary
                  cls
clus                0  1
  OR10A2 MUTATED    2  0
  OR10A2 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A2 MUTATED      2    0
  OR10A2 WILD-TYPE   55    3
   clus
vv  OR10A2 MUTATED OR10A2 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D293V7, binary
                  cls
clus                0  1
  OR10A2 MUTATED    1  3
  OR10A2 WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A2 MUTATED      1    3
  OR10A2 WILD-TYPE   50   72
        clus
vv       OR10A2 MUTATED OR10A2 WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D293V8, binary
                  cls
clus                0  1
  OR10A2 MUTATED    2  1
  OR10A2 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A2 MUTATED      2    1
  OR10A2 WILD-TYPE   86   29
     clus
vv    OR10A2 MUTATED OR10A2 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR10A2 MUTATED                                     2
  OR10A2 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR10A2 MUTATED                                       1
  OR10A2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR10A2 MUTATED                                                  1
  OR10A2 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR10A2 MUTATED                                     0
  OR10A2 WILD-TYPE                                   1
D293V9, multiclass
                                                  clus
vv                                                 OR10A2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 OR10A2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V10, continuous
D293V11, continuous
                  vv
clus               R0 R1 R2 RX
  OR10A2 MUTATED    3  0  0  0
  OR10A2 WILD-TYPE 77 35  4  2
D293V12, multiclass
    clus
vv   OR10A2 MUTATED OR10A2 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR10A2 MUTATED       1                         0     3
  OR10A2 WILD-TYPE     5                         5   111
D293V14, multiclass
                           clus
vv                          OR10A2 MUTATED OR10A2 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V15, binary
                  cls
clus                0  1
  OR10A2 MUTATED    1  2
  OR10A2 WILD-TYPE  4 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A2 MUTATED      1    2
  OR10A2 WILD-TYPE    4   89
                        clus
vv                       OR10A2 MUTATED OR10A2 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(294) Variable = KDM2A MUTATION ANALYSIS
D294V1, survival
                 sevent
clus2              0  1
  KDM2A MUTATED    3  2
  KDM2A WILD-TYPE 60 60
  KDM2A MUTATED KDM2A WILD-TYPE 
              5             120 
  KDM2A MUTATED KDM2A WILD-TYPE 
              2              60 
$`KDM2A MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-IB-7651 TCGA-IB-7652 TCGA-YH-A8SY 
       23.54         4.04        19.82        36.69        12.76 

$`KDM2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       15.95        37.15         7.50        12.53        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  KDM2A MUTATED KDM2A WILD-TYPE 
           4.04            0.23 
  KDM2A MUTATED KDM2A WILD-TYPE 
          36.69           90.12 
  KDM2A MUTATED KDM2A WILD-TYPE 
         19.820          15.205 
[1] "4.0 - 36.7 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D294V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KDM2A MUTATED         0        0        0         0         4         1
  KDM2A WILD-TYPE       1        3       12        19        78         3
                 vv
clus              STAGE IV
  KDM2A MUTATED          0
  KDM2A WILD-TYPE        3
D294V3, multiclass
           clus
vv          KDM2A MUTATED KDM2A WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KDM2A MUTATED    0  1     4
  KDM2A WILD-TYPE  5 16    98
D294V4, multiclass
       clus
vv      KDM2A MUTATED KDM2A WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V5, binary
                 cls
clus               0  1
  KDM2A MUTATED    0  5
  KDM2A WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2A MUTATED      0    5
  KDM2A WILD-TYPE   35   84
   clus
vv  KDM2A MUTATED KDM2A WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D294V6, binary
                 cls
clus               0  1
  KDM2A MUTATED    2  0
  KDM2A WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2A MUTATED      2    0
  KDM2A WILD-TYPE   55    3
   clus
vv  KDM2A MUTATED KDM2A WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D294V7, binary
                 cls
clus               0  1
  KDM2A MUTATED    3  2
  KDM2A WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2A MUTATED      3    2
  KDM2A WILD-TYPE   48   73
        clus
vv       KDM2A MUTATED KDM2A WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D294V8, binary
                 cls
clus               0  1
  KDM2A MUTATED    4  1
  KDM2A WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2A MUTATED      4    1
  KDM2A WILD-TYPE   84   29
     clus
vv    KDM2A MUTATED KDM2A WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KDM2A MUTATED                                     4
  KDM2A WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KDM2A MUTATED                                       0
  KDM2A WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KDM2A MUTATED                                                  0
  KDM2A WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KDM2A MUTATED                                     0
  KDM2A WILD-TYPE                                   1
D294V9, multiclass
                                                  clus
vv                                                 KDM2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KDM2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V10, continuous
[1] "Remove cluster labels:" "KDM2A MUTATED"         
clus
  KDM2A MUTATED KDM2A WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
D294V11, continuous
[1] "Remove cluster labels:" "KDM2A MUTATED"         
clus
  KDM2A MUTATED KDM2A WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" "KDM2A WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KDM2A MUTATED    2  2  0  0
  KDM2A WILD-TYPE 78 33  4  2
D294V12, multiclass
    clus
vv   KDM2A MUTATED KDM2A WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM2A MUTATED       1                         0     4
  KDM2A WILD-TYPE     5                         5   110
D294V14, multiclass
                           clus
vv                          KDM2A MUTATED KDM2A WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V15, binary
                 cls
clus               0  1
  KDM2A MUTATED    0  5
  KDM2A WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2A MUTATED      0    5
  KDM2A WILD-TYPE    5   86
                        clus
vv                       KDM2A MUTATED KDM2A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(295) Variable = RBM45 MUTATION ANALYSIS
D295V1, survival
                 sevent
clus2              0  1
  RBM45 MUTATED    2  3
  RBM45 WILD-TYPE 61 59
  RBM45 MUTATED RBM45 WILD-TYPE 
              5             120 
  RBM45 MUTATED RBM45 WILD-TYPE 
              3              59 
$`RBM45 MUTATED`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-AAPZ TCGA-IB-7651 TCGA-IB-AAUU 
       19.46        16.37        23.54        19.82         8.05 

$`RBM45 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       71.74         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RBM45 MUTATED RBM45 WILD-TYPE 
           8.05            0.23 
  RBM45 MUTATED RBM45 WILD-TYPE 
          23.54           90.12 
  RBM45 MUTATED RBM45 WILD-TYPE 
         19.460          15.155 
[1] "8.1 - 23.5 (19.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D295V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM45 MUTATED         0        0        1         0         4         0
  RBM45 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  RBM45 MUTATED          0
  RBM45 WILD-TYPE        3
D295V3, multiclass
           clus
vv          RBM45 MUTATED RBM45 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM45 MUTATED    0  2     3
  RBM45 WILD-TYPE  5 15    99
D295V4, multiclass
       clus
vv      RBM45 MUTATED RBM45 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V5, binary
                 cls
clus               0  1
  RBM45 MUTATED    1  4
  RBM45 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      1    4
  RBM45 WILD-TYPE   34   85
   clus
vv  RBM45 MUTATED RBM45 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D295V6, binary
                 cls
clus               0  1
  RBM45 MUTATED    4  0
  RBM45 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      4    0
  RBM45 WILD-TYPE   53    3
   clus
vv  RBM45 MUTATED RBM45 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D295V7, binary
                 cls
clus               0  1
  RBM45 MUTATED    1  4
  RBM45 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      1    4
  RBM45 WILD-TYPE   50   71
        clus
vv       RBM45 MUTATED RBM45 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D295V8, binary
                 cls
clus               0  1
  RBM45 MUTATED    4  1
  RBM45 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      4    1
  RBM45 WILD-TYPE   84   29
     clus
vv    RBM45 MUTATED RBM45 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM45 MUTATED                                     5
  RBM45 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM45 MUTATED                                       0
  RBM45 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM45 MUTATED                                                  0
  RBM45 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM45 MUTATED                                     0
  RBM45 WILD-TYPE                                   1
D295V9, multiclass
                                                  clus
vv                                                 RBM45 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RBM45 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V10, continuous
D295V11, continuous
[1] "Remove cluster labels:" "RBM45 MUTATED"         
clus
  RBM45 MUTATED RBM45 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RBM45 MUTATED    4  1  0  0
  RBM45 WILD-TYPE 76 34  4  2
D295V12, multiclass
    clus
vv   RBM45 MUTATED RBM45 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM45 MUTATED       0                         1     4
  RBM45 WILD-TYPE     6                         4   110
D295V14, multiclass
                           clus
vv                          RBM45 MUTATED RBM45 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V15, binary
                 cls
clus               0  1
  RBM45 MUTATED    0  5
  RBM45 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      0    5
  RBM45 WILD-TYPE    5   86
                        clus
vv                       RBM45 MUTATED RBM45 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(296) Variable = PHRF1 MUTATION ANALYSIS
D296V1, survival
                 sevent
clus2              0  1
  PHRF1 MUTATED    2  2
  PHRF1 WILD-TYPE 61 60
  PHRF1 MUTATED PHRF1 WILD-TYPE 
              4             121 
  PHRF1 MUTATED PHRF1 WILD-TYPE 
              2              60 
$`PHRF1 MUTATED`
TCGA-2J-AABP TCGA-3A-A9IR TCGA-FB-A5VM TCGA-IB-7651 
       15.22        50.70        16.37        19.82 

$`PHRF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PHRF1 MUTATED PHRF1 WILD-TYPE 
          15.22            0.23 
  PHRF1 MUTATED PHRF1 WILD-TYPE 
          50.70           90.12 
  PHRF1 MUTATED PHRF1 WILD-TYPE 
         18.095          15.120 
[1] "15.2 - 50.7 (18.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.3"
D296V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHRF1 MUTATED         0        0        2         0         2         0
  PHRF1 WILD-TYPE       1        3       10        19        80         4
                 vv
clus              STAGE IV
  PHRF1 MUTATED          0
  PHRF1 WILD-TYPE        3
D296V3, multiclass
           clus
vv          PHRF1 MUTATED PHRF1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PHRF1 MUTATED     0   2     2
  PHRF1 WILD-TYPE   5  15   100
D296V4, multiclass
       clus
vv      PHRF1 MUTATED PHRF1 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V5, binary
                 cls
clus               0  1
  PHRF1 MUTATED    2  2
  PHRF1 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHRF1 MUTATED      2    2
  PHRF1 WILD-TYPE   33   87
   clus
vv  PHRF1 MUTATED PHRF1 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D296V6, binary
                 cls
clus               0  1
  PHRF1 MUTATED    3  0
  PHRF1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHRF1 MUTATED      3    0
  PHRF1 WILD-TYPE   54    3
   clus
vv  PHRF1 MUTATED PHRF1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D296V7, binary
                 cls
clus               0  1
  PHRF1 MUTATED    3  1
  PHRF1 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHRF1 MUTATED      3    1
  PHRF1 WILD-TYPE   48   74
        clus
vv       PHRF1 MUTATED PHRF1 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D296V8, binary
                 cls
clus               0  1
  PHRF1 MUTATED    4  0
  PHRF1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHRF1 MUTATED      4    0
  PHRF1 WILD-TYPE   84   30
     clus
vv    PHRF1 MUTATED PHRF1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHRF1 MUTATED                                     2
  PHRF1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHRF1 MUTATED                                       1
  PHRF1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHRF1 MUTATED                                                  0
  PHRF1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHRF1 MUTATED                                     1
  PHRF1 WILD-TYPE                                   0
D296V9, multiclass
                                                  clus
vv                                                 PHRF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 PHRF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V10, continuous
[1] "Remove cluster labels:" "PHRF1 MUTATED"         
clus
  PHRF1 MUTATED PHRF1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" "PHRF1 WILD-TYPE" 
     TCGA-YY-A8LH 
"PHRF1 WILD-TYPE" 
D296V11, continuous
                 vv
clus              R0 R1 R2 RX
  PHRF1 MUTATED    4  0  0  0
  PHRF1 WILD-TYPE 76 35  4  2
D296V12, multiclass
    clus
vv   PHRF1 MUTATED PHRF1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHRF1 MUTATED       0                         0     4
  PHRF1 WILD-TYPE     6                         5   110
D296V14, multiclass
                           clus
vv                          PHRF1 MUTATED PHRF1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V15, binary
                 cls
clus               0  1
  PHRF1 MUTATED    0  3
  PHRF1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHRF1 MUTATED      0    3
  PHRF1 WILD-TYPE    5   88
                        clus
vv                       PHRF1 MUTATED PHRF1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(297) Variable = KCND3 MUTATION ANALYSIS
D297V1, survival
                 sevent
clus2              0  1
  KCND3 MUTATED    2  3
  KCND3 WILD-TYPE 61 59
  KCND3 MUTATED KCND3 WILD-TYPE 
              5             120 
  KCND3 MUTATED KCND3 WILD-TYPE 
              3              59 
$`KCND3 MUTATED`
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-IB-7651 TCGA-RL-AAAS TCGA-US-A776 
        3.39        12.95        19.82         0.30        39.98 

$`KCND3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KCND3 MUTATED KCND3 WILD-TYPE 
           0.30            0.23 
  KCND3 MUTATED KCND3 WILD-TYPE 
          39.98           90.12 
  KCND3 MUTATED KCND3 WILD-TYPE 
          12.95           15.27 
[1] "0.3 - 40.0 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D297V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KCND3 MUTATED         0        0        1         1         2         1
  KCND3 WILD-TYPE       1        3       11        18        80         3
                 vv
clus              STAGE IV
  KCND3 MUTATED          0
  KCND3 WILD-TYPE        3
D297V3, multiclass
           clus
vv          KCND3 MUTATED KCND3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KCND3 MUTATED    0  1     4
  KCND3 WILD-TYPE  5 16    98
D297V4, multiclass
       clus
vv      KCND3 MUTATED KCND3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V5, binary
                 cls
clus               0  1
  KCND3 MUTATED    3  2
  KCND3 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND3 MUTATED      3    2
  KCND3 WILD-TYPE   32   87
   clus
vv  KCND3 MUTATED KCND3 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D297V6, binary
                 cls
clus               0  1
  KCND3 MUTATED    2  0
  KCND3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND3 MUTATED      2    0
  KCND3 WILD-TYPE   55    3
   clus
vv  KCND3 MUTATED KCND3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D297V7, binary
                 cls
clus               0  1
  KCND3 MUTATED    3  2
  KCND3 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND3 MUTATED      3    2
  KCND3 WILD-TYPE   48   73
        clus
vv       KCND3 MUTATED KCND3 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D297V8, binary
                 cls
clus               0  1
  KCND3 MUTATED    5  0
  KCND3 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND3 MUTATED      5    0
  KCND3 WILD-TYPE   83   30
     clus
vv    KCND3 MUTATED KCND3 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCND3 MUTATED                                     4
  KCND3 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCND3 MUTATED                                       0
  KCND3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCND3 MUTATED                                                  1
  KCND3 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KCND3 MUTATED                                     0
  KCND3 WILD-TYPE                                   1
D297V9, multiclass
                                                  clus
vv                                                 KCND3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KCND3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V10, continuous
[1] "Remove cluster labels:" "KCND3 MUTATED"         
clus
  KCND3 MUTATED KCND3 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
D297V11, continuous
[1] "Remove cluster labels:" "KCND3 MUTATED"         
clus
  KCND3 MUTATED KCND3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" "KCND3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KCND3 MUTATED    3  2  0  0
  KCND3 WILD-TYPE 77 33  4  2
D297V12, multiclass
    clus
vv   KCND3 MUTATED KCND3 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCND3 MUTATED       0                         0     5
  KCND3 WILD-TYPE     6                         5   109
D297V14, multiclass
                           clus
vv                          KCND3 MUTATED KCND3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V15, binary
                 cls
clus               0  1
  KCND3 MUTATED    0  3
  KCND3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND3 MUTATED      0    3
  KCND3 WILD-TYPE    5   88
                        clus
vv                       KCND3 MUTATED KCND3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(298) Variable = CD1D MUTATION ANALYSIS
D298V1, survival
                sevent
clus2             0  1
  CD1D MUTATED    3  3
  CD1D WILD-TYPE 60 59
  CD1D MUTATED CD1D WILD-TYPE 
             6            119 
  CD1D MUTATED CD1D WILD-TYPE 
             3             59 
$`CD1D MUTATED`
TCGA-2J-AABF TCGA-F2-A8YN TCGA-IB-7651 TCGA-OE-A75W TCGA-XN-A8T5 TCGA-YB-A89D 
       22.72        17.00        19.82         8.78        23.67        11.51 

$`CD1D WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        12.76        66.28        15.35 

  CD1D MUTATED CD1D WILD-TYPE 
          8.78           0.23 
  CD1D MUTATED CD1D WILD-TYPE 
         23.67          90.12 
  CD1D MUTATED CD1D WILD-TYPE 
         18.41          15.19 
[1] "8.8 - 23.7 (18.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D298V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CD1D MUTATED         0        0        1         2         3         0
  CD1D WILD-TYPE       1        3       11        17        79         4
                vv
clus             STAGE IV
  CD1D MUTATED          0
  CD1D WILD-TYPE        3
D298V3, multiclass
           clus
vv          CD1D MUTATED CD1D WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            2             17
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CD1D MUTATED    0  1     5
  CD1D WILD-TYPE  5 16    97
D298V4, multiclass
       clus
vv      CD1D MUTATED CD1D WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V5, binary
                cls
clus              0  1
  CD1D MUTATED    3  3
  CD1D WILD-TYPE 32 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      3    3
  CD1D WILD-TYPE   32   86
   clus
vv  CD1D MUTATED CD1D WILD-TYPE
  0            3             32
  1            3             86
[1] 2 2
[1] FALSE
D298V6, binary
                cls
clus              0  1
  CD1D MUTATED    5  0
  CD1D WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      5    0
  CD1D WILD-TYPE   52    3
   clus
vv  CD1D MUTATED CD1D WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D298V7, binary
                cls
clus              0  1
  CD1D MUTATED    2  4
  CD1D WILD-TYPE 49 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      2    4
  CD1D WILD-TYPE   49   71
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  FEMALE            2             49
  MALE              4             71
[1] 2 2
[1] FALSE
D298V8, binary
                cls
clus              0  1
  CD1D MUTATED    2  4
  CD1D WILD-TYPE 86 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      2    4
  CD1D WILD-TYPE   86   26
     clus
vv    CD1D MUTATED CD1D WILD-TYPE
  NO             2             86
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD1D MUTATED                                     5
  CD1D WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD1D MUTATED                                       1
  CD1D WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD1D MUTATED                                                  0
  CD1D WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CD1D MUTATED                                     0
  CD1D WILD-TYPE                                   1
D298V9, multiclass
                                                  clus
vv                                                 CD1D MUTATED CD1D WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V10, continuous
D298V11, continuous
                vv
clus             R0 R1 R2 RX
  CD1D MUTATED    3  3  0  0
  CD1D WILD-TYPE 77 32  4  2
D298V12, multiclass
    clus
vv   CD1D MUTATED CD1D WILD-TYPE
  R0            3             77
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD1D MUTATED       0                         0     6
  CD1D WILD-TYPE     6                         5   108
D298V14, multiclass
                           clus
vv                          CD1D MUTATED CD1D WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V15, binary
                cls
clus              0  1
  CD1D MUTATED    1  4
  CD1D WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD1D MUTATED      1    4
  CD1D WILD-TYPE    4   87
                        clus
vv                       CD1D MUTATED CD1D WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(299) Variable = PHF21A MUTATION ANALYSIS
D299V1, survival
                  sevent
clus2               0  1
  PHF21A MUTATED    0  4
  PHF21A WILD-TYPE 63 58
  PHF21A MUTATED PHF21A WILD-TYPE 
               4              121 
  PHF21A MUTATED PHF21A WILD-TYPE 
               4               58 
$`PHF21A MUTATED`
TCGA-3A-A9I9 TCGA-IB-7651 TCGA-IB-AAUO TCGA-RB-A7B8 
       20.84        19.82         7.86        15.32 

$`PHF21A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PHF21A MUTATED PHF21A WILD-TYPE 
            7.86             0.23 
  PHF21A MUTATED PHF21A WILD-TYPE 
           20.84            90.12 
  PHF21A MUTATED PHF21A WILD-TYPE 
           17.57            15.19 
[1] "7.9 - 20.8 (17.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.1"
D299V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHF21A MUTATED         0        0        0         1         3         0
  PHF21A WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  PHF21A MUTATED          0
  PHF21A WILD-TYPE        3
D299V3, multiclass
           clus
vv          PHF21A MUTATED PHF21A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PHF21A MUTATED    0  0     4
  PHF21A WILD-TYPE  5 17    98
D299V4, multiclass
       clus
vv      PHF21A MUTATED PHF21A WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V5, binary
                  cls
clus                0  1
  PHF21A MUTATED    1  3
  PHF21A WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      1    3
  PHF21A WILD-TYPE   34   86
   clus
vv  PHF21A MUTATED PHF21A WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D299V6, binary
                  cls
clus                0  1
  PHF21A MUTATED    2  0
  PHF21A WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      2    0
  PHF21A WILD-TYPE   55    3
   clus
vv  PHF21A MUTATED PHF21A WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D299V7, binary
                  cls
clus                0  1
  PHF21A MUTATED    3  1
  PHF21A WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      3    1
  PHF21A WILD-TYPE   48   74
        clus
vv       PHF21A MUTATED PHF21A WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D299V8, binary
                  cls
clus                0  1
  PHF21A MUTATED    3  1
  PHF21A WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      3    1
  PHF21A WILD-TYPE   85   29
     clus
vv    PHF21A MUTATED PHF21A WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF21A MUTATED                                     3
  PHF21A WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF21A MUTATED                                       1
  PHF21A WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF21A MUTATED                                                  0
  PHF21A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHF21A MUTATED                                     0
  PHF21A WILD-TYPE                                   1
D299V9, multiclass
                                                  clus
vv                                                 PHF21A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PHF21A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V10, continuous
[1] "Remove cluster labels:" "PHF21A MUTATED"        
clus
  PHF21A MUTATED PHF21A WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9IB       TCGA-3A-A9IX 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-YY-A8LH 
"PHF21A WILD-TYPE" 
D299V11, continuous
[1] "Remove cluster labels:" "PHF21A MUTATED"        
clus
  PHF21A MUTATED PHF21A WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" "PHF21A WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PHF21A MUTATED    3  1  0  0
  PHF21A WILD-TYPE 77 34  4  2
D299V12, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF21A MUTATED       0                         0     4
  PHF21A WILD-TYPE     6                         5   110
D299V14, multiclass
                           clus
vv                          PHF21A MUTATED PHF21A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V15, binary
                  cls
clus                0  1
  PHF21A MUTATED    0  4
  PHF21A WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      0    4
  PHF21A WILD-TYPE    5   87
                        clus
vv                       PHF21A MUTATED PHF21A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(300) Variable = STEAP2 MUTATION ANALYSIS
D300V1, survival
                  sevent
clus2               0  1
  STEAP2 MUTATED    2  3
  STEAP2 WILD-TYPE 61 59
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               5              120 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               3               59 
$`STEAP2 MUTATED`
TCGA-3A-A9IB TCGA-3A-A9IS TCGA-IB-7651 TCGA-IB-A7LX TCGA-YB-A89D 
        7.36        32.81        19.82         8.22        11.51 

$`STEAP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  STEAP2 MUTATED STEAP2 WILD-TYPE 
            7.36             0.23 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
           32.81            90.12 
  STEAP2 MUTATED STEAP2 WILD-TYPE 
           11.51            15.27 
[1] "7.4 - 32.8 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D300V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  STEAP2 MUTATED         0        0        1         0         4         0
  STEAP2 WILD-TYPE       1        3       11        19        78         4
                  vv
clus               STAGE IV
  STEAP2 MUTATED          0
  STEAP2 WILD-TYPE        3
D300V3, multiclass
           clus
vv          STEAP2 MUTATED STEAP2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  STEAP2 MUTATED    0  1     4
  STEAP2 WILD-TYPE  5 16    98
D300V4, multiclass
       clus
vv      STEAP2 MUTATED STEAP2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V5, binary
                  cls
clus                0  1
  STEAP2 MUTATED    1  4
  STEAP2 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      1    4
  STEAP2 WILD-TYPE   34   85
   clus
vv  STEAP2 MUTATED STEAP2 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D300V6, binary
                  cls
clus                0  1
  STEAP2 MUTATED    1  0
  STEAP2 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      1    0
  STEAP2 WILD-TYPE   56    3
   clus
vv  STEAP2 MUTATED STEAP2 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D300V7, binary
                  cls
clus                0  1
  STEAP2 MUTATED    2  3
  STEAP2 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      2    3
  STEAP2 WILD-TYPE   49   72
        clus
vv       STEAP2 MUTATED STEAP2 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D300V8, binary
                  cls
clus                0  1
  STEAP2 MUTATED    4  1
  STEAP2 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      4    1
  STEAP2 WILD-TYPE   84   29
     clus
vv    STEAP2 MUTATED STEAP2 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STEAP2 MUTATED                                     4
  STEAP2 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STEAP2 MUTATED                                       1
  STEAP2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STEAP2 MUTATED                                                  0
  STEAP2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  STEAP2 MUTATED                                     0
  STEAP2 WILD-TYPE                                   1
D300V9, multiclass
                                                  clus
vv                                                 STEAP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 STEAP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V10, continuous
[1] "Remove cluster labels:" "STEAP2 MUTATED"        
clus
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IX 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-YY-A8LH 
"STEAP2 WILD-TYPE" 
D300V11, continuous
[1] "Remove cluster labels:" "STEAP2 MUTATED"        
clus
  STEAP2 MUTATED STEAP2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IR       TCGA-3A-A9IX 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" "STEAP2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  STEAP2 MUTATED    5  0  0  0
  STEAP2 WILD-TYPE 75 35  4  2
D300V12, multiclass
    clus
vv   STEAP2 MUTATED STEAP2 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STEAP2 MUTATED       0                         0     5
  STEAP2 WILD-TYPE     6                         5   109
D300V14, multiclass
                           clus
vv                          STEAP2 MUTATED STEAP2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V15, binary
                  cls
clus                0  1
  STEAP2 MUTATED    0  5
  STEAP2 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STEAP2 MUTATED      0    5
  STEAP2 WILD-TYPE    5   86
                        clus
vv                       STEAP2 MUTATED STEAP2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(301) Variable = SALL1 MUTATION ANALYSIS
D301V1, survival
                 sevent
clus2              0  1
  SALL1 MUTATED    5  5
  SALL1 WILD-TYPE 58 57
  SALL1 MUTATED SALL1 WILD-TYPE 
             10             115 
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              57 
$`SALL1 MUTATED`
TCGA-2J-AABK TCGA-2J-AABV TCGA-FB-AAPP TCGA-FZ-5921 TCGA-HZ-A49I TCGA-HZ-A77P 
       15.91        21.44        15.95         5.10        10.13        10.85 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A7M4 
       19.82        41.33        15.19        15.88 

$`SALL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
       24.36         2.01        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-A5SO 
       17.00         5.26         0.23        19.82        36.69        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SALL1 MUTATED SALL1 WILD-TYPE 
           5.10            0.23 
  SALL1 MUTATED SALL1 WILD-TYPE 
          41.33           90.12 
  SALL1 MUTATED SALL1 WILD-TYPE 
         15.895          15.120 
[1] "5.1 - 41.3 (15.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D301V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SALL1 MUTATED         0        0        0         0         9         1
  SALL1 WILD-TYPE       1        3       12        19        73         3
                 vv
clus              STAGE IV
  SALL1 MUTATED          0
  SALL1 WILD-TYPE        3
D301V3, multiclass
           clus
vv          SALL1 MUTATED SALL1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             9              73
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SALL1 MUTATED    0  0    10
  SALL1 WILD-TYPE  5 17    92
D301V4, multiclass
       clus
vv      SALL1 MUTATED SALL1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V5, binary
                 cls
clus               0  1
  SALL1 MUTATED    0 10
  SALL1 WILD-TYPE 35 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      0   10
  SALL1 WILD-TYPE   35   79
   clus
vv  SALL1 MUTATED SALL1 WILD-TYPE
  0             0              35
  1            10              79
[1] 2 2
[1] FALSE
D301V6, binary
                 cls
clus               0  1
  SALL1 MUTATED    6  0
  SALL1 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      6    0
  SALL1 WILD-TYPE   51    3
   clus
vv  SALL1 MUTATED SALL1 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D301V7, binary
                 cls
clus               0  1
  SALL1 MUTATED    4  6
  SALL1 WILD-TYPE 47 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      4    6
  SALL1 WILD-TYPE   47   69
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  FEMALE             4              47
  MALE               6              69
[1] 2 2
[1] FALSE
D301V8, binary
                 cls
clus               0  1
  SALL1 MUTATED    6  4
  SALL1 WILD-TYPE 82 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      6    4
  SALL1 WILD-TYPE   82   26
     clus
vv    SALL1 MUTATED SALL1 WILD-TYPE
  NO              6              82
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SALL1 MUTATED                                     9
  SALL1 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SALL1 MUTATED                                       1
  SALL1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SALL1 MUTATED                                                  0
  SALL1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SALL1 MUTATED                                     0
  SALL1 WILD-TYPE                                   1
D301V9, multiclass
                                                  clus
vv                                                 SALL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SALL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V10, continuous
D301V11, continuous
                 vv
clus              R0 R1 R2 RX
  SALL1 MUTATED    5  4  0  0
  SALL1 WILD-TYPE 75 31  4  2
D301V12, multiclass
    clus
vv   SALL1 MUTATED SALL1 WILD-TYPE
  R0             5              75
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SALL1 MUTATED       0                         0     9
  SALL1 WILD-TYPE     6                         5   105
D301V14, multiclass
                           clus
vv                          SALL1 MUTATED SALL1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 9             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V15, binary
                 cls
clus               0  1
  SALL1 MUTATED    0  7
  SALL1 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      0    7
  SALL1 WILD-TYPE    5   84
                        clus
vv                       SALL1 MUTATED SALL1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(302) Variable = DSTN MUTATION ANALYSIS
D302V1, survival
                sevent
clus2             0  1
  DSTN MUTATED    0  3
  DSTN WILD-TYPE 63 59
  DSTN MUTATED DSTN WILD-TYPE 
             3            122 
  DSTN MUTATED DSTN WILD-TYPE 
             3             59 
$`DSTN MUTATED`
TCGA-2J-AABA TCGA-FB-AAPQ TCGA-IB-AAUN 
       19.96        37.15         4.73 

$`DSTN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DSTN MUTATED DSTN WILD-TYPE 
          4.73           0.23 
  DSTN MUTATED DSTN WILD-TYPE 
         37.15          90.12 
  DSTN MUTATED DSTN WILD-TYPE 
        19.960         15.205 
[1] "4.7 - 37.1 (20.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D302V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DSTN MUTATED         0        0        1         0         2         0
  DSTN WILD-TYPE       1        3       11        19        80         4
                vv
clus             STAGE IV
  DSTN MUTATED          0
  DSTN WILD-TYPE        3
D302V3, multiclass
           clus
vv          DSTN MUTATED DSTN WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  DSTN MUTATED     0   1     2
  DSTN WILD-TYPE   5  16   100
D302V4, multiclass
       clus
vv      DSTN MUTATED DSTN WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V5, binary
                cls
clus              0  1
  DSTN MUTATED    1  2
  DSTN WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      1    2
  DSTN WILD-TYPE   34   87
   clus
vv  DSTN MUTATED DSTN WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D302V6, binary
                cls
clus              0  1
  DSTN MUTATED    2  0
  DSTN WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      2    0
  DSTN WILD-TYPE   55    3
   clus
vv  DSTN MUTATED DSTN WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D302V7, binary
                cls
clus              0  1
  DSTN MUTATED    1  2
  DSTN WILD-TYPE 50 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      1    2
  DSTN WILD-TYPE   50   73
        clus
vv       DSTN MUTATED DSTN WILD-TYPE
  FEMALE            1             50
  MALE              2             73
[1] 2 2
[1] FALSE
D302V8, binary
                cls
clus              0  1
  DSTN MUTATED    3  0
  DSTN WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      3    0
  DSTN WILD-TYPE   85   30
     clus
vv    DSTN MUTATED DSTN WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DSTN MUTATED                                     3
  DSTN WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DSTN MUTATED                                       0
  DSTN WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DSTN MUTATED                                                  0
  DSTN WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  DSTN MUTATED                                     0
  DSTN WILD-TYPE                                   1
D302V9, multiclass
                                                  clus
vv                                                 DSTN MUTATED DSTN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V10, continuous
[1] "Remove cluster labels:" "DSTN MUTATED"          
clus
  DSTN MUTATED DSTN WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-YY-A8LH 
"DSTN WILD-TYPE" 
D302V11, continuous
[1] "Remove cluster labels:" "DSTN MUTATED"          
clus
  DSTN MUTATED DSTN WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" "DSTN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  DSTN MUTATED    1  2  0  0
  DSTN WILD-TYPE 79 33  4  2
D302V12, multiclass
    clus
vv   DSTN MUTATED DSTN WILD-TYPE
  R0            1             79
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DSTN MUTATED       0                         0     3
  DSTN WILD-TYPE     6                         5   111
D302V14, multiclass
                           clus
vv                          DSTN MUTATED DSTN WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V15, binary
                cls
clus              0  1
  DSTN MUTATED    0  2
  DSTN WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSTN MUTATED      0    2
  DSTN WILD-TYPE    5   89
                        clus
vv                       DSTN MUTATED DSTN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(303) Variable = C6ORF154 MUTATION ANALYSIS
D303V1, survival
                    sevent
clus2                 0  1
  C6ORF154 MUTATED    1  3
  C6ORF154 WILD-TYPE 62 59
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 4                121 
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 3                 59 
$`C6ORF154 MUTATED`
TCGA-XD-AAUL TCGA-2J-AABU TCGA-3A-A9IC TCGA-FB-AAQ2 
       16.37         9.11        24.26         5.03 

$`C6ORF154 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
              5.03               0.23 
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
             24.26              90.12 
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
             12.74              15.22 
[1] "5.0 - 24.3 (12.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D303V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C6ORF154 MUTATED         0        0        0         1         3         0
  C6ORF154 WILD-TYPE       1        3       12        18        79         4
                    vv
clus                 STAGE IV
  C6ORF154 MUTATED          0
  C6ORF154 WILD-TYPE        3
D303V3, multiclass
           clus
vv          C6ORF154 MUTATED C6ORF154 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C6ORF154 MUTATED    0  0     4
  C6ORF154 WILD-TYPE  5 17    98
D303V4, multiclass
       clus
vv      C6ORF154 MUTATED C6ORF154 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V5, binary
                    cls
clus                  0  1
  C6ORF154 MUTATED    1  3
  C6ORF154 WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF154 MUTATED      1    3
  C6ORF154 WILD-TYPE   34   86
   clus
vv  C6ORF154 MUTATED C6ORF154 WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D303V6, binary
                    cls
clus                  0  1
  C6ORF154 MUTATED    1  0
  C6ORF154 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF154 MUTATED      1    0
  C6ORF154 WILD-TYPE   56    3
   clus
vv  C6ORF154 MUTATED C6ORF154 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D303V7, binary
                    cls
clus                  0  1
  C6ORF154 MUTATED    2  2
  C6ORF154 WILD-TYPE 49 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF154 MUTATED      2    2
  C6ORF154 WILD-TYPE   49   73
        clus
vv       C6ORF154 MUTATED C6ORF154 WILD-TYPE
  FEMALE                2                 49
  MALE                  2                 73
[1] 2 2
[1] FALSE
D303V8, binary
                    cls
clus                  0  1
  C6ORF154 MUTATED    3  1
  C6ORF154 WILD-TYPE 85 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF154 MUTATED      3    1
  C6ORF154 WILD-TYPE   85   29
     clus
vv    C6ORF154 MUTATED C6ORF154 WILD-TYPE
  NO                 3                 85
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C6ORF154 MUTATED                                     4
  C6ORF154 WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C6ORF154 MUTATED                                       0
  C6ORF154 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C6ORF154 MUTATED                                                  0
  C6ORF154 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C6ORF154 MUTATED                                     0
  C6ORF154 WILD-TYPE                                   1
D303V9, multiclass
                                                  clus
vv                                                 C6ORF154 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C6ORF154 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V10, continuous
[1] "Remove cluster labels:" "C6ORF154 MUTATED"      
clus
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-2J-AAB1 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
D303V11, continuous
[1] "Remove cluster labels:" "C6ORF154 MUTATED"      
clus
  C6ORF154 MUTATED C6ORF154 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-2J-AAB1 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C6ORF154 WILD-TYPE" "C6ORF154 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C6ORF154 MUTATED    3  1  0  0
  C6ORF154 WILD-TYPE 77 34  4  2
D303V12, multiclass
    clus
vv   C6ORF154 MUTATED C6ORF154 WILD-TYPE
  R0                3                 77
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C6ORF154 MUTATED       0                         0     4
  C6ORF154 WILD-TYPE     6                         5   110
D303V14, multiclass
                           clus
vv                          C6ORF154 MUTATED C6ORF154 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V15, binary
                    cls
clus                  0  1
  C6ORF154 MUTATED    0  3
  C6ORF154 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF154 MUTATED      0    3
  C6ORF154 WILD-TYPE    5   88
                        clus
vv                       C6ORF154 MUTATED C6ORF154 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(304) Variable = TDRD6 MUTATION ANALYSIS
D304V1, survival
                 sevent
clus2              0  1
  TDRD6 MUTATED    2  6
  TDRD6 WILD-TYPE 61 56
  TDRD6 MUTATED TDRD6 WILD-TYPE 
              8             117 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
              6              56 
$`TDRD6 MUTATED`
TCGA-IB-A5SS TCGA-2J-AAB1 TCGA-3A-A9IZ TCGA-FB-A78T TCGA-HZ-A77O TCGA-IB-7651 
       15.12         2.17        10.13        12.33         5.26        19.82 
TCGA-RB-AA9M TCGA-XN-A8T5 
        9.40        23.67 

$`TDRD6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        31.27        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  TDRD6 MUTATED TDRD6 WILD-TYPE 
           2.17            0.23 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
          23.67           90.12 
  TDRD6 MUTATED TDRD6 WILD-TYPE 
          11.23           15.35 
[1] "2.2 - 23.7 (11.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.3"
D304V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TDRD6 MUTATED         0        0        1         0         7         0
  TDRD6 WILD-TYPE       1        3       11        19        75         4
                 vv
clus              STAGE IV
  TDRD6 MUTATED          0
  TDRD6 WILD-TYPE        3
D304V3, multiclass
           clus
vv          TDRD6 MUTATED TDRD6 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TDRD6 MUTATED    1  2     5
  TDRD6 WILD-TYPE  4 15    97
D304V4, multiclass
       clus
vv      TDRD6 MUTATED TDRD6 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V5, binary
                 cls
clus               0  1
  TDRD6 MUTATED    1  7
  TDRD6 WILD-TYPE 34 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      1    7
  TDRD6 WILD-TYPE   34   82
   clus
vv  TDRD6 MUTATED TDRD6 WILD-TYPE
  0             1              34
  1             7              82
[1] 2 2
[1] FALSE
D304V6, binary
                 cls
clus               0  1
  TDRD6 MUTATED    5  0
  TDRD6 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      5    0
  TDRD6 WILD-TYPE   52    3
   clus
vv  TDRD6 MUTATED TDRD6 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D304V7, binary
                 cls
clus               0  1
  TDRD6 MUTATED    5  3
  TDRD6 WILD-TYPE 46 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      5    3
  TDRD6 WILD-TYPE   46   72
        clus
vv       TDRD6 MUTATED TDRD6 WILD-TYPE
  FEMALE             5              46
  MALE               3              72
[1] 2 2
[1] FALSE
D304V8, binary
                 cls
clus               0  1
  TDRD6 MUTATED    6  2
  TDRD6 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      6    2
  TDRD6 WILD-TYPE   82   28
     clus
vv    TDRD6 MUTATED TDRD6 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TDRD6 MUTATED                                     6
  TDRD6 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TDRD6 MUTATED                                       2
  TDRD6 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TDRD6 MUTATED                                                  0
  TDRD6 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TDRD6 MUTATED                                     0
  TDRD6 WILD-TYPE                                   1
D304V9, multiclass
                                                  clus
vv                                                 TDRD6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TDRD6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V10, continuous
D304V11, continuous
                 vv
clus              R0 R1 R2 RX
  TDRD6 MUTATED    6  2  0  0
  TDRD6 WILD-TYPE 74 33  4  2
D304V12, multiclass
    clus
vv   TDRD6 MUTATED TDRD6 WILD-TYPE
  R0             6              74
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TDRD6 MUTATED       0                         0     8
  TDRD6 WILD-TYPE     6                         5   106
D304V14, multiclass
                           clus
vv                          TDRD6 MUTATED TDRD6 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V15, binary
                 cls
clus               0  1
  TDRD6 MUTATED    2  5
  TDRD6 WILD-TYPE  3 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD6 MUTATED      2    5
  TDRD6 WILD-TYPE    3   86
                        clus
vv                       TDRD6 MUTATED TDRD6 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(305) Variable = SIGLEC11 MUTATION ANALYSIS
D305V1, survival
                    sevent
clus2                 0  1
  SIGLEC11 MUTATED    2  3
  SIGLEC11 WILD-TYPE 61 59
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 5                120 
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 3                 59 
$`SIGLEC11 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AABA TCGA-2L-AAQI TCGA-IB-AAUV 
       23.97         9.63        19.96         3.39        13.28 

$`SIGLEC11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
       14.14        16.37         2.17         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       21.44         4.70        22.49        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40         8.05         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
              3.39               0.23 
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
             23.97              90.12 
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
             13.28              15.27 
[1] "3.4 - 24.0 (13.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D305V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SIGLEC11 MUTATED         0        0        0         1         4         0
  SIGLEC11 WILD-TYPE       1        3       12        18        78         4
                    vv
clus                 STAGE IV
  SIGLEC11 MUTATED          0
  SIGLEC11 WILD-TYPE        3
D305V3, multiclass
           clus
vv          SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  SIGLEC11 MUTATED    0  1     4
  SIGLEC11 WILD-TYPE  5 16    98
D305V4, multiclass
       clus
vv      SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V5, binary
                    cls
clus                  0  1
  SIGLEC11 MUTATED    1  4
  SIGLEC11 WILD-TYPE 34 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC11 MUTATED      1    4
  SIGLEC11 WILD-TYPE   34   85
   clus
vv  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  0                1                 34
  1                4                 85
[1] 2 2
[1] FALSE
D305V6, binary
                    cls
clus                  0  1
  SIGLEC11 MUTATED    4  0
  SIGLEC11 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC11 MUTATED      4    0
  SIGLEC11 WILD-TYPE   53    3
   clus
vv  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D305V7, binary
                    cls
clus                  0  1
  SIGLEC11 MUTATED    0  5
  SIGLEC11 WILD-TYPE 51 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC11 MUTATED      0    5
  SIGLEC11 WILD-TYPE   51   70
        clus
vv       SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  FEMALE                0                 51
  MALE                  5                 70
[1] 2 2
[1] FALSE
D305V8, binary
                    cls
clus                  0  1
  SIGLEC11 MUTATED    5  0
  SIGLEC11 WILD-TYPE 83 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC11 MUTATED      5    0
  SIGLEC11 WILD-TYPE   83   30
     clus
vv    SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  NO                 5                 83
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIGLEC11 MUTATED                                     4
  SIGLEC11 WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIGLEC11 MUTATED                                       1
  SIGLEC11 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIGLEC11 MUTATED                                                  0
  SIGLEC11 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  SIGLEC11 MUTATED                                     0
  SIGLEC11 WILD-TYPE                                   1
D305V9, multiclass
                                                  clus
vv                                                 SIGLEC11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 SIGLEC11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V10, continuous
[1] "Remove cluster labels:" "SIGLEC11 MUTATED"      
clus
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-YY-A8LH 
"SIGLEC11 WILD-TYPE" 
D305V11, continuous
[1] "Remove cluster labels:" "SIGLEC11 MUTATED"      
clus
  SIGLEC11 MUTATED SIGLEC11 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7651         TCGA-IB-7885 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-A6UF         TCGA-IB-A6UG 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUQ         TCGA-IB-AAUS 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"SIGLEC11 WILD-TYPE" "SIGLEC11 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  SIGLEC11 MUTATED    3  2  0  0
  SIGLEC11 WILD-TYPE 77 33  4  2
D305V12, multiclass
    clus
vv   SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  R0                3                 77
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC11 MUTATED       0                         0     5
  SIGLEC11 WILD-TYPE     6                         5   109
D305V14, multiclass
                           clus
vv                          SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V15, binary
                    cls
clus                  0  1
  SIGLEC11 MUTATED    0  1
  SIGLEC11 WILD-TYPE  5 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC11 MUTATED      0    1
  SIGLEC11 WILD-TYPE    5   90
                        clus
vv                       SIGLEC11 MUTATED SIGLEC11 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                1                 90
[1] 2 2
[1] FALSE

Clustering(306) Variable = UGP2 MUTATION ANALYSIS
D306V1, survival
                sevent
clus2             0  1
  UGP2 MUTATED    1  4
  UGP2 WILD-TYPE 62 58
  UGP2 MUTATED UGP2 WILD-TYPE 
             5            120 
  UGP2 MUTATED UGP2 WILD-TYPE 
             4             58 
$`UGP2 MUTATED`
TCGA-LB-A7SX TCGA-FZ-5920 TCGA-HZ-8637 TCGA-HZ-A77P TCGA-IB-7651 
       12.92         2.01        17.00        10.85        19.82 

$`UGP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02        24.36         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        20.19        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  UGP2 MUTATED UGP2 WILD-TYPE 
          2.01           0.23 
  UGP2 MUTATED UGP2 WILD-TYPE 
         19.82          90.12 
  UGP2 MUTATED UGP2 WILD-TYPE 
         12.92          15.27 
[1] "2.0 - 19.8 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D306V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UGP2 MUTATED         0        0        0         0         5         0
  UGP2 WILD-TYPE       1        3       12        19        77         4
                vv
clus             STAGE IV
  UGP2 MUTATED          0
  UGP2 WILD-TYPE        3
D306V3, multiclass
           clus
vv          UGP2 MUTATED UGP2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  UGP2 MUTATED    0  0     5
  UGP2 WILD-TYPE  5 17    97
D306V4, multiclass
       clus
vv      UGP2 MUTATED UGP2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V5, binary
                cls
clus              0  1
  UGP2 MUTATED    0  5
  UGP2 WILD-TYPE 35 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      0    5
  UGP2 WILD-TYPE   35   84
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            0             35
  1            5             84
[1] 2 2
[1] FALSE
D306V6, binary
                cls
clus              0  1
  UGP2 MUTATED    2  0
  UGP2 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      2    0
  UGP2 WILD-TYPE   55    3
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D306V7, binary
                cls
clus              0  1
  UGP2 MUTATED    3  2
  UGP2 WILD-TYPE 48 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      3    2
  UGP2 WILD-TYPE   48   73
        clus
vv       UGP2 MUTATED UGP2 WILD-TYPE
  FEMALE            3             48
  MALE              2             73
[1] 2 2
[1] FALSE
D306V8, binary
                cls
clus              0  1
  UGP2 MUTATED    4  1
  UGP2 WILD-TYPE 84 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      4    1
  UGP2 WILD-TYPE   84   29
     clus
vv    UGP2 MUTATED UGP2 WILD-TYPE
  NO             4             84
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UGP2 MUTATED                                     4
  UGP2 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UGP2 MUTATED                                       1
  UGP2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UGP2 MUTATED                                                  0
  UGP2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  UGP2 MUTATED                                     0
  UGP2 WILD-TYPE                                   1
D306V9, multiclass
                                                  clus
vv                                                 UGP2 MUTATED UGP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V10, continuous
[1] "Remove cluster labels:" "UGP2 MUTATED"          
clus
  UGP2 MUTATED UGP2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-YY-A8LH 
"UGP2 WILD-TYPE" 
D306V11, continuous
[1] "Remove cluster labels:" "UGP2 MUTATED"          
clus
  UGP2 MUTATED UGP2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  UGP2 MUTATED    4  1  0  0
  UGP2 WILD-TYPE 76 34  4  2
D306V12, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  R0            4             76
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UGP2 MUTATED       0                         2     3
  UGP2 WILD-TYPE     6                         3   111
D306V14, multiclass
                           clus
vv                          UGP2 MUTATED UGP2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V15, binary
                cls
clus              0  1
  UGP2 MUTATED    1  4
  UGP2 WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      1    4
  UGP2 WILD-TYPE    4   87
                        clus
vv                       UGP2 MUTATED UGP2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(307) Variable = SCD MUTATION ANALYSIS
D307V1, survival
               sevent
clus2            0  1
  SCD MUTATED    2  2
  SCD WILD-TYPE 61 60
  SCD MUTATED SCD WILD-TYPE 
            4           121 
  SCD MUTATED SCD WILD-TYPE 
            2            60 
$`SCD MUTATED`
TCGA-3A-A9IJ TCGA-FB-AAPP TCGA-HV-A7OP TCGA-IB-7651 
       60.95        15.95        32.15        19.82 

$`SCD WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SCD MUTATED SCD WILD-TYPE 
        15.95          0.23 
  SCD MUTATED SCD WILD-TYPE 
        60.95         90.12 
  SCD MUTATED SCD WILD-TYPE 
       25.985        15.120 
[1] "15.9 - 61.0 (26.0)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.6"
D307V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SCD MUTATED         0        0        1         0         3         0
  SCD WILD-TYPE       1        3       11        19        79         4
               vv
clus            STAGE IV
  SCD MUTATED          0
  SCD WILD-TYPE        3
D307V3, multiclass
           clus
vv          SCD MUTATED SCD WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            1            11
  STAGE IIA           0            19
  STAGE IIB           3            79
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  SCD MUTATED    0  1     3
  SCD WILD-TYPE  5 16    99
D307V4, multiclass
       clus
vv      SCD MUTATED SCD WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           3            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V5, binary
               cls
clus             0  1
  SCD MUTATED    1  3
  SCD WILD-TYPE 34 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      1    3
  SCD WILD-TYPE   34   86
   clus
vv  SCD MUTATED SCD WILD-TYPE
  0           1            34
  1           3            86
[1] 2 2
[1] FALSE
D307V6, binary
               cls
clus             0  1
  SCD MUTATED    2  0
  SCD WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      2    0
  SCD WILD-TYPE   55    3
   clus
vv  SCD MUTATED SCD WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D307V7, binary
               cls
clus             0  1
  SCD MUTATED    1  3
  SCD WILD-TYPE 50 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      1    3
  SCD WILD-TYPE   50   72
        clus
vv       SCD MUTATED SCD WILD-TYPE
  FEMALE           1            50
  MALE             3            72
[1] 2 2
[1] FALSE
D307V8, binary
               cls
clus             0  1
  SCD MUTATED    2  2
  SCD WILD-TYPE 86 28
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      2    2
  SCD WILD-TYPE   86   28
     clus
vv    SCD MUTATED SCD WILD-TYPE
  NO            2            86
  YES           2            28
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SCD MUTATED                                     2
  SCD WILD-TYPE                                 103
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SCD MUTATED                                       2
  SCD WILD-TYPE                                    16
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SCD MUTATED                                                  0
  SCD WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  SCD MUTATED                                     0
  SCD WILD-TYPE                                   1
D307V9, multiclass
                                                  clus
vv                                                 SCD MUTATED SCD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        2           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      2            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V10, continuous
[1] "Remove cluster labels:" "SCD MUTATED"           
clus
  SCD MUTATED SCD WILD-TYPE 
            2            37 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX    TCGA-XD-AAUL 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1    TCGA-IB-7885 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"SCD WILD-TYPE" "SCD WILD-TYPE" 
D307V11, continuous
[1] "Remove cluster labels:" "SCD MUTATED"           
clus
  SCD MUTATED SCD WILD-TYPE 
            2            31 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX    TCGA-XD-AAUL 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO    TCGA-3A-A9IB 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7885    TCGA-IB-8126 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI    TCGA-XN-A8T5 
"SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" "SCD WILD-TYPE" 
   TCGA-YY-A8LH 
"SCD WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  SCD MUTATED    4  0  0  0
  SCD WILD-TYPE 76 35  4  2
D307V12, multiclass
    clus
vv   SCD MUTATED SCD WILD-TYPE
  R0           4            76
  R1           0            35
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCD MUTATED       1                         0     3
  SCD WILD-TYPE     5                         5   111
D307V14, multiclass
                           clus
vv                          SCD MUTATED SCD WILD-TYPE
  ASIAN                               1             5
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V15, binary
               cls
clus             0  1
  SCD MUTATED    0  3
  SCD WILD-TYPE  5 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  SCD MUTATED      0    3
  SCD WILD-TYPE    5   88
                        clus
vv                       SCD MUTATED SCD WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3            88
[1] 2 2
[1] FALSE

Clustering(308) Variable = PANK2 MUTATION ANALYSIS
D308V1, survival
                 sevent
clus2              0  1
  PANK2 MUTATED    3  1
  PANK2 WILD-TYPE 60 61
  PANK2 MUTATED PANK2 WILD-TYPE 
              4             121 
  PANK2 MUTATED PANK2 WILD-TYPE 
              1              61 
$`PANK2 MUTATED`
TCGA-XD-AAUL TCGA-IB-7651 TCGA-IB-8126 TCGA-US-A776 
       16.37        19.82        15.19        39.98 

$`PANK2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PANK2 MUTATED PANK2 WILD-TYPE 
          15.19            0.23 
  PANK2 MUTATED PANK2 WILD-TYPE 
          39.98           90.12 
  PANK2 MUTATED PANK2 WILD-TYPE 
         18.095          15.120 
[1] "15.2 - 40.0 (18.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "2.6"
D308V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PANK2 MUTATED         0        0        0         2         1         1
  PANK2 WILD-TYPE       1        3       12        17        81         3
                 vv
clus              STAGE IV
  PANK2 MUTATED          0
  PANK2 WILD-TYPE        3
D308V3, multiclass
           clus
vv          PANK2 MUTATED PANK2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PANK2 MUTATED    0  0     4
  PANK2 WILD-TYPE  5 17    98
D308V4, multiclass
       clus
vv      PANK2 MUTATED PANK2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V5, binary
                 cls
clus               0  1
  PANK2 MUTATED    2  2
  PANK2 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      2    2
  PANK2 WILD-TYPE   33   87
   clus
vv  PANK2 MUTATED PANK2 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D308V6, binary
                 cls
clus               0  1
  PANK2 MUTATED    2  0
  PANK2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      2    0
  PANK2 WILD-TYPE   55    3
   clus
vv  PANK2 MUTATED PANK2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D308V7, binary
                 cls
clus               0  1
  PANK2 MUTATED    2  2
  PANK2 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      2    2
  PANK2 WILD-TYPE   49   73
        clus
vv       PANK2 MUTATED PANK2 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D308V8, binary
                 cls
clus               0  1
  PANK2 MUTATED    4  0
  PANK2 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      4    0
  PANK2 WILD-TYPE   84   30
     clus
vv    PANK2 MUTATED PANK2 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PANK2 MUTATED                                     3
  PANK2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PANK2 MUTATED                                       0
  PANK2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PANK2 MUTATED                                                  1
  PANK2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PANK2 MUTATED                                     0
  PANK2 WILD-TYPE                                   1
D308V9, multiclass
                                                  clus
vv                                                 PANK2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PANK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V10, continuous
D308V11, continuous
                 vv
clus              R0 R1 R2 RX
  PANK2 MUTATED    3  1  0  0
  PANK2 WILD-TYPE 77 34  4  2
D308V12, multiclass
    clus
vv   PANK2 MUTATED PANK2 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PANK2 MUTATED       0                         0     4
  PANK2 WILD-TYPE     6                         5   110
D308V14, multiclass
                           clus
vv                          PANK2 MUTATED PANK2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V15, binary
                 cls
clus               0  1
  PANK2 MUTATED    0  4
  PANK2 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK2 MUTATED      0    4
  PANK2 WILD-TYPE    5   87
                        clus
vv                       PANK2 MUTATED PANK2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(309) Variable = GOLGA6B MUTATION ANALYSIS
D309V1, survival
                   sevent
clus2                0  1
  GOLGA6B MUTATED    3  3
  GOLGA6B WILD-TYPE 60 59
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                6               119 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                3                59 
$`GOLGA6B MUTATED`
TCGA-3A-A9IO TCGA-FB-A78T TCGA-HZ-A77P TCGA-IB-7651 TCGA-RB-A7B8 TCGA-US-A776 
       63.85        12.33        10.85        19.82        15.32        39.98 

$`GOLGA6B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 
        8.78        13.68         3.12         9.40         0.30        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            10.85              0.23 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            63.85             90.12 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            17.57             15.19 
[1] "10.8 - 63.9 (17.6)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.3"
D309V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GOLGA6B MUTATED         0        0        0         1         4         0
  GOLGA6B WILD-TYPE       1        3       12        18        78         4
                   vv
clus                STAGE IV
  GOLGA6B MUTATED          0
  GOLGA6B WILD-TYPE        3
D309V3, multiclass
           clus
vv          GOLGA6B MUTATED GOLGA6B WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  GOLGA6B MUTATED    0  0     5
  GOLGA6B WILD-TYPE  5 17    97
D309V4, multiclass
       clus
vv      GOLGA6B MUTATED GOLGA6B WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V5, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    1  4
  GOLGA6B WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      1    4
  GOLGA6B WILD-TYPE   34   85
   clus
vv  GOLGA6B MUTATED GOLGA6B WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D309V6, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    2  0
  GOLGA6B WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      2    0
  GOLGA6B WILD-TYPE   55    3
   clus
vv  GOLGA6B MUTATED GOLGA6B WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D309V7, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    3  3
  GOLGA6B WILD-TYPE 48 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      3    3
  GOLGA6B WILD-TYPE   48   72
        clus
vv       GOLGA6B MUTATED GOLGA6B WILD-TYPE
  FEMALE               3                48
  MALE                 3                72
[1] 2 2
[1] FALSE
D309V8, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    6  0
  GOLGA6B WILD-TYPE 82 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      6    0
  GOLGA6B WILD-TYPE   82   30
     clus
vv    GOLGA6B MUTATED GOLGA6B WILD-TYPE
  NO                6                82
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GOLGA6B MUTATED                                     2
  GOLGA6B WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GOLGA6B MUTATED                                       3
  GOLGA6B WILD-TYPE                                    15
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GOLGA6B MUTATED                                                  1
  GOLGA6B WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  GOLGA6B MUTATED                                     0
  GOLGA6B WILD-TYPE                                   1
D309V9, multiclass
                                                  clus
vv                                                 GOLGA6B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 GOLGA6B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V10, continuous
[1] "Remove cluster labels:" "GOLGA6B MUTATED"       
clus
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-AAPQ 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-YY-A8LH 
"GOLGA6B WILD-TYPE" 
D309V11, continuous
[1] "Remove cluster labels:" "GOLGA6B MUTATED"       
clus
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  GOLGA6B MUTATED    6  0  0  0
  GOLGA6B WILD-TYPE 74 35  4  2
D309V12, multiclass
    clus
vv   GOLGA6B MUTATED GOLGA6B WILD-TYPE
  R0               6                74
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GOLGA6B MUTATED       0                         0     6
  GOLGA6B WILD-TYPE     6                         5   108
D309V14, multiclass
                           clus
vv                          GOLGA6B MUTATED GOLGA6B WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V15, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    0  6
  GOLGA6B WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      0    6
  GOLGA6B WILD-TYPE    5   85
                        clus
vv                       GOLGA6B MUTATED GOLGA6B WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(310) Variable = MKI67 MUTATION ANALYSIS
D310V1, survival
                 sevent
clus2              0  1
  MKI67 MUTATED    5  4
  MKI67 WILD-TYPE 58 58
  MKI67 MUTATED MKI67 WILD-TYPE 
              9             116 
  MKI67 MUTATED MKI67 WILD-TYPE 
              4              58 
$`MKI67 MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IO TCGA-FB-AAPZ TCGA-FZ-5919 TCGA-HV-A7OP TCGA-HZ-A77O 
       20.84        63.85        23.54        24.36        32.15         5.26 
TCGA-IB-7651 TCGA-RB-AA9M TCGA-YY-A8LH 
       19.82         9.40        66.28 

$`MKI67 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        15.55         4.04         5.03         1.02 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  MKI67 MUTATED MKI67 WILD-TYPE 
           5.26            0.23 
  MKI67 MUTATED MKI67 WILD-TYPE 
          66.28           90.12 
  MKI67 MUTATED MKI67 WILD-TYPE 
          23.54           15.09 
[1] "5.3 - 66.3 (23.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.7"
D310V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MKI67 MUTATED         0        0        0         1         7         0
  MKI67 WILD-TYPE       1        3       12        18        75         4
                 vv
clus              STAGE IV
  MKI67 MUTATED          0
  MKI67 WILD-TYPE        3
D310V3, multiclass
           clus
vv          MKI67 MUTATED MKI67 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MKI67 MUTATED    1  2     5
  MKI67 WILD-TYPE  4 15    97
D310V4, multiclass
       clus
vv      MKI67 MUTATED MKI67 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V5, binary
                 cls
clus               0  1
  MKI67 MUTATED    1  7
  MKI67 WILD-TYPE 34 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      1    7
  MKI67 WILD-TYPE   34   82
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0             1              34
  1             7              82
[1] 2 2
[1] FALSE
D310V6, binary
                 cls
clus               0  1
  MKI67 MUTATED    2  0
  MKI67 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      2    0
  MKI67 WILD-TYPE   55    3
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D310V7, binary
                 cls
clus               0  1
  MKI67 MUTATED    4  5
  MKI67 WILD-TYPE 47 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      4    5
  MKI67 WILD-TYPE   47   70
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  FEMALE             4              47
  MALE               5              70
[1] 2 2
[1] FALSE
D310V8, binary
                 cls
clus               0  1
  MKI67 MUTATED    5  4
  MKI67 WILD-TYPE 83 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      5    4
  MKI67 WILD-TYPE   83   26
     clus
vv    MKI67 MUTATED MKI67 WILD-TYPE
  NO              5              83
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MKI67 MUTATED                                     7
  MKI67 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MKI67 MUTATED                                       2
  MKI67 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MKI67 MUTATED                                                  0
  MKI67 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MKI67 MUTATED                                     0
  MKI67 WILD-TYPE                                   1
D310V9, multiclass
                                                  clus
vv                                                 MKI67 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MKI67 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V10, continuous
D310V11, continuous
[1] "Remove cluster labels:" "MKI67 MUTATED"         
clus
  MKI67 MUTATED MKI67 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"MKI67 WILD-TYPE" "MKI67 WILD-TYPE" "MKI67 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MKI67 MUTATED    8  0  0  0
  MKI67 WILD-TYPE 72 35  4  2
D310V12, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0             8              72
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MKI67 MUTATED       1                         0     8
  MKI67 WILD-TYPE     5                         5   106
D310V14, multiclass
                           clus
vv                          MKI67 MUTATED MKI67 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V15, binary
                 cls
clus               0  1
  MKI67 MUTATED    0  8
  MKI67 WILD-TYPE  5 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      0    8
  MKI67 WILD-TYPE    5   83
                        clus
vv                       MKI67 MUTATED MKI67 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              83
[1] 2 2
[1] FALSE

Clustering(311) Variable = STK19 MUTATION ANALYSIS
D311V1, survival
                 sevent
clus2              0  1
  STK19 MUTATED    2  2
  STK19 WILD-TYPE 61 60
  STK19 MUTATED STK19 WILD-TYPE 
              4             121 
  STK19 MUTATED STK19 WILD-TYPE 
              2              60 
$`STK19 MUTATED`
TCGA-2J-AABR TCGA-XD-AAUL TCGA-2L-AAQE TCGA-US-A77J 
       14.40        16.37        22.49        18.67 

$`STK19 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  STK19 MUTATED STK19 WILD-TYPE 
          14.40            0.23 
  STK19 MUTATED STK19 WILD-TYPE 
          22.49           90.12 
  STK19 MUTATED STK19 WILD-TYPE 
          17.52           15.19 
[1] "14.4 - 22.5 (17.5)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D311V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  STK19 MUTATED         0        0        0         2         2         0
  STK19 WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  STK19 MUTATED          0
  STK19 WILD-TYPE        3
D311V3, multiclass
           clus
vv          STK19 MUTATED STK19 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  STK19 MUTATED    0  0     4
  STK19 WILD-TYPE  5 17    98
D311V4, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V5, binary
                 cls
clus               0  1
  STK19 MUTATED    2  2
  STK19 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    2
  STK19 WILD-TYPE   33   87
   clus
vv  STK19 MUTATED STK19 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D311V6, binary
                 cls
clus               0  1
  STK19 MUTATED    2  0
  STK19 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    0
  STK19 WILD-TYPE   55    3
   clus
vv  STK19 MUTATED STK19 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D311V7, binary
                 cls
clus               0  1
  STK19 MUTATED    2  2
  STK19 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      2    2
  STK19 WILD-TYPE   49   73
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D311V8, binary
                 cls
clus               0  1
  STK19 MUTATED    3  0
  STK19 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3    0
  STK19 WILD-TYPE   85   30
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STK19 MUTATED                                     4
  STK19 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STK19 MUTATED                                       0
  STK19 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STK19 MUTATED                                                  0
  STK19 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  STK19 MUTATED                                     0
  STK19 WILD-TYPE                                   1
D311V9, multiclass
                                                  clus
vv                                                 STK19 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 STK19 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V10, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-YY-A8LH 
"STK19 WILD-TYPE" 
D311V11, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  STK19 MUTATED    4  0  0  0
  STK19 WILD-TYPE 76 35  4  2
D311V12, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK19 MUTATED       0                         0     4
  STK19 WILD-TYPE     6                         5   110
D311V14, multiclass
                           clus
vv                          STK19 MUTATED STK19 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V15, binary
                 cls
clus               0  1
  STK19 MUTATED    0  2
  STK19 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    2
  STK19 WILD-TYPE    5   89
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(312) Variable = SPANXN3 MUTATION ANALYSIS
D312V1, survival
                   sevent
clus2                0  1
  SPANXN3 MUTATED    3  1
  SPANXN3 WILD-TYPE 60 61
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                4               121 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                1                61 
$`SPANXN3 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABE TCGA-FB-AAQ3 TCGA-US-A776 
       23.97        22.22         1.02        39.98 

$`SPANXN3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
             1.02              0.23 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
            39.98             90.12 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
           23.095            15.190 
[1] "1.0 - 40.0 (23.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.8"
D312V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SPANXN3 MUTATED         0        0        0         2         3         0
  SPANXN3 WILD-TYPE       1        3       12        17        79         4
                   vv
clus                STAGE IV
  SPANXN3 MUTATED          0
  SPANXN3 WILD-TYPE        3
D312V3, multiclass
           clus
vv          SPANXN3 MUTATED SPANXN3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               2                17
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SPANXN3 MUTATED    0  1     4
  SPANXN3 WILD-TYPE  5 16    98
D312V4, multiclass
       clus
vv      SPANXN3 MUTATED SPANXN3 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V5, binary
                   cls
clus                 0  1
  SPANXN3 MUTATED    2  3
  SPANXN3 WILD-TYPE 33 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      2    3
  SPANXN3 WILD-TYPE   33   86
   clus
vv  SPANXN3 MUTATED SPANXN3 WILD-TYPE
  0               2                33
  1               3                86
[1] 2 2
[1] FALSE
D312V6, binary
                   cls
clus                 0  1
  SPANXN3 MUTATED    2  0
  SPANXN3 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      2    0
  SPANXN3 WILD-TYPE   55    3
   clus
vv  SPANXN3 MUTATED SPANXN3 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D312V7, binary
                   cls
clus                 0  1
  SPANXN3 MUTATED    1  4
  SPANXN3 WILD-TYPE 50 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      1    4
  SPANXN3 WILD-TYPE   50   71
        clus
vv       SPANXN3 MUTATED SPANXN3 WILD-TYPE
  FEMALE               1                50
  MALE                 4                71
[1] 2 2
[1] FALSE
D312V8, binary
                   cls
clus                 0  1
  SPANXN3 MUTATED    3  1
  SPANXN3 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      3    1
  SPANXN3 WILD-TYPE   85   29
     clus
vv    SPANXN3 MUTATED SPANXN3 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPANXN3 MUTATED                                     3
  SPANXN3 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPANXN3 MUTATED                                       1
  SPANXN3 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPANXN3 MUTATED                                                  1
  SPANXN3 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SPANXN3 MUTATED                                     0
  SPANXN3 WILD-TYPE                                   1
D312V9, multiclass
                                                  clus
vv                                                 SPANXN3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SPANXN3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V10, continuous
[1] "Remove cluster labels:" "SPANXN3 MUTATED"       
clus
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABF 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1        TCGA-IB-7651 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-YY-A8LH 
"SPANXN3 WILD-TYPE" 
D312V11, continuous
[1] "Remove cluster labels:" "SPANXN3 MUTATED"       
clus
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABF        TCGA-2J-AABO 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX        TCGA-FB-A5VM 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" "SPANXN3 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SPANXN3 MUTATED    5  0  0  0
  SPANXN3 WILD-TYPE 75 35  4  2
D312V12, multiclass
    clus
vv   SPANXN3 MUTATED SPANXN3 WILD-TYPE
  R0               5                75
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPANXN3 MUTATED       0                         0     5
  SPANXN3 WILD-TYPE     6                         5   109
D312V14, multiclass
                           clus
vv                          SPANXN3 MUTATED SPANXN3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V15, binary
                   cls
clus                 0  1
  SPANXN3 MUTATED    0  3
  SPANXN3 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      0    3
  SPANXN3 WILD-TYPE    5   88
                        clus
vv                       SPANXN3 MUTATED SPANXN3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(313) Variable = RTEL1 MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2              0  1
  RTEL1 MUTATED    1  5
  RTEL1 WILD-TYPE 62 57
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              6             119 
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              5              57 
$`RTEL1 MUTATED`
TCGA-US-A77E TCGA-FB-A5VM TCGA-HZ-A49I TCGA-HZ-A77P TCGA-IB-7651 TCGA-RB-A7B8 
       14.14        16.37        10.13        10.85        19.82        15.32 

$`RTEL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        20.19        17.00         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  RTEL1 MUTATED RTEL1 WILD-TYPE 
          10.13            0.23 
  RTEL1 MUTATED RTEL1 WILD-TYPE 
          19.82           90.12 
  RTEL1 MUTATED RTEL1 WILD-TYPE 
          14.73           15.22 
[1] "10.1 - 19.8 (14.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.2"
D313V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RTEL1 MUTATED         0        0        1         0         5         0
  RTEL1 WILD-TYPE       1        3       11        19        77         4
                 vv
clus              STAGE IV
  RTEL1 MUTATED          0
  RTEL1 WILD-TYPE        3
D313V3, multiclass
           clus
vv          RTEL1 MUTATED RTEL1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RTEL1 MUTATED    0  1     5
  RTEL1 WILD-TYPE  5 16    97
D313V4, multiclass
       clus
vv      RTEL1 MUTATED RTEL1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V5, binary
                 cls
clus               0  1
  RTEL1 MUTATED    1  5
  RTEL1 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTEL1 MUTATED      1    5
  RTEL1 WILD-TYPE   34   84
   clus
vv  RTEL1 MUTATED RTEL1 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D313V6, binary
                 cls
clus               0  1
  RTEL1 MUTATED    2  0
  RTEL1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTEL1 MUTATED      2    0
  RTEL1 WILD-TYPE   55    3
   clus
vv  RTEL1 MUTATED RTEL1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D313V7, binary
                 cls
clus               0  1
  RTEL1 MUTATED    2  4
  RTEL1 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTEL1 MUTATED      2    4
  RTEL1 WILD-TYPE   49   71
        clus
vv       RTEL1 MUTATED RTEL1 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D313V8, binary
                 cls
clus               0  1
  RTEL1 MUTATED    5  1
  RTEL1 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTEL1 MUTATED      5    1
  RTEL1 WILD-TYPE   83   29
     clus
vv    RTEL1 MUTATED RTEL1 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RTEL1 MUTATED                                     3
  RTEL1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RTEL1 MUTATED                                       3
  RTEL1 WILD-TYPE                                    15
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RTEL1 MUTATED                                                  0
  RTEL1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RTEL1 MUTATED                                     0
  RTEL1 WILD-TYPE                                   1
D313V9, multiclass
                                                  clus
vv                                                 RTEL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RTEL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V10, continuous
[1] "Remove cluster labels:" "RTEL1 MUTATED"         
clus
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-YY-A8LH 
"RTEL1 WILD-TYPE" 
D313V11, continuous
[1] "Remove cluster labels:" "RTEL1 MUTATED"         
clus
  RTEL1 MUTATED RTEL1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" "RTEL1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RTEL1 MUTATED    4  2  0  0
  RTEL1 WILD-TYPE 76 33  4  2
D313V12, multiclass
    clus
vv   RTEL1 MUTATED RTEL1 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RTEL1 MUTATED       0                         0     6
  RTEL1 WILD-TYPE     6                         5   108
D313V14, multiclass
                           clus
vv                          RTEL1 MUTATED RTEL1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V15, binary
                 cls
clus               0  1
  RTEL1 MUTATED    0  6
  RTEL1 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RTEL1 MUTATED      0    6
  RTEL1 WILD-TYPE    5   85
                        clus
vv                       RTEL1 MUTATED RTEL1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(314) Variable = NWD1 MUTATION ANALYSIS
D314V1, survival
                sevent
clus2             0  1
  NWD1 MUTATED    5  3
  NWD1 WILD-TYPE 58 59
  NWD1 MUTATED NWD1 WILD-TYPE 
             8            117 
  NWD1 MUTATED NWD1 WILD-TYPE 
             3             59 
$`NWD1 MUTATED`
TCGA-2J-AAB8 TCGA-3E-AAAY TCGA-F2-A7TX TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-AAUP 
        2.63        75.12         3.12        17.00        19.82        14.17 
TCGA-US-A77J TCGA-YB-A89D 
       18.67        11.51 

$`NWD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        24.43        71.74        19.46 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NWD1 MUTATED NWD1 WILD-TYPE 
          2.63           0.23 
  NWD1 MUTATED NWD1 WILD-TYPE 
         75.12          90.12 
  NWD1 MUTATED NWD1 WILD-TYPE 
        15.585         15.220 
[1] "2.6 - 75.1 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D314V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NWD1 MUTATED         0        0        0         1         7         0
  NWD1 WILD-TYPE       1        3       12        18        75         4
                vv
clus             STAGE IV
  NWD1 MUTATED          0
  NWD1 WILD-TYPE        3
D314V3, multiclass
           clus
vv          NWD1 MUTATED NWD1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NWD1 MUTATED    0  0     8
  NWD1 WILD-TYPE  5 17    94
D314V4, multiclass
       clus
vv      NWD1 MUTATED NWD1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V5, binary
                cls
clus              0  1
  NWD1 MUTATED    1  7
  NWD1 WILD-TYPE 34 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      1    7
  NWD1 WILD-TYPE   34   82
   clus
vv  NWD1 MUTATED NWD1 WILD-TYPE
  0            1             34
  1            7             82
[1] 2 2
[1] FALSE
D314V6, binary
                cls
clus              0  1
  NWD1 MUTATED    5  0
  NWD1 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      5    0
  NWD1 WILD-TYPE   52    3
   clus
vv  NWD1 MUTATED NWD1 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D314V7, binary
                cls
clus              0  1
  NWD1 MUTATED    2  6
  NWD1 WILD-TYPE 49 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      2    6
  NWD1 WILD-TYPE   49   69
        clus
vv       NWD1 MUTATED NWD1 WILD-TYPE
  FEMALE            2             49
  MALE              6             69
[1] 2 2
[1] FALSE
D314V8, binary
                cls
clus              0  1
  NWD1 MUTATED    5  1
  NWD1 WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      5    1
  NWD1 WILD-TYPE   83   29
     clus
vv    NWD1 MUTATED NWD1 WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NWD1 MUTATED                                     8
  NWD1 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NWD1 MUTATED                                       0
  NWD1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NWD1 MUTATED                                                  0
  NWD1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NWD1 MUTATED                                     0
  NWD1 WILD-TYPE                                   1
D314V9, multiclass
                                                  clus
vv                                                 NWD1 MUTATED NWD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V10, continuous
[1] "Remove cluster labels:" "NWD1 MUTATED"          
clus
  NWD1 MUTATED NWD1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-YY-A8LH 
"NWD1 WILD-TYPE" 
D314V11, continuous
[1] "Remove cluster labels:" "NWD1 MUTATED"          
clus
  NWD1 MUTATED NWD1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" "NWD1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  NWD1 MUTATED    3  4  0  0
  NWD1 WILD-TYPE 77 31  4  2
D314V12, multiclass
    clus
vv   NWD1 MUTATED NWD1 WILD-TYPE
  R0            3             77
  R1            4             31
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NWD1 MUTATED       0                         0     8
  NWD1 WILD-TYPE     6                         5   106
D314V14, multiclass
                           clus
vv                          NWD1 MUTATED NWD1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V15, binary
                cls
clus              0  1
  NWD1 MUTATED    0  6
  NWD1 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  NWD1 MUTATED      0    6
  NWD1 WILD-TYPE    5   85
                        clus
vv                       NWD1 MUTATED NWD1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(315) Variable = NBPF1 MUTATION ANALYSIS
D315V1, survival
                 sevent
clus2              0  1
  NBPF1 MUTATED    2  3
  NBPF1 WILD-TYPE 61 59
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              5             120 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              3              59 
$`NBPF1 MUTATED`
TCGA-HZ-A77Q TCGA-2L-AAQL TCGA-3A-A9IX TCGA-FB-AAPU TCGA-IB-7651 
        1.08         9.60        34.09        12.53        19.82 

$`NBPF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           1.08            0.23 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          34.09           90.12 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          12.53           15.27 
[1] "1.1 - 34.1 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D315V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NBPF1 MUTATED         0        1        0         1         3         0
  NBPF1 WILD-TYPE       1        2       12        18        79         4
                 vv
clus              STAGE IV
  NBPF1 MUTATED          0
  NBPF1 WILD-TYPE        3
D315V3, multiclass
           clus
vv          NBPF1 MUTATED NBPF1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NBPF1 MUTATED    1  0     4
  NBPF1 WILD-TYPE  4 17    98
D315V4, multiclass
       clus
vv      NBPF1 MUTATED NBPF1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V5, binary
                 cls
clus               0  1
  NBPF1 MUTATED    2  3
  NBPF1 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      2    3
  NBPF1 WILD-TYPE   33   86
   clus
vv  NBPF1 MUTATED NBPF1 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D315V6, binary
                 cls
clus               0  1
  NBPF1 MUTATED    1  0
  NBPF1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      1    0
  NBPF1 WILD-TYPE   56    3
   clus
vv  NBPF1 MUTATED NBPF1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D315V7, binary
                 cls
clus               0  1
  NBPF1 MUTATED    3  2
  NBPF1 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      3    2
  NBPF1 WILD-TYPE   48   73
        clus
vv       NBPF1 MUTATED NBPF1 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D315V8, binary
                 cls
clus               0  1
  NBPF1 MUTATED    3  1
  NBPF1 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      3    1
  NBPF1 WILD-TYPE   85   29
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF1 MUTATED                                     4
  NBPF1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF1 MUTATED                                       1
  NBPF1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF1 MUTATED                                                  0
  NBPF1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NBPF1 MUTATED                                     0
  NBPF1 WILD-TYPE                                   1
D315V9, multiclass
                                                  clus
vv                                                 NBPF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NBPF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V10, continuous
D315V11, continuous
                 vv
clus              R0 R1 R2 RX
  NBPF1 MUTATED    3  1  0  1
  NBPF1 WILD-TYPE 77 34  4  1
D315V12, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF1 MUTATED       1                         0     4
  NBPF1 WILD-TYPE     5                         5   110
D315V14, multiclass
                           clus
vv                          NBPF1 MUTATED NBPF1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V15, binary
                 cls
clus               0  1
  NBPF1 MUTATED    0  4
  NBPF1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      0    4
  NBPF1 WILD-TYPE    5   87
                        clus
vv                       NBPF1 MUTATED NBPF1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(316) Variable = PPP1R10 MUTATION ANALYSIS
D316V1, survival
                   sevent
clus2                0  1
  PPP1R10 MUTATED    2  2
  PPP1R10 WILD-TYPE 61 60
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                4               121 
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                2                60 
$`PPP1R10 MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9IZ TCGA-FB-AAQ1 TCGA-HZ-A77P 
       60.95        10.13         4.04        10.85 

$`PPP1R10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
             4.04              0.23 
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
            60.95             90.12 
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
            10.49             15.32 
[1] "4.0 - 61.0 (10.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D316V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPP1R10 MUTATED         0        0        1         0         3         0
  PPP1R10 WILD-TYPE       1        3       11        19        79         4
                   vv
clus                STAGE IV
  PPP1R10 MUTATED          0
  PPP1R10 WILD-TYPE        3
D316V3, multiclass
           clus
vv          PPP1R10 MUTATED PPP1R10 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  PPP1R10 MUTATED    0  1     3
  PPP1R10 WILD-TYPE  5 16    99
D316V4, multiclass
       clus
vv      PPP1R10 MUTATED PPP1R10 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V5, binary
                   cls
clus                 0  1
  PPP1R10 MUTATED    1  3
  PPP1R10 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R10 MUTATED      1    3
  PPP1R10 WILD-TYPE   34   86
   clus
vv  PPP1R10 MUTATED PPP1R10 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D316V6, binary
                   cls
clus                 0  1
  PPP1R10 MUTATED    0  0
  PPP1R10 WILD-TYPE 57  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R10 MUTATED      0    0
  PPP1R10 WILD-TYPE   57    3
D316V7, binary
                   cls
clus                 0  1
  PPP1R10 MUTATED    0  4
  PPP1R10 WILD-TYPE 51 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R10 MUTATED      0    4
  PPP1R10 WILD-TYPE   51   71
        clus
vv       PPP1R10 MUTATED PPP1R10 WILD-TYPE
  FEMALE               0                51
  MALE                 4                71
[1] 2 2
[1] FALSE
D316V8, binary
                   cls
clus                 0  1
  PPP1R10 MUTATED    4  0
  PPP1R10 WILD-TYPE 84 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R10 MUTATED      4    0
  PPP1R10 WILD-TYPE   84   30
     clus
vv    PPP1R10 MUTATED PPP1R10 WILD-TYPE
  NO                4                84
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPP1R10 MUTATED                                     2
  PPP1R10 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPP1R10 MUTATED                                       2
  PPP1R10 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPP1R10 MUTATED                                                  0
  PPP1R10 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPP1R10 MUTATED                                     0
  PPP1R10 WILD-TYPE                                   1
D316V9, multiclass
                                                  clus
vv                                                 PPP1R10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PPP1R10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V10, continuous
[1] "Remove cluster labels:" "PPP1R10 MUTATED"       
clus
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                1                38 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
D316V11, continuous
[1] "Remove cluster labels:" "PPP1R10 MUTATED"       
clus
  PPP1R10 MUTATED PPP1R10 WILD-TYPE 
                1                32 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" "PPP1R10 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  PPP1R10 MUTATED    2  2  0  0
  PPP1R10 WILD-TYPE 78 33  4  2
D316V12, multiclass
    clus
vv   PPP1R10 MUTATED PPP1R10 WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP1R10 MUTATED       0                         0     4
  PPP1R10 WILD-TYPE     6                         5   110
D316V14, multiclass
                           clus
vv                          PPP1R10 MUTATED PPP1R10 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V15, binary
                   cls
clus                 0  1
  PPP1R10 MUTATED    1  3
  PPP1R10 WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R10 MUTATED      1    3
  PPP1R10 WILD-TYPE    4   88
                        clus
vv                       PPP1R10 MUTATED PPP1R10 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(317) Variable = DDX50 MUTATION ANALYSIS
D317V1, survival
                 sevent
clus2              0  1
  DDX50 MUTATED    2  3
  DDX50 WILD-TYPE 61 59
  DDX50 MUTATED DDX50 WILD-TYPE 
              5             120 
  DDX50 MUTATED DDX50 WILD-TYPE 
              3              59 
$`DDX50 MUTATED`
TCGA-2J-AABA TCGA-IB-7651 TCGA-IB-A7M4 TCGA-IB-AAUW TCGA-YB-A89D 
       19.96        19.82        15.88         7.56        11.51 

$`DDX50 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  DDX50 MUTATED DDX50 WILD-TYPE 
           7.56            0.23 
  DDX50 MUTATED DDX50 WILD-TYPE 
          19.96           90.12 
  DDX50 MUTATED DDX50 WILD-TYPE 
         15.880          15.205 
[1] "7.6 - 20.0 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D317V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DDX50 MUTATED         0        0        0         0         5         0
  DDX50 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  DDX50 MUTATED          0
  DDX50 WILD-TYPE        3
D317V3, multiclass
           clus
vv          DDX50 MUTATED DDX50 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DDX50 MUTATED    0  0     5
  DDX50 WILD-TYPE  5 17    97
D317V4, multiclass
       clus
vv      DDX50 MUTATED DDX50 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V5, binary
                 cls
clus               0  1
  DDX50 MUTATED    0  5
  DDX50 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      0    5
  DDX50 WILD-TYPE   35   84
   clus
vv  DDX50 MUTATED DDX50 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D317V6, binary
                 cls
clus               0  1
  DDX50 MUTATED    3  0
  DDX50 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      3    0
  DDX50 WILD-TYPE   54    3
   clus
vv  DDX50 MUTATED DDX50 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D317V7, binary
                 cls
clus               0  1
  DDX50 MUTATED    2  3
  DDX50 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      2    3
  DDX50 WILD-TYPE   49   72
        clus
vv       DDX50 MUTATED DDX50 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D317V8, binary
                 cls
clus               0  1
  DDX50 MUTATED    4  1
  DDX50 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      4    1
  DDX50 WILD-TYPE   84   29
     clus
vv    DDX50 MUTATED DDX50 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DDX50 MUTATED                                     5
  DDX50 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DDX50 MUTATED                                       0
  DDX50 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DDX50 MUTATED                                                  0
  DDX50 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DDX50 MUTATED                                     0
  DDX50 WILD-TYPE                                   1
D317V9, multiclass
                                                  clus
vv                                                 DDX50 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DDX50 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V10, continuous
D317V11, continuous
[1] "Remove cluster labels:" "DDX50 MUTATED"         
clus
  DDX50 MUTATED DDX50 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-AAUQ 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"DDX50 WILD-TYPE" "DDX50 WILD-TYPE" "DDX50 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DDX50 MUTATED    4  1  0  0
  DDX50 WILD-TYPE 76 34  4  2
D317V12, multiclass
    clus
vv   DDX50 MUTATED DDX50 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX50 MUTATED       0                         0     5
  DDX50 WILD-TYPE     6                         5   109
D317V14, multiclass
                           clus
vv                          DDX50 MUTATED DDX50 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V15, binary
                 cls
clus               0  1
  DDX50 MUTATED    0  4
  DDX50 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX50 MUTATED      0    4
  DDX50 WILD-TYPE    5   87
                        clus
vv                       DDX50 MUTATED DDX50 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(318) Variable = HOXA1 MUTATION ANALYSIS
D318V1, survival
                 sevent
clus2              0  1
  HOXA1 MUTATED    2  2
  HOXA1 WILD-TYPE 61 60
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              4             121 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              2              60 
$`HOXA1 MUTATED`
TCGA-LB-A7SX TCGA-3A-A9IV TCGA-IB-7651 TCGA-LB-A8F3 
       12.92        36.26        19.82        12.46 

$`HOXA1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HOXA1 MUTATED HOXA1 WILD-TYPE 
          12.46            0.23 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
          36.26           90.12 
  HOXA1 MUTATED HOXA1 WILD-TYPE 
          16.37           15.22 
[1] "12.5 - 36.3 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D318V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HOXA1 MUTATED         0        0        1         1         2         0
  HOXA1 WILD-TYPE       1        3       11        18        80         4
                 vv
clus              STAGE IV
  HOXA1 MUTATED          0
  HOXA1 WILD-TYPE        3
D318V3, multiclass
           clus
vv          HOXA1 MUTATED HOXA1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HOXA1 MUTATED    0  1     3
  HOXA1 WILD-TYPE  5 16    99
D318V4, multiclass
       clus
vv      HOXA1 MUTATED HOXA1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V5, binary
                 cls
clus               0  1
  HOXA1 MUTATED    2  2
  HOXA1 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      2    2
  HOXA1 WILD-TYPE   33   87
   clus
vv  HOXA1 MUTATED HOXA1 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D318V6, binary
                 cls
clus               0  1
  HOXA1 MUTATED    1  0
  HOXA1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      1    0
  HOXA1 WILD-TYPE   56    3
   clus
vv  HOXA1 MUTATED HOXA1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D318V7, binary
                 cls
clus               0  1
  HOXA1 MUTATED    4  0
  HOXA1 WILD-TYPE 47 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      4    0
  HOXA1 WILD-TYPE   47   75
        clus
vv       HOXA1 MUTATED HOXA1 WILD-TYPE
  FEMALE             4              47
  MALE               0              75
[1] 2 2
[1] FALSE
D318V8, binary
                 cls
clus               0  1
  HOXA1 MUTATED    3  1
  HOXA1 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      3    1
  HOXA1 WILD-TYPE   85   29
     clus
vv    HOXA1 MUTATED HOXA1 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HOXA1 MUTATED                                     3
  HOXA1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HOXA1 MUTATED                                       1
  HOXA1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HOXA1 MUTATED                                                  0
  HOXA1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HOXA1 MUTATED                                     0
  HOXA1 WILD-TYPE                                   1
D318V9, multiclass
                                                  clus
vv                                                 HOXA1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HOXA1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V10, continuous
[1] "Remove cluster labels:" "HOXA1 MUTATED"         
clus
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-YY-A8LH 
"HOXA1 WILD-TYPE" 
D318V11, continuous
[1] "Remove cluster labels:" "HOXA1 MUTATED"         
clus
  HOXA1 MUTATED HOXA1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" "HOXA1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HOXA1 MUTATED    3  1  0  0
  HOXA1 WILD-TYPE 77 34  4  2
D318V12, multiclass
    clus
vv   HOXA1 MUTATED HOXA1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HOXA1 MUTATED       0                         2     2
  HOXA1 WILD-TYPE     6                         3   112
D318V14, multiclass
                           clus
vv                          HOXA1 MUTATED HOXA1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V15, binary
                 cls
clus               0  1
  HOXA1 MUTATED    0  4
  HOXA1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA1 MUTATED      0    4
  HOXA1 WILD-TYPE    5   87
                        clus
vv                       HOXA1 MUTATED HOXA1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(319) Variable = SLC4A3 MUTATION ANALYSIS
D319V1, survival
                  sevent
clus2               0  1
  SLC4A3 MUTATED    5  1
  SLC4A3 WILD-TYPE 58 61
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               6              119 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               1               61 
$`SLC4A3 MUTATED`
TCGA-2J-AABE TCGA-2J-AABH TCGA-3A-A9IH TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-A6UF 
       22.22        42.31        33.57        19.82        36.69        21.90 

$`SLC4A3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       20.61        19.96        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           19.82             0.23 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           42.31            90.12 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
          27.895           15.060 
[1] "19.8 - 42.3 (27.9)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "5.6"
D319V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC4A3 MUTATED         0        1        0         2         3         0
  SLC4A3 WILD-TYPE       1        2       12        17        79         4
                  vv
clus               STAGE IV
  SLC4A3 MUTATED          0
  SLC4A3 WILD-TYPE        3
D319V3, multiclass
           clus
vv          SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SLC4A3 MUTATED    1  0     5
  SLC4A3 WILD-TYPE  4 17    97
D319V4, multiclass
       clus
vv      SLC4A3 MUTATED SLC4A3 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V5, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    3  3
  SLC4A3 WILD-TYPE 32 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      3    3
  SLC4A3 WILD-TYPE   32   86
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0              3               32
  1              3               86
[1] 2 2
[1] FALSE
D319V6, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    5  0
  SLC4A3 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      5    0
  SLC4A3 WILD-TYPE   52    3
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D319V7, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    3  3
  SLC4A3 WILD-TYPE 48 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      3    3
  SLC4A3 WILD-TYPE   48   72
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE              3               48
  MALE                3               72
[1] 2 2
[1] FALSE
D319V8, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    5  1
  SLC4A3 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      5    1
  SLC4A3 WILD-TYPE   83   29
     clus
vv    SLC4A3 MUTATED SLC4A3 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC4A3 MUTATED                                     5
  SLC4A3 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC4A3 MUTATED                                       1
  SLC4A3 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC4A3 MUTATED                                                  0
  SLC4A3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC4A3 MUTATED                                     0
  SLC4A3 WILD-TYPE                                   1
D319V9, multiclass
                                                  clus
vv                                                 SLC4A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SLC4A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V10, continuous
D319V11, continuous
                  vv
clus               R0 R1 R2 RX
  SLC4A3 MUTATED    4  2  0  0
  SLC4A3 WILD-TYPE 76 33  4  2
D319V12, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0              4               76
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC4A3 MUTATED       1                         0     5
  SLC4A3 WILD-TYPE     5                         5   109
D319V14, multiclass
                           clus
vv                          SLC4A3 MUTATED SLC4A3 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V15, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    0  4
  SLC4A3 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      0    4
  SLC4A3 WILD-TYPE    5   87
                        clus
vv                       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(320) Variable = XPA MUTATION ANALYSIS
D320V1, survival
               sevent
clus2            0  1
  XPA MUTATED    1  2
  XPA WILD-TYPE 62 60
  XPA MUTATED XPA WILD-TYPE 
            3           122 
  XPA MUTATED XPA WILD-TYPE 
            2            60 
$`XPA MUTATED`
TCGA-F2-A44G TCGA-3A-A9IV TCGA-FZ-5922 
        7.66        36.26        36.20 

$`XPA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  XPA MUTATED XPA WILD-TYPE 
         7.66          0.23 
  XPA MUTATED XPA WILD-TYPE 
        36.26         90.12 
  XPA MUTATED XPA WILD-TYPE 
       36.200        15.205 
[1] "7.7 - 36.3 (36.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D320V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XPA MUTATED         0        0        1         1         1         0
  XPA WILD-TYPE       1        3       11        18        81         4
               vv
clus            STAGE IV
  XPA MUTATED          0
  XPA WILD-TYPE        3
D320V3, multiclass
           clus
vv          XPA MUTATED XPA WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            1            11
  STAGE IIA           1            18
  STAGE IIB           1            81
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  XPA MUTATED     0   1     2
  XPA WILD-TYPE   5  16   100
D320V4, multiclass
       clus
vv      XPA MUTATED XPA WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           2           100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V5, binary
               cls
clus             0  1
  XPA MUTATED    2  1
  XPA WILD-TYPE 33 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  XPA MUTATED      2    1
  XPA WILD-TYPE   33   88
   clus
vv  XPA MUTATED XPA WILD-TYPE
  0           2            33
  1           1            88
[1] 2 2
[1] FALSE
D320V6, binary
               cls
clus             0  1
  XPA MUTATED    2  0
  XPA WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  XPA MUTATED      2    0
  XPA WILD-TYPE   55    3
   clus
vv  XPA MUTATED XPA WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D320V7, binary
               cls
clus             0  1
  XPA MUTATED    2  1
  XPA WILD-TYPE 49 74
[1] "tbl2"
               cls
clus            [,1] [,2]
  XPA MUTATED      2    1
  XPA WILD-TYPE   49   74
        clus
vv       XPA MUTATED XPA WILD-TYPE
  FEMALE           2            49
  MALE             1            74
[1] 2 2
[1] FALSE
D320V8, binary
               cls
clus             0  1
  XPA MUTATED    2  1
  XPA WILD-TYPE 86 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  XPA MUTATED      2    1
  XPA WILD-TYPE   86   29
     clus
vv    XPA MUTATED XPA WILD-TYPE
  NO            2            86
  YES           1            29
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XPA MUTATED                                     2
  XPA WILD-TYPE                                 103
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XPA MUTATED                                       1
  XPA WILD-TYPE                                    17
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XPA MUTATED                                                  0
  XPA WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  XPA MUTATED                                     0
  XPA WILD-TYPE                                   1
D320V9, multiclass
                                                  clus
vv                                                 XPA MUTATED XPA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        2           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      1            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V10, continuous
D320V11, continuous
               vv
clus            R0 R1 R2 RX
  XPA MUTATED    2  1  0  0
  XPA WILD-TYPE 78 34  4  2
D320V12, multiclass
    clus
vv   XPA MUTATED XPA WILD-TYPE
  R0           2            78
  R1           1            34
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XPA MUTATED       0                         0     3
  XPA WILD-TYPE     6                         5   111
D320V14, multiclass
                           clus
vv                          XPA MUTATED XPA WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V15, binary
               cls
clus             0  1
  XPA MUTATED    0  3
  XPA WILD-TYPE  5 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  XPA MUTATED      0    3
  XPA WILD-TYPE    5   88
                        clus
vv                       XPA MUTATED XPA WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3            88
[1] 2 2
[1] FALSE

Clustering(321) Variable = FADS2 MUTATION ANALYSIS
D321V1, survival
                 sevent
clus2              0  1
  FADS2 MUTATED    1  3
  FADS2 WILD-TYPE 62 59
  FADS2 MUTATED FADS2 WILD-TYPE 
              4             121 
  FADS2 MUTATED FADS2 WILD-TYPE 
              3              59 
$`FADS2 MUTATED`
TCGA-2J-AAB6 TCGA-FZ-5922 TCGA-IB-AAUS TCGA-RB-A7B8 
        9.63        36.20         7.40        15.32 

$`FADS2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FADS2 MUTATED FADS2 WILD-TYPE 
           7.40            0.23 
  FADS2 MUTATED FADS2 WILD-TYPE 
          36.20           90.12 
  FADS2 MUTATED FADS2 WILD-TYPE 
         12.475          15.220 
[1] "7.4 - 36.2 (12.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D321V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FADS2 MUTATED         0        0        0         2         2         0
  FADS2 WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  FADS2 MUTATED          0
  FADS2 WILD-TYPE        3
D321V3, multiclass
           clus
vv          FADS2 MUTATED FADS2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FADS2 MUTATED    0  0     4
  FADS2 WILD-TYPE  5 17    98
D321V4, multiclass
       clus
vv      FADS2 MUTATED FADS2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V5, binary
                 cls
clus               0  1
  FADS2 MUTATED    2  2
  FADS2 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FADS2 MUTATED      2    2
  FADS2 WILD-TYPE   33   87
   clus
vv  FADS2 MUTATED FADS2 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D321V6, binary
                 cls
clus               0  1
  FADS2 MUTATED    3  0
  FADS2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FADS2 MUTATED      3    0
  FADS2 WILD-TYPE   54    3
   clus
vv  FADS2 MUTATED FADS2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D321V7, binary
                 cls
clus               0  1
  FADS2 MUTATED    2  2
  FADS2 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FADS2 MUTATED      2    2
  FADS2 WILD-TYPE   49   73
        clus
vv       FADS2 MUTATED FADS2 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D321V8, binary
                 cls
clus               0  1
  FADS2 MUTATED    4  0
  FADS2 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FADS2 MUTATED      4    0
  FADS2 WILD-TYPE   84   30
     clus
vv    FADS2 MUTATED FADS2 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FADS2 MUTATED                                     3
  FADS2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FADS2 MUTATED                                       1
  FADS2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FADS2 MUTATED                                                  0
  FADS2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FADS2 MUTATED                                     0
  FADS2 WILD-TYPE                                   1
D321V9, multiclass
                                                  clus
vv                                                 FADS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FADS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V10, continuous
[1] "Remove cluster labels:" "FADS2 MUTATED"         
clus
  FADS2 MUTATED FADS2 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
D321V11, continuous
[1] "Remove cluster labels:" "FADS2 MUTATED"         
clus
  FADS2 MUTATED FADS2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" "FADS2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  FADS2 MUTATED    3  1  0  0
  FADS2 WILD-TYPE 77 34  4  2
D321V12, multiclass
    clus
vv   FADS2 MUTATED FADS2 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FADS2 MUTATED       0                         0     4
  FADS2 WILD-TYPE     6                         5   110
D321V14, multiclass
                           clus
vv                          FADS2 MUTATED FADS2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V15, binary
                 cls
clus               0  1
  FADS2 MUTATED    0  3
  FADS2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FADS2 MUTATED      0    3
  FADS2 WILD-TYPE    5   88
                        clus
vv                       FADS2 MUTATED FADS2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(322) Variable = SYT2 MUTATION ANALYSIS
D322V1, survival
                sevent
clus2             0  1
  SYT2 MUTATED    1  2
  SYT2 WILD-TYPE 62 60
  SYT2 MUTATED SYT2 WILD-TYPE 
             3            122 
  SYT2 MUTATED SYT2 WILD-TYPE 
             2             60 
$`SYT2 MUTATED`
TCGA-FB-A5VM TCGA-HV-AA8X TCGA-YH-A8SY 
       16.37        17.49        12.76 

$`SYT2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SYT2 MUTATED SYT2 WILD-TYPE 
         12.76           0.23 
  SYT2 MUTATED SYT2 WILD-TYPE 
         17.49          90.12 
  SYT2 MUTATED SYT2 WILD-TYPE 
        16.370         15.205 
[1] "12.8 - 17.5 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.5"
D322V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYT2 MUTATED         0        0        1         0         2         1
  SYT2 WILD-TYPE       1        3       11        19        80         3
                vv
clus             STAGE IV
  SYT2 MUTATED          0
  SYT2 WILD-TYPE        3
D322V3, multiclass
           clus
vv          SYT2 MUTATED SYT2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  SYT2 MUTATED     0   2     2
  SYT2 WILD-TYPE   5  15   100
D322V4, multiclass
       clus
vv      SYT2 MUTATED SYT2 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V5, binary
                cls
clus              0  1
  SYT2 MUTATED    1  3
  SYT2 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      1    3
  SYT2 WILD-TYPE   34   86
   clus
vv  SYT2 MUTATED SYT2 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D322V6, binary
                cls
clus              0  1
  SYT2 MUTATED    1  0
  SYT2 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      1    0
  SYT2 WILD-TYPE   56    3
   clus
vv  SYT2 MUTATED SYT2 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D322V7, binary
                cls
clus              0  1
  SYT2 MUTATED    2  2
  SYT2 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      2    2
  SYT2 WILD-TYPE   49   73
        clus
vv       SYT2 MUTATED SYT2 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D322V8, binary
                cls
clus              0  1
  SYT2 MUTATED    2  1
  SYT2 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      2    1
  SYT2 WILD-TYPE   86   29
     clus
vv    SYT2 MUTATED SYT2 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYT2 MUTATED                                     3
  SYT2 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYT2 MUTATED                                       0
  SYT2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYT2 MUTATED                                                  0
  SYT2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYT2 MUTATED                                     0
  SYT2 WILD-TYPE                                   1
D322V9, multiclass
                                                  clus
vv                                                 SYT2 MUTATED SYT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V10, continuous
[1] "Remove cluster labels:" "SYT2 MUTATED"          
clus
  SYT2 MUTATED SYT2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-YY-A8LH 
"SYT2 WILD-TYPE" 
D322V11, continuous
[1] "Remove cluster labels:" "SYT2 MUTATED"          
clus
  SYT2 MUTATED SYT2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"SYT2 WILD-TYPE" "SYT2 WILD-TYPE" "SYT2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  SYT2 MUTATED    2  0  1  0
  SYT2 WILD-TYPE 78 35  3  2
D322V12, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  R0            2             78
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYT2 MUTATED       1                         0     3
  SYT2 WILD-TYPE     5                         5   111
D322V14, multiclass
                           clus
vv                          SYT2 MUTATED SYT2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V15, binary
                cls
clus              0  1
  SYT2 MUTATED    0  3
  SYT2 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      0    3
  SYT2 WILD-TYPE    5   88
                        clus
vv                       SYT2 MUTATED SYT2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(323) Variable = RBM33 MUTATION ANALYSIS
D323V1, survival
                 sevent
clus2              0  1
  RBM33 MUTATED    4  2
  RBM33 WILD-TYPE 59 60
  RBM33 MUTATED RBM33 WILD-TYPE 
              6             119 
  RBM33 MUTATED RBM33 WILD-TYPE 
              2              60 
$`RBM33 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABP TCGA-HV-A7OL TCGA-IB-7651 TCGA-XN-A8T3 TCGA-YH-A8SY 
        9.63        15.22         8.28        19.82        31.27        12.76 

$`RBM33 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        23.67        11.51        66.28        15.35 

  RBM33 MUTATED RBM33 WILD-TYPE 
           8.28            0.23 
  RBM33 MUTATED RBM33 WILD-TYPE 
          31.27           90.12 
  RBM33 MUTATED RBM33 WILD-TYPE 
          13.99           15.32 
[1] "8.3 - 31.3 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D323V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM33 MUTATED         0        0        1         2         2         1
  RBM33 WILD-TYPE       1        3       11        17        80         3
                 vv
clus              STAGE IV
  RBM33 MUTATED          0
  RBM33 WILD-TYPE        3
D323V3, multiclass
           clus
vv          RBM33 MUTATED RBM33 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM33 MUTATED    0  1     5
  RBM33 WILD-TYPE  5 16    97
D323V4, multiclass
       clus
vv      RBM33 MUTATED RBM33 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V5, binary
                 cls
clus               0  1
  RBM33 MUTATED    3  3
  RBM33 WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      3    3
  RBM33 WILD-TYPE   32   86
   clus
vv  RBM33 MUTATED RBM33 WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D323V6, binary
                 cls
clus               0  1
  RBM33 MUTATED    4  0
  RBM33 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      4    0
  RBM33 WILD-TYPE   53    3
   clus
vv  RBM33 MUTATED RBM33 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D323V7, binary
                 cls
clus               0  1
  RBM33 MUTATED    3  3
  RBM33 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      3    3
  RBM33 WILD-TYPE   48   72
        clus
vv       RBM33 MUTATED RBM33 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D323V8, binary
                 cls
clus               0  1
  RBM33 MUTATED    4  2
  RBM33 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      4    2
  RBM33 WILD-TYPE   84   28
     clus
vv    RBM33 MUTATED RBM33 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM33 MUTATED                                     4
  RBM33 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM33 MUTATED                                       0
  RBM33 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM33 MUTATED                                                  0
  RBM33 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM33 MUTATED                                     1
  RBM33 WILD-TYPE                                   0
D323V9, multiclass
                                                  clus
vv                                                 RBM33 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 RBM33 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V10, continuous
[1] "Remove cluster labels:" "RBM33 MUTATED"         
clus
  RBM33 MUTATED RBM33 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
D323V11, continuous
[1] "Remove cluster labels:" "RBM33 MUTATED"         
clus
  RBM33 MUTATED RBM33 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" "RBM33 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RBM33 MUTATED    3  1  1  0
  RBM33 WILD-TYPE 77 34  3  2
D323V12, multiclass
    clus
vv   RBM33 MUTATED RBM33 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM33 MUTATED       1                         0     5
  RBM33 WILD-TYPE     5                         5   109
D323V14, multiclass
                           clus
vv                          RBM33 MUTATED RBM33 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V15, binary
                 cls
clus               0  1
  RBM33 MUTATED    1  2
  RBM33 WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM33 MUTATED      1    2
  RBM33 WILD-TYPE    4   89
                        clus
vv                       RBM33 MUTATED RBM33 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(324) Variable = ESD MUTATION ANALYSIS
D324V1, survival
               sevent
clus2            0  1
  ESD MUTATED    2  3
  ESD WILD-TYPE 61 59
  ESD MUTATED ESD WILD-TYPE 
            5           120 
  ESD MUTATED ESD WILD-TYPE 
            3            59 
$`ESD MUTATED`
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-IB-7651 TCGA-IB-A7LX TCGA-IB-AAUO 
       63.85        50.70        19.82         8.22         7.86 

$`ESD WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
        7.36        24.26        33.57        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ESD MUTATED ESD WILD-TYPE 
         7.86          0.23 
  ESD MUTATED ESD WILD-TYPE 
        63.85         90.12 
  ESD MUTATED ESD WILD-TYPE 
       19.820        15.205 
[1] "7.9 - 63.9 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D324V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ESD MUTATED         0        0        1         0         3         0
  ESD WILD-TYPE       1        3       11        19        79         4
               vv
clus            STAGE IV
  ESD MUTATED          0
  ESD WILD-TYPE        3
D324V3, multiclass
           clus
vv          ESD MUTATED ESD WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            1            11
  STAGE IIA           0            19
  STAGE IIB           3            79
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  ESD MUTATED    0  1     3
  ESD WILD-TYPE  5 16    99
D324V4, multiclass
       clus
vv      ESD MUTATED ESD WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           3            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V5, binary
               cls
clus             0  1
  ESD MUTATED    1  3
  ESD WILD-TYPE 34 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  ESD MUTATED      1    3
  ESD WILD-TYPE   34   86
   clus
vv  ESD MUTATED ESD WILD-TYPE
  0           1            34
  1           3            86
[1] 2 2
[1] FALSE
D324V6, binary
               cls
clus             0  1
  ESD MUTATED    2  0
  ESD WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  ESD MUTATED      2    0
  ESD WILD-TYPE   55    3
   clus
vv  ESD MUTATED ESD WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D324V7, binary
               cls
clus             0  1
  ESD MUTATED    3  2
  ESD WILD-TYPE 48 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  ESD MUTATED      3    2
  ESD WILD-TYPE   48   73
        clus
vv       ESD MUTATED ESD WILD-TYPE
  FEMALE           3            48
  MALE             2            73
[1] 2 2
[1] FALSE
D324V8, binary
               cls
clus             0  1
  ESD MUTATED    5  0
  ESD WILD-TYPE 83 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  ESD MUTATED      5    0
  ESD WILD-TYPE   83   30
     clus
vv    ESD MUTATED ESD WILD-TYPE
  NO            5            83
  YES           0            30
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ESD MUTATED                                     3
  ESD WILD-TYPE                                 102
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ESD MUTATED                                       2
  ESD WILD-TYPE                                    16
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ESD MUTATED                                                  0
  ESD WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  ESD MUTATED                                     0
  ESD WILD-TYPE                                   1
D324V9, multiclass
                                                  clus
vv                                                 ESD MUTATED ESD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        3           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      2            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V10, continuous
[1] "Remove cluster labels:" "ESD MUTATED"           
clus
  ESD MUTATED ESD WILD-TYPE 
            1            38 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-OE-A75W    TCGA-XN-A8T5    TCGA-YY-A8LH 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
D324V11, continuous
[1] "Remove cluster labels:" "ESD MUTATED"           
clus
  ESD MUTATED ESD WILD-TYPE 
            2            31 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7885    TCGA-IB-8126 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI    TCGA-XN-A8T5 
"ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" "ESD WILD-TYPE" 
   TCGA-YY-A8LH 
"ESD WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  ESD MUTATED    4  1  0  0
  ESD WILD-TYPE 76 34  4  2
D324V12, multiclass
    clus
vv   ESD MUTATED ESD WILD-TYPE
  R0           4            76
  R1           1            34
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESD MUTATED       0                         0     5
  ESD WILD-TYPE     6                         5   109
D324V14, multiclass
                           clus
vv                          ESD MUTATED ESD WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               5           109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V15, binary
               cls
clus             0  1
  ESD MUTATED    0  5
  ESD WILD-TYPE  5 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  ESD MUTATED      0    5
  ESD WILD-TYPE    5   86
                        clus
vv                       ESD MUTATED ESD WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           5            86
[1] 2 2
[1] FALSE

Clustering(325) Variable = RANBP2 MUTATION ANALYSIS
D325V1, survival
                  sevent
clus2               0  1
  RANBP2 MUTATED    7  7
  RANBP2 WILD-TYPE 56 55
  RANBP2 MUTATED RANBP2 WILD-TYPE 
              14              111 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               7               55 
$`RANBP2 MUTATED`
TCGA-2J-AABR TCGA-LB-A7SX TCGA-XD-AAUL TCGA-2J-AABU TCGA-FB-A5VM TCGA-FB-A78T 
       14.40        12.92        16.37         9.11        16.37        12.33 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-A6UF 
       32.15        30.25         5.26        19.82        19.82        21.90 
TCGA-LB-A9Q5 TCGA-US-A776 
       10.29        39.98 

$`RANBP2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-2J-AAB1 
       15.78         1.08        15.12        17.26        14.14         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV 
       22.72        42.31        15.91        14.47        15.22        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8X 
       36.20        20.35        17.79        22.06         8.28        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RANBP2 MUTATED RANBP2 WILD-TYPE 
            5.26             0.23 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
           39.98            90.12 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
           16.37            15.19 
[1] "5.3 - 40.0 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D325V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RANBP2 MUTATED         0        0        1         3         9         0
  RANBP2 WILD-TYPE       1        3       11        16        73         4
                  vv
clus               STAGE IV
  RANBP2 MUTATED          1
  RANBP2 WILD-TYPE        2
D325V3, multiclass
           clus
vv          RANBP2 MUTATED RANBP2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              3               16
  STAGE IIB              9               73
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RANBP2 MUTATED    0  2    12
  RANBP2 WILD-TYPE  5 15    90
D325V4, multiclass
       clus
vv      RANBP2 MUTATED RANBP2 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4             12               90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V5, binary
                  cls
clus                0  1
  RANBP2 MUTATED    5  9
  RANBP2 WILD-TYPE 30 80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      5    9
  RANBP2 WILD-TYPE   30   80
   clus
vv  RANBP2 MUTATED RANBP2 WILD-TYPE
  0              5               30
  1              9               80
[1] 2 2
[1] FALSE
D325V6, binary
                  cls
clus                0  1
  RANBP2 MUTATED    7  1
  RANBP2 WILD-TYPE 50  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      7    1
  RANBP2 WILD-TYPE   50    2
   clus
vv  RANBP2 MUTATED RANBP2 WILD-TYPE
  0              7               50
  1              1                2
[1] 2 2
[1] FALSE
D325V7, binary
                  cls
clus                0  1
  RANBP2 MUTATED    6  8
  RANBP2 WILD-TYPE 45 67
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      6    8
  RANBP2 WILD-TYPE   45   67
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  FEMALE              6               45
  MALE                8               67
[1] 2 2
[1] FALSE
D325V8, binary
                  cls
clus                0  1
  RANBP2 MUTATED   12  2
  RANBP2 WILD-TYPE 76 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED     12    2
  RANBP2 WILD-TYPE   76   28
     clus
vv    RANBP2 MUTATED RANBP2 WILD-TYPE
  NO              12               76
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RANBP2 MUTATED                                    11
  RANBP2 WILD-TYPE                                  94
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RANBP2 MUTATED                                       2
  RANBP2 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RANBP2 MUTATED                                                  1
  RANBP2 WILD-TYPE                                                0
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RANBP2 MUTATED                                     0
  RANBP2 WILD-TYPE                                   1
D325V9, multiclass
                                                  clus
vv                                                 RANBP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RANBP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V10, continuous
D325V11, continuous
                  vv
clus               R0 R1 R2 RX
  RANBP2 MUTATED   11  2  1  0
  RANBP2 WILD-TYPE 69 33  3  2
D325V12, multiclass
    clus
vv   RANBP2 MUTATED RANBP2 WILD-TYPE
  R0             11               69
  R1              2               33
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RANBP2 MUTATED       2                         1    11
  RANBP2 WILD-TYPE     4                         4   103
D325V14, multiclass
                           clus
vv                          RANBP2 MUTATED RANBP2 WILD-TYPE
  ASIAN                                  2                4
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                 11              103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V15, binary
                  cls
clus                0  1
  RANBP2 MUTATED    0 10
  RANBP2 WILD-TYPE  5 81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      0   10
  RANBP2 WILD-TYPE    5   81
                        clus
vv                       RANBP2 MUTATED RANBP2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             10               81
[1] 2 2
[1] FALSE

Clustering(326) Variable = ABCB4 MUTATION ANALYSIS
D326V1, survival
                 sevent
clus2              0  1
  ABCB4 MUTATED    4  1
  ABCB4 WILD-TYPE 59 61
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              5             120 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              1              61 
$`ABCB4 MUTATED`
TCGA-3A-A9I5 TCGA-FZ-5921 TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-A5ST 
       58.98         5.10        10.85         0.23        20.88 

$`ABCB4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A9TJ 
       31.86        20.19        17.00        10.13         5.26        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           0.23            0.26 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          58.98           90.12 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          10.85           15.27 
[1] "0.2 - 59.0 (10.8)" "0.3 - 90.1 (15.3)"
[1] "hr=" "2.2"
D326V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ABCB4 MUTATED         0        0        1         0         3         0
  ABCB4 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  ABCB4 MUTATED          0
  ABCB4 WILD-TYPE        3
D326V3, multiclass
           clus
vv          ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ABCB4 MUTATED    0  1     3
  ABCB4 WILD-TYPE  5 16    99
D326V4, multiclass
       clus
vv      ABCB4 MUTATED ABCB4 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V5, binary
                 cls
clus               0  1
  ABCB4 MUTATED    2  3
  ABCB4 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      2    3
  ABCB4 WILD-TYPE   33   86
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D326V6, binary
                 cls
clus               0  1
  ABCB4 MUTATED    2  0
  ABCB4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      2    0
  ABCB4 WILD-TYPE   55    3
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D326V7, binary
                 cls
clus               0  1
  ABCB4 MUTATED    2  3
  ABCB4 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      2    3
  ABCB4 WILD-TYPE   49   72
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D326V8, binary
                 cls
clus               0  1
  ABCB4 MUTATED    2  2
  ABCB4 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      2    2
  ABCB4 WILD-TYPE   86   28
     clus
vv    ABCB4 MUTATED ABCB4 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ABCB4 MUTATED                                     4
  ABCB4 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ABCB4 MUTATED                                       1
  ABCB4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ABCB4 MUTATED                                                  0
  ABCB4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ABCB4 MUTATED                                     0
  ABCB4 WILD-TYPE                                   1
D326V9, multiclass
                                                  clus
vv                                                 ABCB4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ABCB4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V10, continuous
[1] "Remove cluster labels:" "ABCB4 MUTATED"         
clus
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
D326V11, continuous
[1] "Remove cluster labels:" "ABCB4 MUTATED"         
clus
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-IB-7651      TCGA-IB-7885 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" "ABCB4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ABCB4 MUTATED    4  0  0  0
  ABCB4 WILD-TYPE 76 35  4  2
D326V12, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCB4 MUTATED       0                         0     4
  ABCB4 WILD-TYPE     6                         5   110
D326V14, multiclass
                           clus
vv                          ABCB4 MUTATED ABCB4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V15, binary
                 cls
clus               0  1
  ABCB4 MUTATED    0  4
  ABCB4 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED      0    4
  ABCB4 WILD-TYPE    5   87
                        clus
vv                       ABCB4 MUTATED ABCB4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(327) Variable = FHL3 MUTATION ANALYSIS
D327V1, survival
                sevent
clus2             0  1
  FHL3 MUTATED    1  3
  FHL3 WILD-TYPE 62 59
  FHL3 MUTATED FHL3 WILD-TYPE 
             4            121 
  FHL3 MUTATED FHL3 WILD-TYPE 
             3             59 
$`FHL3 MUTATED`
TCGA-2L-AAQE TCGA-FB-A78T TCGA-IB-7651 TCGA-IB-A5ST 
       22.49        12.33        19.82        20.88 

$`FHL3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FHL3 MUTATED FHL3 WILD-TYPE 
         12.33           0.23 
  FHL3 MUTATED FHL3 WILD-TYPE 
         22.49          90.12 
  FHL3 MUTATED FHL3 WILD-TYPE 
         20.35          15.19 
[1] "12.3 - 22.5 (20.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D327V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FHL3 MUTATED         0        0        0         0         4         0
  FHL3 WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  FHL3 MUTATED          0
  FHL3 WILD-TYPE        3
D327V3, multiclass
           clus
vv          FHL3 MUTATED FHL3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  FHL3 MUTATED    0  0     4
  FHL3 WILD-TYPE  5 17    98
D327V4, multiclass
       clus
vv      FHL3 MUTATED FHL3 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V5, binary
                cls
clus              0  1
  FHL3 MUTATED    0  4
  FHL3 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  FHL3 MUTATED      0    4
  FHL3 WILD-TYPE   35   85
   clus
vv  FHL3 MUTATED FHL3 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D327V6, binary
                cls
clus              0  1
  FHL3 MUTATED    4  0
  FHL3 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FHL3 MUTATED      4    0
  FHL3 WILD-TYPE   53    3
   clus
vv  FHL3 MUTATED FHL3 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D327V7, binary
                cls
clus              0  1
  FHL3 MUTATED    3  1
  FHL3 WILD-TYPE 48 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  FHL3 MUTATED      3    1
  FHL3 WILD-TYPE   48   74
        clus
vv       FHL3 MUTATED FHL3 WILD-TYPE
  FEMALE            3             48
  MALE              1             74
[1] 2 2
[1] FALSE
D327V8, binary
                cls
clus              0  1
  FHL3 MUTATED    4  0
  FHL3 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  FHL3 MUTATED      4    0
  FHL3 WILD-TYPE   84   30
     clus
vv    FHL3 MUTATED FHL3 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FHL3 MUTATED                                     4
  FHL3 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FHL3 MUTATED                                       0
  FHL3 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FHL3 MUTATED                                                  0
  FHL3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  FHL3 MUTATED                                     0
  FHL3 WILD-TYPE                                   1
D327V9, multiclass
                                                  clus
vv                                                 FHL3 MUTATED FHL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V10, continuous
D327V11, continuous
[1] "Remove cluster labels:" "FHL3 MUTATED"          
clus
  FHL3 MUTATED FHL3 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"FHL3 WILD-TYPE" "FHL3 WILD-TYPE" "FHL3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  FHL3 MUTATED    4  0  0  0
  FHL3 WILD-TYPE 76 35  4  2
D327V12, multiclass
    clus
vv   FHL3 MUTATED FHL3 WILD-TYPE
  R0            4             76
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FHL3 MUTATED       0                         0     4
  FHL3 WILD-TYPE     6                         5   110
D327V14, multiclass
                           clus
vv                          FHL3 MUTATED FHL3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V15, binary
                cls
clus              0  1
  FHL3 MUTATED    0  3
  FHL3 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  FHL3 MUTATED      0    3
  FHL3 WILD-TYPE    5   88
                        clus
vv                       FHL3 MUTATED FHL3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(328) Variable = NAP1L3 MUTATION ANALYSIS
D328V1, survival
                  sevent
clus2               0  1
  NAP1L3 MUTATED    2  2
  NAP1L3 WILD-TYPE 61 60
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               4              121 
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               2               60 
$`NAP1L3 MUTATED`
TCGA-IB-A7LX TCGA-LB-A9Q5 TCGA-Q3-AA2A TCGA-RL-AAAS 
        8.22        10.29         3.12         0.30 

$`NAP1L3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
        7.56        12.46         8.78        13.68        15.32         9.40 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
            0.30             0.23 
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
           10.29            90.12 
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
            5.67            15.35 
[1] "0.3 - 10.3 (5.7)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.1"
D328V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NAP1L3 MUTATED         0        0        2         0         2         0
  NAP1L3 WILD-TYPE       1        3       10        19        80         4
                  vv
clus               STAGE IV
  NAP1L3 MUTATED          0
  NAP1L3 WILD-TYPE        3
D328V3, multiclass
           clus
vv          NAP1L3 MUTATED NAP1L3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NAP1L3 MUTATED    0  1     3
  NAP1L3 WILD-TYPE  5 16    99
D328V4, multiclass
       clus
vv      NAP1L3 MUTATED NAP1L3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V5, binary
                  cls
clus                0  1
  NAP1L3 MUTATED    1  3
  NAP1L3 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L3 MUTATED      1    3
  NAP1L3 WILD-TYPE   34   86
   clus
vv  NAP1L3 MUTATED NAP1L3 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D328V6, binary
                  cls
clus                0  1
  NAP1L3 MUTATED    1  0
  NAP1L3 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L3 MUTATED      1    0
  NAP1L3 WILD-TYPE   56    3
   clus
vv  NAP1L3 MUTATED NAP1L3 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D328V7, binary
                  cls
clus                0  1
  NAP1L3 MUTATED    3  1
  NAP1L3 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L3 MUTATED      3    1
  NAP1L3 WILD-TYPE   48   74
        clus
vv       NAP1L3 MUTATED NAP1L3 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D328V8, binary
                  cls
clus                0  1
  NAP1L3 MUTATED    3  1
  NAP1L3 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L3 MUTATED      3    1
  NAP1L3 WILD-TYPE   85   29
     clus
vv    NAP1L3 MUTATED NAP1L3 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAP1L3 MUTATED                                     4
  NAP1L3 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAP1L3 MUTATED                                       0
  NAP1L3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAP1L3 MUTATED                                                  0
  NAP1L3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NAP1L3 MUTATED                                     0
  NAP1L3 WILD-TYPE                                   1
D328V9, multiclass
                                                  clus
vv                                                 NAP1L3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NAP1L3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V10, continuous
[1] "Remove cluster labels:" "NAP1L3 MUTATED"        
clus
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-OE-A75W 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
D328V11, continuous
[1] "Remove cluster labels:" "NAP1L3 MUTATED"        
clus
  NAP1L3 MUTATED NAP1L3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" "NAP1L3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NAP1L3 MUTATED    3  0  0  1
  NAP1L3 WILD-TYPE 77 35  4  1
D328V12, multiclass
    clus
vv   NAP1L3 MUTATED NAP1L3 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAP1L3 MUTATED       0                         0     4
  NAP1L3 WILD-TYPE     6                         5   110
D328V14, multiclass
                           clus
vv                          NAP1L3 MUTATED NAP1L3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V15, binary
                  cls
clus                0  1
  NAP1L3 MUTATED    0  4
  NAP1L3 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L3 MUTATED      0    4
  NAP1L3 WILD-TYPE    5   87
                        clus
vv                       NAP1L3 MUTATED NAP1L3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(329) Variable = GNAS MUTATION ANALYSIS
D329V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    2  7
  GNAS WILD-TYPE 61 55
  GNAS MUTATED GNAS WILD-TYPE 
             9            116 
  GNAS MUTATED GNAS WILD-TYPE 
             7             55 
$`GNAS MUTATED`
TCGA-F2-A44G TCGA-US-A77E TCGA-2J-AAB1 TCGA-FB-AAPP TCGA-HV-AA8V TCGA-IB-7651 
        7.66        14.14         2.17        15.95        30.25        19.82 
TCGA-IB-A5SO TCGA-IB-AAUW TCGA-US-A776 
       12.00         7.56        39.98 

$`GNAS WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        17.26        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        12.33        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  GNAS MUTATED GNAS WILD-TYPE 
          2.17           0.23 
  GNAS MUTATED GNAS WILD-TYPE 
         39.98          90.12 
  GNAS MUTATED GNAS WILD-TYPE 
         14.14          15.27 
[1] "2.2 - 40.0 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D329V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GNAS MUTATED         0        0        0         1         8         0
  GNAS WILD-TYPE       1        3       12        18        74         4
                vv
clus             STAGE IV
  GNAS MUTATED          0
  GNAS WILD-TYPE        3
D329V3, multiclass
           clus
vv          GNAS MUTATED GNAS WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  GNAS MUTATED    0  0     9
  GNAS WILD-TYPE  5 17    93
D329V4, multiclass
       clus
vv      GNAS MUTATED GNAS WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            9             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V5, binary
                cls
clus              0  1
  GNAS MUTATED    1  8
  GNAS WILD-TYPE 34 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      1    8
  GNAS WILD-TYPE   34   81
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            1             34
  1            8             81
[1] 2 2
[1] FALSE
D329V6, binary
                cls
clus              0  1
  GNAS MUTATED    5  0
  GNAS WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      5    0
  GNAS WILD-TYPE   52    3
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D329V7, binary
                cls
clus              0  1
  GNAS MUTATED    3  6
  GNAS WILD-TYPE 48 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      3    6
  GNAS WILD-TYPE   48   69
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            3             48
  MALE              6             69
[1] 2 2
[1] FALSE
D329V8, binary
                cls
clus              0  1
  GNAS MUTATED    7  2
  GNAS WILD-TYPE 81 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      7    2
  GNAS WILD-TYPE   81   28
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO             7             81
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNAS MUTATED                                     6
  GNAS WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNAS MUTATED                                       2
  GNAS WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNAS MUTATED                                                  1
  GNAS WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  GNAS MUTATED                                     0
  GNAS WILD-TYPE                                   1
D329V9, multiclass
                                                  clus
vv                                                 GNAS MUTATED GNAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V10, continuous
D329V11, continuous
[1] "Remove cluster labels:" "GNAS MUTATED"          
clus
  GNAS MUTATED GNAS WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  GNAS MUTATED    6  2  1  0
  GNAS WILD-TYPE 74 33  3  2
D329V12, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            6             74
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED       1                         0     8
  GNAS WILD-TYPE     5                         5   106
D329V14, multiclass
                           clus
vv                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V15, binary
                cls
clus              0  1
  GNAS MUTATED    0  6
  GNAS WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0    6
  GNAS WILD-TYPE    5   85
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(330) Variable = PARP14 MUTATION ANALYSIS
D330V1, survival
                  sevent
clus2               0  1
  PARP14 MUTATED    1  4
  PARP14 WILD-TYPE 62 58
  PARP14 MUTATED PARP14 WILD-TYPE 
               5              120 
  PARP14 MUTATED PARP14 WILD-TYPE 
               4               58 
$`PARP14 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-3A-A9IU TCGA-IB-7651 TCGA-IB-A5SQ 
       20.61        22.22        15.06        19.82         7.20 

$`PARP14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  PARP14 MUTATED PARP14 WILD-TYPE 
            7.20             0.23 
  PARP14 MUTATED PARP14 WILD-TYPE 
           22.22            90.12 
  PARP14 MUTATED PARP14 WILD-TYPE 
          19.820           15.205 
[1] "7.2 - 22.2 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D330V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PARP14 MUTATED         0        0        1         1         3         0
  PARP14 WILD-TYPE       1        3       11        18        79         4
                  vv
clus               STAGE IV
  PARP14 MUTATED          0
  PARP14 WILD-TYPE        3
D330V3, multiclass
           clus
vv          PARP14 MUTATED PARP14 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PARP14 MUTATED    0  1     4
  PARP14 WILD-TYPE  5 16    98
D330V4, multiclass
       clus
vv      PARP14 MUTATED PARP14 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V5, binary
                  cls
clus                0  1
  PARP14 MUTATED    2  3
  PARP14 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP14 MUTATED      2    3
  PARP14 WILD-TYPE   33   86
   clus
vv  PARP14 MUTATED PARP14 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D330V6, binary
                  cls
clus                0  1
  PARP14 MUTATED    4  0
  PARP14 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP14 MUTATED      4    0
  PARP14 WILD-TYPE   53    3
   clus
vv  PARP14 MUTATED PARP14 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D330V7, binary
                  cls
clus                0  1
  PARP14 MUTATED    3  2
  PARP14 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP14 MUTATED      3    2
  PARP14 WILD-TYPE   48   73
        clus
vv       PARP14 MUTATED PARP14 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D330V8, binary
                  cls
clus                0  1
  PARP14 MUTATED    3  2
  PARP14 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP14 MUTATED      3    2
  PARP14 WILD-TYPE   85   28
     clus
vv    PARP14 MUTATED PARP14 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PARP14 MUTATED                                     5
  PARP14 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PARP14 MUTATED                                       0
  PARP14 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PARP14 MUTATED                                                  0
  PARP14 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PARP14 MUTATED                                     0
  PARP14 WILD-TYPE                                   1
D330V9, multiclass
                                                  clus
vv                                                 PARP14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PARP14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V10, continuous
[1] "Remove cluster labels:" "PARP14 MUTATED"        
clus
  PARP14 MUTATED PARP14 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-YY-A8LH 
"PARP14 WILD-TYPE" 
D330V11, continuous
[1] "Remove cluster labels:" "PARP14 MUTATED"        
clus
  PARP14 MUTATED PARP14 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABF 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PARP14 WILD-TYPE" "PARP14 WILD-TYPE" "PARP14 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PARP14 MUTATED    5  0  0  0
  PARP14 WILD-TYPE 75 35  4  2
D330V12, multiclass
    clus
vv   PARP14 MUTATED PARP14 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARP14 MUTATED       0                         0     5
  PARP14 WILD-TYPE     6                         5   109
D330V14, multiclass
                           clus
vv                          PARP14 MUTATED PARP14 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V15, binary
                  cls
clus                0  1
  PARP14 MUTATED    0  3
  PARP14 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP14 MUTATED      0    3
  PARP14 WILD-TYPE    5   88
                        clus
vv                       PARP14 MUTATED PARP14 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(331) Variable = SLCO1B3 MUTATION ANALYSIS
D331V1, survival
                   sevent
clus2                0  1
  SLCO1B3 MUTATED    2  5
  SLCO1B3 WILD-TYPE 61 57
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
                7               118 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
                5                57 
$`SLCO1B3 MUTATED`
TCGA-2L-AAQL TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-AAUS TCGA-LB-A9Q5 
        9.60        19.82        12.00         7.20         7.40        10.29 
TCGA-RL-AAAS 
        0.30 

$`SLCO1B3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         9.40        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
             0.30              0.23 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
            19.82             90.12 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
             9.60             15.45 
[1] "0.3 - 19.8 (9.6)"  "0.2 - 90.1 (15.4)"
[1] "hr=" "3.2"
D331V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLCO1B3 MUTATED         0        0        2         0         5         0
  SLCO1B3 WILD-TYPE       1        3       10        19        77         4
                   vv
clus                STAGE IV
  SLCO1B3 MUTATED          0
  SLCO1B3 WILD-TYPE        3
D331V3, multiclass
           clus
vv          SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLCO1B3 MUTATED    0  2     5
  SLCO1B3 WILD-TYPE  5 15    97
D331V4, multiclass
       clus
vv      SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V5, binary
                   cls
clus                 0  1
  SLCO1B3 MUTATED    2  5
  SLCO1B3 WILD-TYPE 33 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED      2    5
  SLCO1B3 WILD-TYPE   33   84
   clus
vv  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  0               2                33
  1               5                84
[1] 2 2
[1] FALSE
D331V6, binary
                   cls
clus                 0  1
  SLCO1B3 MUTATED    5  0
  SLCO1B3 WILD-TYPE 52  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED      5    0
  SLCO1B3 WILD-TYPE   52    3
   clus
vv  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  0               5                52
  1               0                 3
[1] 2 2
[1] FALSE
D331V7, binary
                   cls
clus                 0  1
  SLCO1B3 MUTATED    5  2
  SLCO1B3 WILD-TYPE 46 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED      5    2
  SLCO1B3 WILD-TYPE   46   73
        clus
vv       SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  FEMALE               5                46
  MALE                 2                73
[1] 2 2
[1] FALSE
D331V8, binary
                   cls
clus                 0  1
  SLCO1B3 MUTATED    6  1
  SLCO1B3 WILD-TYPE 82 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED      6    1
  SLCO1B3 WILD-TYPE   82   29
     clus
vv    SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  NO                6                82
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLCO1B3 MUTATED                                     7
  SLCO1B3 WILD-TYPE                                  98
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLCO1B3 MUTATED                                       0
  SLCO1B3 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLCO1B3 MUTATED                                                  0
  SLCO1B3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLCO1B3 MUTATED                                     0
  SLCO1B3 WILD-TYPE                                   1
D331V9, multiclass
                                                  clus
vv                                                 SLCO1B3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLCO1B3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V10, continuous
D331V11, continuous
                   vv
clus                R0 R1 R2 RX
  SLCO1B3 MUTATED    5  1  0  1
  SLCO1B3 WILD-TYPE 75 34  4  1
D331V12, multiclass
    clus
vv   SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  R0               5                75
  R1               1                34
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLCO1B3 MUTATED       0                         0     7
  SLCO1B3 WILD-TYPE     6                         5   107
D331V14, multiclass
                           clus
vv                          SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   7               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V15, binary
                   cls
clus                 0  1
  SLCO1B3 MUTATED    0  5
  SLCO1B3 WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED      0    5
  SLCO1B3 WILD-TYPE    5   86
                        clus
vv                       SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(332) Variable = BCL9L MUTATION ANALYSIS
D332V1, survival
                 sevent
clus2              0  1
  BCL9L MUTATED    5  1
  BCL9L WILD-TYPE 58 61
  BCL9L MUTATED BCL9L WILD-TYPE 
              6             119 
  BCL9L MUTATED BCL9L WILD-TYPE 
              1              61 
$`BCL9L MUTATED`
TCGA-2J-AABT TCGA-HV-A7OP TCGA-HV-AA8V TCGA-IB-7651 TCGA-RB-AA9M TCGA-YB-A89D 
       10.49        32.15        30.25        19.82         9.40        11.51 

$`BCL9L WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79        22.06         8.28        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  BCL9L MUTATED BCL9L WILD-TYPE 
           9.40            0.23 
  BCL9L MUTATED BCL9L WILD-TYPE 
          32.15           90.12 
  BCL9L MUTATED BCL9L WILD-TYPE 
         15.665          15.220 
[1] "9.4 - 32.1 (15.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.4"
D332V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BCL9L MUTATED         0        0        0         0         7         0
  BCL9L WILD-TYPE       1        3       12        19        75         4
                 vv
clus              STAGE IV
  BCL9L MUTATED          0
  BCL9L WILD-TYPE        3
D332V3, multiclass
           clus
vv          BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  BCL9L MUTATED    1  0     6
  BCL9L WILD-TYPE  4 17    96
D332V4, multiclass
       clus
vv      BCL9L MUTATED BCL9L WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V5, binary
                 cls
clus               0  1
  BCL9L MUTATED    0  7
  BCL9L WILD-TYPE 35 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      0    7
  BCL9L WILD-TYPE   35   82
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0             0              35
  1             7              82
[1] 2 2
[1] FALSE
D332V6, binary
                 cls
clus               0  1
  BCL9L MUTATED    3  0
  BCL9L WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      3    0
  BCL9L WILD-TYPE   54    3
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D332V7, binary
                 cls
clus               0  1
  BCL9L MUTATED    2  5
  BCL9L WILD-TYPE 49 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      2    5
  BCL9L WILD-TYPE   49   70
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             2              49
  MALE               5              70
[1] 2 2
[1] FALSE
D332V8, binary
                 cls
clus               0  1
  BCL9L MUTATED    2  3
  BCL9L WILD-TYPE 86 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      2    3
  BCL9L WILD-TYPE   86   27
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO              2              86
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCL9L MUTATED                                     6
  BCL9L WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCL9L MUTATED                                       1
  BCL9L WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCL9L MUTATED                                                  0
  BCL9L WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  BCL9L MUTATED                                     0
  BCL9L WILD-TYPE                                   1
D332V9, multiclass
                                                  clus
vv                                                 BCL9L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 BCL9L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V10, continuous
D332V11, continuous
[1] "Remove cluster labels:" "BCL9L MUTATED"         
clus
  BCL9L MUTATED BCL9L WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-IB-A5SS      TCGA-LB-A7SX 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"BCL9L WILD-TYPE" "BCL9L WILD-TYPE" "BCL9L WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  BCL9L MUTATED    6  0  1  0
  BCL9L WILD-TYPE 74 35  3  2
D332V12, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0             6              74
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL9L MUTATED       2                         0     5
  BCL9L WILD-TYPE     4                         5   109
D332V14, multiclass
                           clus
vv                          BCL9L MUTATED BCL9L WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V15, binary
                 cls
clus               0  1
  BCL9L MUTATED    0  4
  BCL9L WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      0    4
  BCL9L WILD-TYPE    5   87
                        clus
vv                       BCL9L MUTATED BCL9L WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(333) Variable = ZNF428 MUTATION ANALYSIS
D333V1, survival
                  sevent
clus2               0  1
  ZNF428 MUTATED    2  1
  ZNF428 WILD-TYPE 61 61
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               3              122 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               1               61 
$`ZNF428 MUTATED`
TCGA-FZ-5924 TCGA-XD-AAUL TCGA-3A-A9I7 
       15.78        16.37        43.50 

$`ZNF428 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF428 MUTATED ZNF428 WILD-TYPE 
           15.78             0.23 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
           43.50            90.12 
  ZNF428 MUTATED ZNF428 WILD-TYPE 
          16.370           15.155 
[1] "15.8 - 43.5 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2"  
D333V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF428 MUTATED         0        0        0         2         1         0
  ZNF428 WILD-TYPE       1        3       12        17        81         4
                  vv
clus               STAGE IV
  ZNF428 MUTATED          0
  ZNF428 WILD-TYPE        3
D333V3, multiclass
           clus
vv          ZNF428 MUTATED ZNF428 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF428 MUTATED    0  0     3
  ZNF428 WILD-TYPE  5 17    99
D333V4, multiclass
       clus
vv      ZNF428 MUTATED ZNF428 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V5, binary
                  cls
clus                0  1
  ZNF428 MUTATED    1  2
  ZNF428 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      1    2
  ZNF428 WILD-TYPE   34   87
   clus
vv  ZNF428 MUTATED ZNF428 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D333V6, binary
                  cls
clus                0  1
  ZNF428 MUTATED    1  0
  ZNF428 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      1    0
  ZNF428 WILD-TYPE   56    3
   clus
vv  ZNF428 MUTATED ZNF428 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D333V7, binary
                  cls
clus                0  1
  ZNF428 MUTATED    0  3
  ZNF428 WILD-TYPE 51 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      0    3
  ZNF428 WILD-TYPE   51   72
        clus
vv       ZNF428 MUTATED ZNF428 WILD-TYPE
  FEMALE              0               51
  MALE                3               72
[1] 2 2
[1] FALSE
D333V8, binary
                  cls
clus                0  1
  ZNF428 MUTATED    2  1
  ZNF428 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      2    1
  ZNF428 WILD-TYPE   86   29
     clus
vv    ZNF428 MUTATED ZNF428 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF428 MUTATED                                     3
  ZNF428 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF428 MUTATED                                       0
  ZNF428 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF428 MUTATED                                                  0
  ZNF428 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF428 MUTATED                                     0
  ZNF428 WILD-TYPE                                   1
D333V9, multiclass
                                                  clus
vv                                                 ZNF428 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF428 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V10, continuous
[1] "Remove cluster labels:" "ZNF428 MUTATED"        
clus
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
D333V11, continuous
[1] "Remove cluster labels:" "ZNF428 MUTATED"        
clus
  ZNF428 MUTATED ZNF428 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" "ZNF428 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF428 MUTATED    3  0  0  0
  ZNF428 WILD-TYPE 77 35  4  2
D333V12, multiclass
    clus
vv   ZNF428 MUTATED ZNF428 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF428 MUTATED       0                         1     2
  ZNF428 WILD-TYPE     6                         4   112
D333V14, multiclass
                           clus
vv                          ZNF428 MUTATED ZNF428 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V15, binary
                  cls
clus                0  1
  ZNF428 MUTATED    0  3
  ZNF428 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF428 MUTATED      0    3
  ZNF428 WILD-TYPE    5   88
                        clus
vv                       ZNF428 MUTATED ZNF428 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(334) Variable = ARFGAP3 MUTATION ANALYSIS
D334V1, survival
                   sevent
clus2                0  1
  ARFGAP3 MUTATED    2  2
  ARFGAP3 WILD-TYPE 61 60
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                4               121 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                2                60 
$`ARFGAP3 MUTATED`
TCGA-3A-A9IH TCGA-F2-7273 TCGA-IB-A6UG TCGA-RB-AA9M 
       33.57        19.46         1.35         9.40 

$`ARFGAP3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
             1.35              0.23 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
            33.57             90.12 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
            14.43             15.22 
[1] "1.4 - 33.6 (14.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D334V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ARFGAP3 MUTATED         0        1        0         0         3         0
  ARFGAP3 WILD-TYPE       1        2       12        19        79         4
                   vv
clus                STAGE IV
  ARFGAP3 MUTATED          0
  ARFGAP3 WILD-TYPE        3
D334V3, multiclass
           clus
vv          ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  ARFGAP3 MUTATED     2   0     2
  ARFGAP3 WILD-TYPE   3  17   100
D334V4, multiclass
       clus
vv      ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  T1                  2                 3
  T2                  0                17
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V5, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    1  3
  ARFGAP3 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      1    3
  ARFGAP3 WILD-TYPE   34   86
   clus
vv  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D334V6, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    2  0
  ARFGAP3 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      2    0
  ARFGAP3 WILD-TYPE   55    3
   clus
vv  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D334V7, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    1  3
  ARFGAP3 WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      1    3
  ARFGAP3 WILD-TYPE   50   72
        clus
vv       ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D334V8, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    2  2
  ARFGAP3 WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      2    2
  ARFGAP3 WILD-TYPE   86   28
     clus
vv    ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARFGAP3 MUTATED                                     4
  ARFGAP3 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARFGAP3 MUTATED                                       0
  ARFGAP3 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARFGAP3 MUTATED                                                  0
  ARFGAP3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ARFGAP3 MUTATED                                     0
  ARFGAP3 WILD-TYPE                                   1
D334V9, multiclass
                                                  clus
vv                                                 ARFGAP3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ARFGAP3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V10, continuous
[1] "Remove cluster labels:" "ARFGAP3 MUTATED"       
clus
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
D334V11, continuous
[1] "Remove cluster labels:" "ARFGAP3 MUTATED"       
clus
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A7M4 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ARFGAP3 MUTATED    2  2  0  0
  ARFGAP3 WILD-TYPE 78 33  4  2
D334V12, multiclass
    clus
vv   ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARFGAP3 MUTATED       0                         1     3
  ARFGAP3 WILD-TYPE     6                         4   111
D334V14, multiclass
                           clus
vv                          ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V15, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    0  4
  ARFGAP3 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      0    4
  ARFGAP3 WILD-TYPE    5   87
                        clus
vv                       ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(335) Variable = SALL2 MUTATION ANALYSIS
D335V1, survival
                 sevent
clus2              0  1
  SALL2 MUTATED    4  1
  SALL2 WILD-TYPE 59 61
  SALL2 MUTATED SALL2 WILD-TYPE 
              5             120 
  SALL2 MUTATED SALL2 WILD-TYPE 
              1              61 
$`SALL2 MUTATED`
TCGA-3A-A9IJ TCGA-2L-AAQJ TCGA-US-A776 TCGA-XN-A8T3 TCGA-YB-A89D 
       60.95        12.95        39.98        31.27        11.51 

$`SALL2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        23.67        12.76        66.28        15.35 

  SALL2 MUTATED SALL2 WILD-TYPE 
          11.51            0.23 
  SALL2 MUTATED SALL2 WILD-TYPE 
          60.95           90.12 
  SALL2 MUTATED SALL2 WILD-TYPE 
         31.270          15.205 
[1] "11.5 - 61.0 (31.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3.8"
D335V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SALL2 MUTATED         0        0        2         1         1         1
  SALL2 WILD-TYPE       1        3       10        18        81         3
                 vv
clus              STAGE IV
  SALL2 MUTATED          0
  SALL2 WILD-TYPE        3
D335V3, multiclass
           clus
vv          SALL2 MUTATED SALL2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SALL2 MUTATED    0  2     3
  SALL2 WILD-TYPE  5 15    99
D335V4, multiclass
       clus
vv      SALL2 MUTATED SALL2 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V5, binary
                 cls
clus               0  1
  SALL2 MUTATED    4  1
  SALL2 WILD-TYPE 31 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      4    1
  SALL2 WILD-TYPE   31   88
   clus
vv  SALL2 MUTATED SALL2 WILD-TYPE
  0             4              31
  1             1              88
[1] 2 2
[1] FALSE
D335V6, binary
                 cls
clus               0  1
  SALL2 MUTATED    1  0
  SALL2 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      1    0
  SALL2 WILD-TYPE   56    3
   clus
vv  SALL2 MUTATED SALL2 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D335V7, binary
                 cls
clus               0  1
  SALL2 MUTATED    1  4
  SALL2 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      1    4
  SALL2 WILD-TYPE   50   71
        clus
vv       SALL2 MUTATED SALL2 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D335V8, binary
                 cls
clus               0  1
  SALL2 MUTATED    3  2
  SALL2 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      3    2
  SALL2 WILD-TYPE   85   28
     clus
vv    SALL2 MUTATED SALL2 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SALL2 MUTATED                                     3
  SALL2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SALL2 MUTATED                                       1
  SALL2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SALL2 MUTATED                                                  1
  SALL2 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SALL2 MUTATED                                     0
  SALL2 WILD-TYPE                                   1
D335V9, multiclass
                                                  clus
vv                                                 SALL2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SALL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V10, continuous
[1] "Remove cluster labels:" "SALL2 MUTATED"         
clus
  SALL2 MUTATED SALL2 WILD-TYPE 
              1              38 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
D335V11, continuous
[1] "Remove cluster labels:" "SALL2 MUTATED"         
clus
  SALL2 MUTATED SALL2 WILD-TYPE 
              1              32 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" "SALL2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SALL2 MUTATED    3  2  0  0
  SALL2 WILD-TYPE 77 33  4  2
D335V12, multiclass
    clus
vv   SALL2 MUTATED SALL2 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SALL2 MUTATED       0                         0     5
  SALL2 WILD-TYPE     6                         5   109
D335V14, multiclass
                           clus
vv                          SALL2 MUTATED SALL2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V15, binary
                 cls
clus               0  1
  SALL2 MUTATED    1  3
  SALL2 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL2 MUTATED      1    3
  SALL2 WILD-TYPE    4   88
                        clus
vv                       SALL2 MUTATED SALL2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(336) Variable = BMP2K MUTATION ANALYSIS
D336V1, survival
                 sevent
clus2              0  1
  BMP2K MUTATED    2  3
  BMP2K WILD-TYPE 61 59
  BMP2K MUTATED BMP2K WILD-TYPE 
              5             120 
  BMP2K MUTATED BMP2K WILD-TYPE 
              3              59 
$`BMP2K MUTATED`
TCGA-US-A77E TCGA-3A-A9J0 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A6UF 
       14.14        24.43        20.19        19.82        21.90 

$`BMP2K WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  BMP2K MUTATED BMP2K WILD-TYPE 
          14.14            0.23 
  BMP2K MUTATED BMP2K WILD-TYPE 
          24.43           90.12 
  BMP2K MUTATED BMP2K WILD-TYPE 
         20.190          15.155 
[1] "14.1 - 24.4 (20.2)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D336V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BMP2K MUTATED         0        0        0         0         5         0
  BMP2K WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  BMP2K MUTATED          0
  BMP2K WILD-TYPE        3
D336V3, multiclass
           clus
vv          BMP2K MUTATED BMP2K WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  BMP2K MUTATED    0  0     5
  BMP2K WILD-TYPE  5 17    97
D336V4, multiclass
       clus
vv      BMP2K MUTATED BMP2K WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V5, binary
                 cls
clus               0  1
  BMP2K MUTATED    0  5
  BMP2K WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      0    5
  BMP2K WILD-TYPE   35   84
   clus
vv  BMP2K MUTATED BMP2K WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D336V6, binary
                 cls
clus               0  1
  BMP2K MUTATED    2  0
  BMP2K WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      2    0
  BMP2K WILD-TYPE   55    3
   clus
vv  BMP2K MUTATED BMP2K WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D336V7, binary
                 cls
clus               0  1
  BMP2K MUTATED    1  4
  BMP2K WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      1    4
  BMP2K WILD-TYPE   50   71
        clus
vv       BMP2K MUTATED BMP2K WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D336V8, binary
                 cls
clus               0  1
  BMP2K MUTATED    5  0
  BMP2K WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      5    0
  BMP2K WILD-TYPE   83   30
     clus
vv    BMP2K MUTATED BMP2K WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BMP2K MUTATED                                     4
  BMP2K WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BMP2K MUTATED                                       1
  BMP2K WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BMP2K MUTATED                                                  0
  BMP2K WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  BMP2K MUTATED                                     0
  BMP2K WILD-TYPE                                   1
D336V9, multiclass
                                                  clus
vv                                                 BMP2K MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 BMP2K WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V10, continuous
[1] "Remove cluster labels:" "BMP2K MUTATED"         
clus
  BMP2K MUTATED BMP2K WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-YY-A8LH 
"BMP2K WILD-TYPE" 
D336V11, continuous
[1] "Remove cluster labels:" "BMP2K MUTATED"         
clus
  BMP2K MUTATED BMP2K WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  BMP2K MUTATED    3  2  0  0
  BMP2K WILD-TYPE 77 33  4  2
D336V12, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BMP2K MUTATED       0                         0     5
  BMP2K WILD-TYPE     6                         5   109
D336V14, multiclass
                           clus
vv                          BMP2K MUTATED BMP2K WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V15, binary
                 cls
clus               0  1
  BMP2K MUTATED    0  5
  BMP2K WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      0    5
  BMP2K WILD-TYPE    5   86
                        clus
vv                       BMP2K MUTATED BMP2K WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(337) Variable = RAI2 MUTATION ANALYSIS
D337V1, survival
                sevent
clus2             0  1
  RAI2 MUTATED    2  2
  RAI2 WILD-TYPE 61 60
  RAI2 MUTATED RAI2 WILD-TYPE 
             4            121 
  RAI2 MUTATED RAI2 WILD-TYPE 
             2             60 
$`RAI2 MUTATED`
TCGA-IB-7885 TCGA-IB-AAUO TCGA-LB-A8F3 TCGA-LB-A9Q5 
       41.33         7.86        12.46        10.29 

$`RAI2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         4.73        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RAI2 MUTATED RAI2 WILD-TYPE 
          7.86           0.23 
  RAI2 MUTATED RAI2 WILD-TYPE 
         41.33          90.12 
  RAI2 MUTATED RAI2 WILD-TYPE 
        11.375         15.320 
[1] "7.9 - 41.3 (11.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D337V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RAI2 MUTATED         0        0        0         1         3         0
  RAI2 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  RAI2 MUTATED          0
  RAI2 WILD-TYPE        3
D337V3, multiclass
           clus
vv          RAI2 MUTATED RAI2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RAI2 MUTATED    0  0     4
  RAI2 WILD-TYPE  5 17    98
D337V4, multiclass
       clus
vv      RAI2 MUTATED RAI2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V5, binary
                cls
clus              0  1
  RAI2 MUTATED    1  3
  RAI2 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      1    3
  RAI2 WILD-TYPE   34   86
   clus
vv  RAI2 MUTATED RAI2 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D337V6, binary
                cls
clus              0  1
  RAI2 MUTATED    2  0
  RAI2 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      2    0
  RAI2 WILD-TYPE   55    3
   clus
vv  RAI2 MUTATED RAI2 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D337V7, binary
                cls
clus              0  1
  RAI2 MUTATED    4  0
  RAI2 WILD-TYPE 47 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      4    0
  RAI2 WILD-TYPE   47   75
        clus
vv       RAI2 MUTATED RAI2 WILD-TYPE
  FEMALE            4             47
  MALE              0             75
[1] 2 2
[1] FALSE
D337V8, binary
                cls
clus              0  1
  RAI2 MUTATED    2  2
  RAI2 WILD-TYPE 86 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      2    2
  RAI2 WILD-TYPE   86   28
     clus
vv    RAI2 MUTATED RAI2 WILD-TYPE
  NO             2             86
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAI2 MUTATED                                     4
  RAI2 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAI2 MUTATED                                       0
  RAI2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAI2 MUTATED                                                  0
  RAI2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RAI2 MUTATED                                     0
  RAI2 WILD-TYPE                                   1
D337V9, multiclass
                                                  clus
vv                                                 RAI2 MUTATED RAI2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V10, continuous
[1] "Remove cluster labels:" "RAI2 MUTATED"          
clus
  RAI2 MUTATED RAI2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-8126     TCGA-IB-A6UF 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-OE-A75W     TCGA-XN-A8T5 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-YY-A8LH 
"RAI2 WILD-TYPE" 
D337V11, continuous
[1] "Remove cluster labels:" "RAI2 MUTATED"          
clus
  RAI2 MUTATED RAI2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-OE-A75W 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"RAI2 WILD-TYPE" "RAI2 WILD-TYPE" "RAI2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RAI2 MUTATED    3  1  0  0
  RAI2 WILD-TYPE 77 34  4  2
D337V12, multiclass
    clus
vv   RAI2 MUTATED RAI2 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAI2 MUTATED       0                         1     3
  RAI2 WILD-TYPE     6                         4   111
D337V14, multiclass
                           clus
vv                          RAI2 MUTATED RAI2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V15, binary
                cls
clus              0  1
  RAI2 MUTATED    0  4
  RAI2 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI2 MUTATED      0    4
  RAI2 WILD-TYPE    5   87
                        clus
vv                       RAI2 MUTATED RAI2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(338) Variable = COL27A1 MUTATION ANALYSIS
D338V1, survival
                   sevent
clus2                0  1
  COL27A1 MUTATED    2  2
  COL27A1 WILD-TYPE 61 60
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                4               121 
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                2                60 
$`COL27A1 MUTATED`
TCGA-2J-AAB1 TCGA-HV-A7OP TCGA-HZ-A77P TCGA-IB-7651 
        2.17        32.15        10.85        19.82 

$`COL27A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  COL27A1 MUTATED COL27A1 WILD-TYPE 
             2.17              0.23 
  COL27A1 MUTATED COL27A1 WILD-TYPE 
            32.15             90.12 
  COL27A1 MUTATED COL27A1 WILD-TYPE 
           15.335            15.220 
[1] "2.2 - 32.1 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D338V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  COL27A1 MUTATED         0        0        0         0         4         0
  COL27A1 WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  COL27A1 MUTATED          0
  COL27A1 WILD-TYPE        3
D338V3, multiclass
           clus
vv          COL27A1 MUTATED COL27A1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  COL27A1 MUTATED    0  0     4
  COL27A1 WILD-TYPE  5 17    98
D338V4, multiclass
       clus
vv      COL27A1 MUTATED COL27A1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V5, binary
                   cls
clus                 0  1
  COL27A1 MUTATED    0  4
  COL27A1 WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL27A1 MUTATED      0    4
  COL27A1 WILD-TYPE   35   85
   clus
vv  COL27A1 MUTATED COL27A1 WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D338V6, binary
                   cls
clus                 0  1
  COL27A1 MUTATED    3  0
  COL27A1 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL27A1 MUTATED      3    0
  COL27A1 WILD-TYPE   54    3
   clus
vv  COL27A1 MUTATED COL27A1 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D338V7, binary
                   cls
clus                 0  1
  COL27A1 MUTATED    1  3
  COL27A1 WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL27A1 MUTATED      1    3
  COL27A1 WILD-TYPE   50   72
        clus
vv       COL27A1 MUTATED COL27A1 WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D338V8, binary
                   cls
clus                 0  1
  COL27A1 MUTATED    3  1
  COL27A1 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL27A1 MUTATED      3    1
  COL27A1 WILD-TYPE   85   29
     clus
vv    COL27A1 MUTATED COL27A1 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COL27A1 MUTATED                                     1
  COL27A1 WILD-TYPE                                 104
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COL27A1 MUTATED                                       3
  COL27A1 WILD-TYPE                                    15
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COL27A1 MUTATED                                                  0
  COL27A1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  COL27A1 MUTATED                                     0
  COL27A1 WILD-TYPE                                   1
D338V9, multiclass
                                                  clus
vv                                                 COL27A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 COL27A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V10, continuous
[1] "Remove cluster labels:" "COL27A1 MUTATED"       
clus
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AABA        TCGA-2J-AABE 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-YY-A8LH 
"COL27A1 WILD-TYPE" 
D338V11, continuous
[1] "Remove cluster labels:" "COL27A1 MUTATED"       
clus
  COL27A1 MUTATED COL27A1 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AABE        TCGA-2J-AABF 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" "COL27A1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  COL27A1 MUTATED    4  0  0  0
  COL27A1 WILD-TYPE 76 35  4  2
D338V12, multiclass
    clus
vv   COL27A1 MUTATED COL27A1 WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL27A1 MUTATED       1                         0     3
  COL27A1 WILD-TYPE     5                         5   111
D338V14, multiclass
                           clus
vv                          COL27A1 MUTATED COL27A1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V15, binary
                   cls
clus                 0  1
  COL27A1 MUTATED    0  2
  COL27A1 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL27A1 MUTATED      0    2
  COL27A1 WILD-TYPE    5   89
                        clus
vv                       COL27A1 MUTATED COL27A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(339) Variable = CCPG1 MUTATION ANALYSIS
D339V1, survival
                 sevent
clus2              0  1
  CCPG1 MUTATED    2  3
  CCPG1 WILD-TYPE 61 59
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              5             120 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              3              59 
$`CCPG1 MUTATED`
TCGA-US-A77E TCGA-2J-AAB9 TCGA-2L-AAQA TCGA-XN-A8T3 TCGA-YB-A89D 
       14.14        20.61         4.70        31.27        11.51 

$`CCPG1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.99        12.03        23.67        12.76        66.28        15.35 

  CCPG1 MUTATED CCPG1 WILD-TYPE 
           4.70            0.23 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
          31.27           90.12 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
          14.14           15.27 
[1] "4.7 - 31.3 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D339V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCPG1 MUTATED         0        0        1         0         4         0
  CCPG1 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  CCPG1 MUTATED          0
  CCPG1 WILD-TYPE        3
D339V3, multiclass
           clus
vv          CCPG1 MUTATED CCPG1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CCPG1 MUTATED    0  1     4
  CCPG1 WILD-TYPE  5 16    98
D339V4, multiclass
       clus
vv      CCPG1 MUTATED CCPG1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V5, binary
                 cls
clus               0  1
  CCPG1 MUTATED    1  4
  CCPG1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      1    4
  CCPG1 WILD-TYPE   34   85
   clus
vv  CCPG1 MUTATED CCPG1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D339V6, binary
                 cls
clus               0  1
  CCPG1 MUTATED    2  0
  CCPG1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      2    0
  CCPG1 WILD-TYPE   55    3
   clus
vv  CCPG1 MUTATED CCPG1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D339V7, binary
                 cls
clus               0  1
  CCPG1 MUTATED    1  4
  CCPG1 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      1    4
  CCPG1 WILD-TYPE   50   71
        clus
vv       CCPG1 MUTATED CCPG1 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D339V8, binary
                 cls
clus               0  1
  CCPG1 MUTATED    2  3
  CCPG1 WILD-TYPE 86 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      2    3
  CCPG1 WILD-TYPE   86   27
     clus
vv    CCPG1 MUTATED CCPG1 WILD-TYPE
  NO              2              86
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCPG1 MUTATED                                     4
  CCPG1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCPG1 MUTATED                                       1
  CCPG1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCPG1 MUTATED                                                  0
  CCPG1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCPG1 MUTATED                                     0
  CCPG1 WILD-TYPE                                   1
D339V9, multiclass
                                                  clus
vv                                                 CCPG1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CCPG1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V10, continuous
[1] "Remove cluster labels:" "CCPG1 MUTATED"         
clus
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CCPG1 WILD-TYPE" "CCPG1 WILD-TYPE" 
D339V11, continuous
                 vv
clus              R0 R1 R2 RX
  CCPG1 MUTATED    2  3  0  0
  CCPG1 WILD-TYPE 78 32  4  2
D339V12, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCPG1 MUTATED       0                         0     5
  CCPG1 WILD-TYPE     6                         5   109
D339V14, multiclass
                           clus
vv                          CCPG1 MUTATED CCPG1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V15, binary
                 cls
clus               0  1
  CCPG1 MUTATED    1  2
  CCPG1 WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      1    2
  CCPG1 WILD-TYPE    4   89
                        clus
vv                       CCPG1 MUTATED CCPG1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(340) Variable = TERF1 MUTATION ANALYSIS
D340V1, survival
                 sevent
clus2              0  1
  TERF1 MUTATED    1  2
  TERF1 WILD-TYPE 62 60
  TERF1 MUTATED TERF1 WILD-TYPE 
              3             122 
  TERF1 MUTATED TERF1 WILD-TYPE 
              2              60 
$`TERF1 MUTATED`
TCGA-LB-A7SX TCGA-FB-A78T TCGA-Q3-A5QY 
       12.92        12.33        13.68 

$`TERF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TERF1 MUTATED TERF1 WILD-TYPE 
          12.33            0.23 
  TERF1 MUTATED TERF1 WILD-TYPE 
          13.68           90.12 
  TERF1 MUTATED TERF1 WILD-TYPE 
         12.920          15.335 
[1] "12.3 - 13.7 (12.9)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "2.1"
D340V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TERF1 MUTATED         0        0        0         0         3         0
  TERF1 WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  TERF1 MUTATED          0
  TERF1 WILD-TYPE        3
D340V3, multiclass
           clus
vv          TERF1 MUTATED TERF1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TERF1 MUTATED    0  0     3
  TERF1 WILD-TYPE  5 17    99
D340V4, multiclass
       clus
vv      TERF1 MUTATED TERF1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V5, binary
                 cls
clus               0  1
  TERF1 MUTATED    0  3
  TERF1 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      0    3
  TERF1 WILD-TYPE   35   86
   clus
vv  TERF1 MUTATED TERF1 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D340V6, binary
                 cls
clus               0  1
  TERF1 MUTATED    1  0
  TERF1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      1    0
  TERF1 WILD-TYPE   56    3
   clus
vv  TERF1 MUTATED TERF1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D340V7, binary
                 cls
clus               0  1
  TERF1 MUTATED    2  1
  TERF1 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      2    1
  TERF1 WILD-TYPE   49   74
        clus
vv       TERF1 MUTATED TERF1 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D340V8, binary
                 cls
clus               0  1
  TERF1 MUTATED    3  0
  TERF1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      3    0
  TERF1 WILD-TYPE   85   30
     clus
vv    TERF1 MUTATED TERF1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TERF1 MUTATED                                     3
  TERF1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TERF1 MUTATED                                       0
  TERF1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TERF1 MUTATED                                                  0
  TERF1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TERF1 MUTATED                                     0
  TERF1 WILD-TYPE                                   1
D340V9, multiclass
                                                  clus
vv                                                 TERF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TERF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V10, continuous
[1] "Remove cluster labels:" "TERF1 MUTATED"         
clus
  TERF1 MUTATED TERF1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-YY-A8LH 
"TERF1 WILD-TYPE" 
D340V11, continuous
[1] "Remove cluster labels:" "TERF1 MUTATED"         
clus
  TERF1 MUTATED TERF1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TERF1 WILD-TYPE" "TERF1 WILD-TYPE" "TERF1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TERF1 MUTATED    2  1  0  0
  TERF1 WILD-TYPE 78 34  4  2
D340V12, multiclass
    clus
vv   TERF1 MUTATED TERF1 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TERF1 MUTATED       0                         1     2
  TERF1 WILD-TYPE     6                         4   112
D340V14, multiclass
                           clus
vv                          TERF1 MUTATED TERF1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V15, binary
                 cls
clus               0  1
  TERF1 MUTATED    0  3
  TERF1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TERF1 MUTATED      0    3
  TERF1 WILD-TYPE    5   88
                        clus
vv                       TERF1 MUTATED TERF1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(341) Variable = HIST1H1B MUTATION ANALYSIS
D341V1, survival
                    sevent
clus2                 0  1
  HIST1H1B MUTATED    4  1
  HIST1H1B WILD-TYPE 59 61
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 5                120 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 1                 61 
$`HIST1H1B MUTATED`
TCGA-2J-AABE TCGA-3A-A9I7 TCGA-IB-7651 TCGA-IB-AAUU TCGA-XN-A8T3 
       22.22        43.50        19.82         8.05        31.27 

$`HIST1H1B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        23.67        11.51        12.76        66.28        15.35 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              8.05               0.23 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             43.50              90.12 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
            22.220             15.155 
[1] "8.1 - 43.5 (22.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.7"
D341V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIST1H1B MUTATED         0        0        1         1         3         0
  HIST1H1B WILD-TYPE       1        3       11        18        79         4
                    vv
clus                 STAGE IV
  HIST1H1B MUTATED          0
  HIST1H1B WILD-TYPE        3
D341V3, multiclass
           clus
vv          HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  HIST1H1B MUTATED    0  1     4
  HIST1H1B WILD-TYPE  5 16    98
D341V4, multiclass
       clus
vv      HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V5, binary
                    cls
clus                  0  1
  HIST1H1B MUTATED    2  3
  HIST1H1B WILD-TYPE 33 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      2    3
  HIST1H1B WILD-TYPE   33   86
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                2                 33
  1                3                 86
[1] 2 2
[1] FALSE
D341V6, binary
                    cls
clus                  0  1
  HIST1H1B MUTATED    4  0
  HIST1H1B WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      4    0
  HIST1H1B WILD-TYPE   53    3
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D341V7, binary
                    cls
clus                  0  1
  HIST1H1B MUTATED    1  4
  HIST1H1B WILD-TYPE 50 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      1    4
  HIST1H1B WILD-TYPE   50   71
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  FEMALE                1                 50
  MALE                  4                 71
[1] 2 2
[1] FALSE
D341V8, binary
                    cls
clus                  0  1
  HIST1H1B MUTATED    2  3
  HIST1H1B WILD-TYPE 86 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      2    3
  HIST1H1B WILD-TYPE   86   27
     clus
vv    HIST1H1B MUTATED HIST1H1B WILD-TYPE
  NO                 2                 86
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H1B MUTATED                                     5
  HIST1H1B WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H1B MUTATED                                       0
  HIST1H1B WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H1B MUTATED                                                  0
  HIST1H1B WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIST1H1B MUTATED                                     0
  HIST1H1B WILD-TYPE                                   1
D341V9, multiclass
                                                  clus
vv                                                 HIST1H1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 HIST1H1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V10, continuous
D341V11, continuous
[1] "Remove cluster labels:" "HIST1H1B MUTATED"      
clus
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABF         TCGA-2J-AABO 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" "HIST1H1B WILD-TYPE" 
        TCGA-YY-A8LH 
"HIST1H1B WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  HIST1H1B MUTATED    4  1  0  0
  HIST1H1B WILD-TYPE 76 34  4  2
D341V12, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0                4                 76
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1B MUTATED       0                         1     4
  HIST1H1B WILD-TYPE     6                         4   110
D341V14, multiclass
                           clus
vv                          HIST1H1B MUTATED HIST1H1B WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V15, binary
                    cls
clus                  0  1
  HIST1H1B MUTATED    1  3
  HIST1H1B WILD-TYPE  4 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      1    3
  HIST1H1B WILD-TYPE    4   88
                        clus
vv                       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(342) Variable = ZMYM4 MUTATION ANALYSIS
D342V1, survival
                 sevent
clus2              0  1
  ZMYM4 MUTATED    2  2
  ZMYM4 WILD-TYPE 61 60
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              4             121 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              2              60 
$`ZMYM4 MUTATED`
TCGA-3A-A9IV TCGA-IB-7651 TCGA-IB-A5SQ TCGA-US-A776 
       36.26        19.82         7.20        39.98 

$`ZMYM4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
           7.20            0.23 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          39.98           90.12 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          28.04           15.19 
[1] "7.2 - 40.0 (28.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D342V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZMYM4 MUTATED         0        0        2         1         1         0
  ZMYM4 WILD-TYPE       1        3       10        18        81         4
                 vv
clus              STAGE IV
  ZMYM4 MUTATED          0
  ZMYM4 WILD-TYPE        3
D342V3, multiclass
           clus
vv          ZMYM4 MUTATED ZMYM4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ZMYM4 MUTATED     0   2     2
  ZMYM4 WILD-TYPE   5  15   100
D342V4, multiclass
       clus
vv      ZMYM4 MUTATED ZMYM4 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V5, binary
                 cls
clus               0  1
  ZMYM4 MUTATED    3  1
  ZMYM4 WILD-TYPE 32 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      3    1
  ZMYM4 WILD-TYPE   32   88
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0             3              32
  1             1              88
[1] 2 2
[1] FALSE
D342V6, binary
                 cls
clus               0  1
  ZMYM4 MUTATED    2  0
  ZMYM4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      2    0
  ZMYM4 WILD-TYPE   55    3
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D342V7, binary
                 cls
clus               0  1
  ZMYM4 MUTATED    3  1
  ZMYM4 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      3    1
  ZMYM4 WILD-TYPE   48   74
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D342V8, binary
                 cls
clus               0  1
  ZMYM4 MUTATED    4  0
  ZMYM4 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      4    0
  ZMYM4 WILD-TYPE   84   30
     clus
vv    ZMYM4 MUTATED ZMYM4 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYM4 MUTATED                                     2
  ZMYM4 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYM4 MUTATED                                       1
  ZMYM4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYM4 MUTATED                                                  1
  ZMYM4 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZMYM4 MUTATED                                     0
  ZMYM4 WILD-TYPE                                   1
D342V9, multiclass
                                                  clus
vv                                                 ZMYM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZMYM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V10, continuous
[1] "Remove cluster labels:" "ZMYM4 MUTATED"         
clus
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
D342V11, continuous
[1] "Remove cluster labels:" "ZMYM4 MUTATED"         
clus
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" "ZMYM4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZMYM4 MUTATED    4  0  0  0
  ZMYM4 WILD-TYPE 76 35  4  2
D342V12, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM4 MUTATED       0                         0     4
  ZMYM4 WILD-TYPE     6                         5   110
D342V14, multiclass
                           clus
vv                          ZMYM4 MUTATED ZMYM4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V15, binary
                 cls
clus               0  1
  ZMYM4 MUTATED    0  4
  ZMYM4 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED      0    4
  ZMYM4 WILD-TYPE    5   87
                        clus
vv                       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(343) Variable = TSPYL6 MUTATION ANALYSIS
D343V1, survival
                  sevent
clus2               0  1
  TSPYL6 MUTATED    2  2
  TSPYL6 WILD-TYPE 61 60
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               4              121 
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               2               60 
$`TSPYL6 MUTATED`
TCGA-FB-AAPU TCGA-IB-7651 TCGA-Q3-AA2A TCGA-XD-AAUG 
       12.53        19.82         3.12        13.81 

$`TSPYL6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        18.67        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
            3.12             0.23 
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
           19.82            90.12 
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
           13.17            15.32 
[1] "3.1 - 19.8 (13.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D343V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TSPYL6 MUTATED         0        0        1         1         1         0
  TSPYL6 WILD-TYPE       1        3       11        18        81         4
                  vv
clus               STAGE IV
  TSPYL6 MUTATED          1
  TSPYL6 WILD-TYPE        2
D343V3, multiclass
           clus
vv          TSPYL6 MUTATED TSPYL6 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TSPYL6 MUTATED    0  0     4
  TSPYL6 WILD-TYPE  5 17    98
D343V4, multiclass
       clus
vv      TSPYL6 MUTATED TSPYL6 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V5, binary
                  cls
clus                0  1
  TSPYL6 MUTATED    1  3
  TSPYL6 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL6 MUTATED      1    3
  TSPYL6 WILD-TYPE   34   86
   clus
vv  TSPYL6 MUTATED TSPYL6 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D343V6, binary
                  cls
clus                0  1
  TSPYL6 MUTATED    1  1
  TSPYL6 WILD-TYPE 56  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL6 MUTATED      1    1
  TSPYL6 WILD-TYPE   56    2
   clus
vv  TSPYL6 MUTATED TSPYL6 WILD-TYPE
  0              1               56
  1              1                2
[1] 2 2
[1] FALSE
D343V7, binary
                  cls
clus                0  1
  TSPYL6 MUTATED    4  0
  TSPYL6 WILD-TYPE 47 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL6 MUTATED      4    0
  TSPYL6 WILD-TYPE   47   75
        clus
vv       TSPYL6 MUTATED TSPYL6 WILD-TYPE
  FEMALE              4               47
  MALE                0               75
[1] 2 2
[1] FALSE
D343V8, binary
                  cls
clus                0  1
  TSPYL6 MUTATED    4  0
  TSPYL6 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL6 MUTATED      4    0
  TSPYL6 WILD-TYPE   84   30
     clus
vv    TSPYL6 MUTATED TSPYL6 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TSPYL6 MUTATED                                     4
  TSPYL6 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TSPYL6 MUTATED                                       0
  TSPYL6 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TSPYL6 MUTATED                                                  0
  TSPYL6 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TSPYL6 MUTATED                                     0
  TSPYL6 WILD-TYPE                                   1
D343V9, multiclass
                                                  clus
vv                                                 TSPYL6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TSPYL6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V10, continuous
[1] "Remove cluster labels:" "TSPYL6 MUTATED"        
clus
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
D343V11, continuous
[1] "Remove cluster labels:" "TSPYL6 MUTATED"        
clus
  TSPYL6 MUTATED TSPYL6 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" "TSPYL6 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TSPYL6 MUTATED    2  1  0  1
  TSPYL6 WILD-TYPE 78 34  4  1
D343V12, multiclass
    clus
vv   TSPYL6 MUTATED TSPYL6 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSPYL6 MUTATED       1                         0     3
  TSPYL6 WILD-TYPE     5                         5   111
D343V14, multiclass
                           clus
vv                          TSPYL6 MUTATED TSPYL6 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V15, binary
                  cls
clus                0  1
  TSPYL6 MUTATED    0  4
  TSPYL6 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL6 MUTATED      0    4
  TSPYL6 WILD-TYPE    5   87
                        clus
vv                       TSPYL6 MUTATED TSPYL6 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(344) Variable = SULT1C3 MUTATION ANALYSIS
D344V1, survival
                   sevent
clus2                0  1
  SULT1C3 MUTATED    1  3
  SULT1C3 WILD-TYPE 62 59
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                4               121 
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                3                59 
$`SULT1C3 MUTATED`
TCGA-HZ-A77Q TCGA-2L-AAQJ TCGA-3A-A9IU TCGA-RB-A7B8 
        1.08        12.95        15.06        15.32 

$`SULT1C3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
             1.08              0.23 
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
            15.32             90.12 
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
           14.005            15.350 
[1] "1.1 - 15.3 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.8"
D344V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SULT1C3 MUTATED         0        0        0         0         3         1
  SULT1C3 WILD-TYPE       1        3       12        19        79         3
                   vv
clus                STAGE IV
  SULT1C3 MUTATED          0
  SULT1C3 WILD-TYPE        3
D344V3, multiclass
           clus
vv          SULT1C3 MUTATED SULT1C3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SULT1C3 MUTATED    0  0     4
  SULT1C3 WILD-TYPE  5 17    98
D344V4, multiclass
       clus
vv      SULT1C3 MUTATED SULT1C3 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V5, binary
                   cls
clus                 0  1
  SULT1C3 MUTATED    1  3
  SULT1C3 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C3 MUTATED      1    3
  SULT1C3 WILD-TYPE   34   86
   clus
vv  SULT1C3 MUTATED SULT1C3 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D344V6, binary
                   cls
clus                 0  1
  SULT1C3 MUTATED    0  0
  SULT1C3 WILD-TYPE 57  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C3 MUTATED      0    0
  SULT1C3 WILD-TYPE   57    3
D344V7, binary
                   cls
clus                 0  1
  SULT1C3 MUTATED    3  1
  SULT1C3 WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C3 MUTATED      3    1
  SULT1C3 WILD-TYPE   48   74
        clus
vv       SULT1C3 MUTATED SULT1C3 WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D344V8, binary
                   cls
clus                 0  1
  SULT1C3 MUTATED    3  0
  SULT1C3 WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C3 MUTATED      3    0
  SULT1C3 WILD-TYPE   85   30
     clus
vv    SULT1C3 MUTATED SULT1C3 WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SULT1C3 MUTATED                                     2
  SULT1C3 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SULT1C3 MUTATED                                       2
  SULT1C3 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SULT1C3 MUTATED                                                  0
  SULT1C3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SULT1C3 MUTATED                                     0
  SULT1C3 WILD-TYPE                                   1
D344V9, multiclass
                                                  clus
vv                                                 SULT1C3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SULT1C3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V10, continuous
[1] "Remove cluster labels:" "SULT1C3 MUTATED"       
clus
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
D344V11, continuous
[1] "Remove cluster labels:" "SULT1C3 MUTATED"       
clus
  SULT1C3 MUTATED SULT1C3 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" "SULT1C3 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SULT1C3 MUTATED    3  1  0  0
  SULT1C3 WILD-TYPE 77 34  4  2
D344V12, multiclass
    clus
vv   SULT1C3 MUTATED SULT1C3 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SULT1C3 MUTATED       0                         0     4
  SULT1C3 WILD-TYPE     6                         5   110
D344V14, multiclass
                           clus
vv                          SULT1C3 MUTATED SULT1C3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V15, binary
                   cls
clus                 0  1
  SULT1C3 MUTATED    0  3
  SULT1C3 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C3 MUTATED      0    3
  SULT1C3 WILD-TYPE    5   88
                        clus
vv                       SULT1C3 MUTATED SULT1C3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(345) Variable = SH3PXD2A MUTATION ANALYSIS
D345V1, survival
                    sevent
clus2                 0  1
  SH3PXD2A MUTATED    2  5
  SH3PXD2A WILD-TYPE 61 57
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
                 7                118 
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
                 5                 57 
$`SH3PXD2A MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQI TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-A6UG TCGA-IB-AAUP 
       12.92         3.39        19.82         7.20         1.35        14.17 
TCGA-IB-AAUU 
        8.05 

$`SH3PXD2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        4.73         7.86         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
              1.35               0.23 
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
             19.82              90.12 
  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE 
              8.05              15.45 
[1] "1.4 - 19.8 (8.1)"  "0.2 - 90.1 (15.4)"
[1] "hr=" "3.1"
D345V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SH3PXD2A MUTATED         0        0        1         0         6         0
  SH3PXD2A WILD-TYPE       1        3       11        19        76         4
                    vv
clus                 STAGE IV
  SH3PXD2A MUTATED          0
  SH3PXD2A WILD-TYPE        3
D345V3, multiclass
           clus
vv          SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                0                 19
  STAGE IIB                6                 76
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  SH3PXD2A MUTATED    0  1     6
  SH3PXD2A WILD-TYPE  5 16    96
D345V4, multiclass
       clus
vv      SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V5, binary
                    cls
clus                  0  1
  SH3PXD2A MUTATED    1  6
  SH3PXD2A WILD-TYPE 34 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SH3PXD2A MUTATED      1    6
  SH3PXD2A WILD-TYPE   34   83
   clus
vv  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  0                1                 34
  1                6                 83
[1] 2 2
[1] FALSE
D345V6, binary
                    cls
clus                  0  1
  SH3PXD2A MUTATED    5  0
  SH3PXD2A WILD-TYPE 52  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SH3PXD2A MUTATED      5    0
  SH3PXD2A WILD-TYPE   52    3
   clus
vv  SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  0                5                 52
  1                0                  3
[1] 2 2
[1] FALSE
D345V7, binary
                    cls
clus                  0  1
  SH3PXD2A MUTATED    3  4
  SH3PXD2A WILD-TYPE 48 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SH3PXD2A MUTATED      3    4
  SH3PXD2A WILD-TYPE   48   71
        clus
vv       SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  FEMALE                3                 48
  MALE                  4                 71
[1] 2 2
[1] FALSE
D345V8, binary
                    cls
clus                  0  1
  SH3PXD2A MUTATED    7  0
  SH3PXD2A WILD-TYPE 81 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SH3PXD2A MUTATED      7    0
  SH3PXD2A WILD-TYPE   81   30
     clus
vv    SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  NO                 7                 81
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SH3PXD2A MUTATED                                     7
  SH3PXD2A WILD-TYPE                                  98
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SH3PXD2A MUTATED                                       0
  SH3PXD2A WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SH3PXD2A MUTATED                                                  0
  SH3PXD2A WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  SH3PXD2A MUTATED                                     0
  SH3PXD2A WILD-TYPE                                   1
D345V9, multiclass
                                                  clus
vv                                                 SH3PXD2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 SH3PXD2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V10, continuous
D345V11, continuous
                    vv
clus                 R0 R1 R2 RX
  SH3PXD2A MUTATED    3  4  0  0
  SH3PXD2A WILD-TYPE 77 31  4  2
D345V12, multiclass
    clus
vv   SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  R0                3                 77
  R1                4                 31
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SH3PXD2A MUTATED       0                         1     6
  SH3PXD2A WILD-TYPE     6                         4   108
D345V14, multiclass
                           clus
vv                          SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    6                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V15, binary
                    cls
clus                  0  1
  SH3PXD2A MUTATED    0  6
  SH3PXD2A WILD-TYPE  5 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SH3PXD2A MUTATED      0    6
  SH3PXD2A WILD-TYPE    5   85
                        clus
vv                       SH3PXD2A MUTATED SH3PXD2A WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                6                 85
[1] 2 2
[1] FALSE

Clustering(346) Variable = ZSWIM4 MUTATION ANALYSIS
D346V1, survival
                  sevent
clus2               0  1
  ZSWIM4 MUTATED    1  4
  ZSWIM4 WILD-TYPE 62 58
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
               5              120 
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
               4               58 
$`ZSWIM4 MUTATED`
TCGA-2J-AABA TCGA-FZ-5920 TCGA-IB-7651 TCGA-IB-AAUQ TCGA-IB-AAUU 
       19.96         2.01        19.82         6.02         8.05 

$`ZSWIM4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02        24.36         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
            2.01             0.23 
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
           19.96            90.12 
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
            8.05            15.27 
[1] "2.0 - 20.0 (8.1)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.6"
D346V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZSWIM4 MUTATED         0        0        0         0         5         0
  ZSWIM4 WILD-TYPE       1        3       12        19        77         4
                  vv
clus               STAGE IV
  ZSWIM4 MUTATED          0
  ZSWIM4 WILD-TYPE        3
D346V3, multiclass
           clus
vv          ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZSWIM4 MUTATED    0  0     5
  ZSWIM4 WILD-TYPE  5 17    97
D346V4, multiclass
       clus
vv      ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V5, binary
                  cls
clus                0  1
  ZSWIM4 MUTATED    0  5
  ZSWIM4 WILD-TYPE 35 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM4 MUTATED      0    5
  ZSWIM4 WILD-TYPE   35   84
   clus
vv  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  0              0               35
  1              5               84
[1] 2 2
[1] FALSE
D346V6, binary
                  cls
clus                0  1
  ZSWIM4 MUTATED    5  0
  ZSWIM4 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM4 MUTATED      5    0
  ZSWIM4 WILD-TYPE   52    3
   clus
vv  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D346V7, binary
                  cls
clus                0  1
  ZSWIM4 MUTATED    1  4
  ZSWIM4 WILD-TYPE 50 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM4 MUTATED      1    4
  ZSWIM4 WILD-TYPE   50   71
        clus
vv       ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  FEMALE              1               50
  MALE                4               71
[1] 2 2
[1] FALSE
D346V8, binary
                  cls
clus                0  1
  ZSWIM4 MUTATED    5  0
  ZSWIM4 WILD-TYPE 83 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM4 MUTATED      5    0
  ZSWIM4 WILD-TYPE   83   30
     clus
vv    ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  NO               5               83
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZSWIM4 MUTATED                                     5
  ZSWIM4 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZSWIM4 MUTATED                                       0
  ZSWIM4 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZSWIM4 MUTATED                                                  0
  ZSWIM4 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZSWIM4 MUTATED                                     0
  ZSWIM4 WILD-TYPE                                   1
D346V9, multiclass
                                                  clus
vv                                                 ZSWIM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZSWIM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V10, continuous
D346V11, continuous
[1] "Remove cluster labels:" "ZSWIM4 MUTATED"        
clus
  ZSWIM4 MUTATED ZSWIM4 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" "ZSWIM4 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZSWIM4 MUTATED    3  2  0  0
  ZSWIM4 WILD-TYPE 77 33  4  2
D346V12, multiclass
    clus
vv   ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  R0              3               77
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZSWIM4 MUTATED       0                         1     4
  ZSWIM4 WILD-TYPE     6                         4   110
D346V14, multiclass
                           clus
vv                          ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V15, binary
                  cls
clus                0  1
  ZSWIM4 MUTATED    0  4
  ZSWIM4 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM4 MUTATED      0    4
  ZSWIM4 WILD-TYPE    5   87
                        clus
vv                       ZSWIM4 MUTATED ZSWIM4 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(347) Variable = CCR3 MUTATION ANALYSIS
D347V1, survival
                sevent
clus2             0  1
  CCR3 MUTATED    4  0
  CCR3 WILD-TYPE 59 62
  CCR3 MUTATED CCR3 WILD-TYPE 
             4            121 
  CCR3 MUTATED CCR3 WILD-TYPE 
             0             62 
$`CCR3 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9I7 TCGA-IB-A5SP TCGA-Q3-A5QY 
        1.08        43.50        15.85        13.68 

$`CCR3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CCR3 MUTATED CCR3 WILD-TYPE 
          1.08           0.23 
  CCR3 MUTATED CCR3 WILD-TYPE 
         43.50          90.12 
  CCR3 MUTATED CCR3 WILD-TYPE 
        14.765         15.220 
[1] "1.1 - 43.5 (14.8)" "0.2 - 90.1 (15.2)"
[1] "hr="     "2.5e+07"
D347V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCR3 MUTATED         0        0        0         1         3         0
  CCR3 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  CCR3 MUTATED          0
  CCR3 WILD-TYPE        3
D347V3, multiclass
           clus
vv          CCR3 MUTATED CCR3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CCR3 MUTATED    0  0     4
  CCR3 WILD-TYPE  5 17    98
D347V4, multiclass
       clus
vv      CCR3 MUTATED CCR3 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V5, binary
                cls
clus              0  1
  CCR3 MUTATED    1  3
  CCR3 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      1    3
  CCR3 WILD-TYPE   34   86
   clus
vv  CCR3 MUTATED CCR3 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D347V6, binary
                cls
clus              0  1
  CCR3 MUTATED    1  0
  CCR3 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      1    0
  CCR3 WILD-TYPE   56    3
   clus
vv  CCR3 MUTATED CCR3 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D347V7, binary
                cls
clus              0  1
  CCR3 MUTATED    1  3
  CCR3 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      1    3
  CCR3 WILD-TYPE   50   72
        clus
vv       CCR3 MUTATED CCR3 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D347V8, binary
                cls
clus              0  1
  CCR3 MUTATED    2  1
  CCR3 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      2    1
  CCR3 WILD-TYPE   86   29
     clus
vv    CCR3 MUTATED CCR3 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCR3 MUTATED                                     3
  CCR3 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCR3 MUTATED                                       1
  CCR3 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCR3 MUTATED                                                  0
  CCR3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCR3 MUTATED                                     0
  CCR3 WILD-TYPE                                   1
D347V9, multiclass
                                                  clus
vv                                                 CCR3 MUTATED CCR3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V10, continuous
[1] "Remove cluster labels:" "CCR3 MUTATED"          
clus
  CCR3 MUTATED CCR3 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
D347V11, continuous
[1] "Remove cluster labels:" "CCR3 MUTATED"          
clus
  CCR3 MUTATED CCR3 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" "CCR3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CCR3 MUTATED    3  1  0  0
  CCR3 WILD-TYPE 77 34  4  2
D347V12, multiclass
    clus
vv   CCR3 MUTATED CCR3 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCR3 MUTATED       0                         1     3
  CCR3 WILD-TYPE     6                         4   111
D347V14, multiclass
                           clus
vv                          CCR3 MUTATED CCR3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V15, binary
                cls
clus              0  1
  CCR3 MUTATED    0  3
  CCR3 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR3 MUTATED      0    3
  CCR3 WILD-TYPE    5   88
                        clus
vv                       CCR3 MUTATED CCR3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(348) Variable = CPLX3 MUTATION ANALYSIS
D348V1, survival
                 sevent
clus2              0  1
  CPLX3 MUTATED    2  2
  CPLX3 WILD-TYPE 61 60
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              4             121 
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              2              60 
$`CPLX3 MUTATED`
TCGA-2J-AABK TCGA-2L-AAQE TCGA-IB-A6UG TCGA-US-A776 
       15.91        22.49         1.35        39.98 

$`CPLX3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CPLX3 MUTATED CPLX3 WILD-TYPE 
           1.35            0.23 
  CPLX3 MUTATED CPLX3 WILD-TYPE 
          39.98           90.12 
  CPLX3 MUTATED CPLX3 WILD-TYPE 
          19.20           15.19 
[1] "1.4 - 40.0 (19.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D348V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CPLX3 MUTATED         0        0        0         1         3         0
  CPLX3 WILD-TYPE       1        3       12        18        79         4
                 vv
clus              STAGE IV
  CPLX3 MUTATED          0
  CPLX3 WILD-TYPE        3
D348V3, multiclass
           clus
vv          CPLX3 MUTATED CPLX3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CPLX3 MUTATED    0  0     4
  CPLX3 WILD-TYPE  5 17    98
D348V4, multiclass
       clus
vv      CPLX3 MUTATED CPLX3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V5, binary
                 cls
clus               0  1
  CPLX3 MUTATED    1  3
  CPLX3 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX3 MUTATED      1    3
  CPLX3 WILD-TYPE   34   86
   clus
vv  CPLX3 MUTATED CPLX3 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D348V6, binary
                 cls
clus               0  1
  CPLX3 MUTATED    3  0
  CPLX3 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX3 MUTATED      3    0
  CPLX3 WILD-TYPE   54    3
   clus
vv  CPLX3 MUTATED CPLX3 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D348V7, binary
                 cls
clus               0  1
  CPLX3 MUTATED    0  4
  CPLX3 WILD-TYPE 51 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX3 MUTATED      0    4
  CPLX3 WILD-TYPE   51   71
        clus
vv       CPLX3 MUTATED CPLX3 WILD-TYPE
  FEMALE             0              51
  MALE               4              71
[1] 2 2
[1] FALSE
D348V8, binary
                 cls
clus               0  1
  CPLX3 MUTATED    3  1
  CPLX3 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX3 MUTATED      3    1
  CPLX3 WILD-TYPE   85   29
     clus
vv    CPLX3 MUTATED CPLX3 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CPLX3 MUTATED                                     3
  CPLX3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CPLX3 MUTATED                                       0
  CPLX3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CPLX3 MUTATED                                                  1
  CPLX3 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CPLX3 MUTATED                                     0
  CPLX3 WILD-TYPE                                   1
D348V9, multiclass
                                                  clus
vv                                                 CPLX3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CPLX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V10, continuous
[1] "Remove cluster labels:" "CPLX3 MUTATED"         
clus
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-YY-A8LH 
"CPLX3 WILD-TYPE" 
D348V11, continuous
[1] "Remove cluster labels:" "CPLX3 MUTATED"         
clus
  CPLX3 MUTATED CPLX3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A7M4 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" "CPLX3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CPLX3 MUTATED    2  2  0  0
  CPLX3 WILD-TYPE 78 33  4  2
D348V12, multiclass
    clus
vv   CPLX3 MUTATED CPLX3 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPLX3 MUTATED       0                         0     4
  CPLX3 WILD-TYPE     6                         5   110
D348V14, multiclass
                           clus
vv                          CPLX3 MUTATED CPLX3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V15, binary
                 cls
clus               0  1
  CPLX3 MUTATED    0  2
  CPLX3 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX3 MUTATED      0    2
  CPLX3 WILD-TYPE    5   89
                        clus
vv                       CPLX3 MUTATED CPLX3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(349) Variable = RAD17 MUTATION ANALYSIS
D349V1, survival
                 sevent
clus2              0  1
  RAD17 MUTATED    2  3
  RAD17 WILD-TYPE 61 59
  RAD17 MUTATED RAD17 WILD-TYPE 
              5             120 
  RAD17 MUTATED RAD17 WILD-TYPE 
              3              59 
$`RAD17 MUTATED`
TCGA-F2-A44G TCGA-2J-AABA TCGA-FB-AAPP TCGA-IB-7885 TCGA-IB-AAUP 
        7.66        19.96        15.95        41.33        14.17 

$`RAD17 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        19.82        36.69        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RAD17 MUTATED RAD17 WILD-TYPE 
           7.66            0.23 
  RAD17 MUTATED RAD17 WILD-TYPE 
          41.33           90.12 
  RAD17 MUTATED RAD17 WILD-TYPE 
         15.950          15.205 
[1] "7.7 - 41.3 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D349V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RAD17 MUTATED         0        0        0         0         5         0
  RAD17 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  RAD17 MUTATED          0
  RAD17 WILD-TYPE        3
D349V3, multiclass
           clus
vv          RAD17 MUTATED RAD17 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RAD17 MUTATED    0  0     5
  RAD17 WILD-TYPE  5 17    97
D349V4, multiclass
       clus
vv      RAD17 MUTATED RAD17 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V5, binary
                 cls
clus               0  1
  RAD17 MUTATED    0  5
  RAD17 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      0    5
  RAD17 WILD-TYPE   35   84
   clus
vv  RAD17 MUTATED RAD17 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D349V6, binary
                 cls
clus               0  1
  RAD17 MUTATED    4  0
  RAD17 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      4    0
  RAD17 WILD-TYPE   53    3
   clus
vv  RAD17 MUTATED RAD17 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D349V7, binary
                 cls
clus               0  1
  RAD17 MUTATED    2  3
  RAD17 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      2    3
  RAD17 WILD-TYPE   49   72
        clus
vv       RAD17 MUTATED RAD17 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D349V8, binary
                 cls
clus               0  1
  RAD17 MUTATED    3  2
  RAD17 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      3    2
  RAD17 WILD-TYPE   85   28
     clus
vv    RAD17 MUTATED RAD17 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAD17 MUTATED                                     5
  RAD17 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAD17 MUTATED                                       0
  RAD17 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAD17 MUTATED                                                  0
  RAD17 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RAD17 MUTATED                                     0
  RAD17 WILD-TYPE                                   1
D349V9, multiclass
                                                  clus
vv                                                 RAD17 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RAD17 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V10, continuous
[1] "Remove cluster labels:" "RAD17 MUTATED"         
clus
  RAD17 MUTATED RAD17 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-YY-A8LH 
"RAD17 WILD-TYPE" 
D349V11, continuous
[1] "Remove cluster labels:" "RAD17 MUTATED"         
clus
  RAD17 MUTATED RAD17 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" "RAD17 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RAD17 MUTATED    2  3  0  0
  RAD17 WILD-TYPE 78 32  4  2
D349V12, multiclass
    clus
vv   RAD17 MUTATED RAD17 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD17 MUTATED       0                         0     5
  RAD17 WILD-TYPE     6                         5   109
D349V14, multiclass
                           clus
vv                          RAD17 MUTATED RAD17 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V15, binary
                 cls
clus               0  1
  RAD17 MUTATED    0  4
  RAD17 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD17 MUTATED      0    4
  RAD17 WILD-TYPE    5   87
                        clus
vv                       RAD17 MUTATED RAD17 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(350) Variable = RANBP9 MUTATION ANALYSIS
D350V1, survival
                  sevent
clus2               0  1
  RANBP9 MUTATED    1  4
  RANBP9 WILD-TYPE 62 58
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               5              120 
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               4               58 
$`RANBP9 MUTATED`
TCGA-IB-A5SS TCGA-3A-A9IV TCGA-FZ-5920 TCGA-HZ-8637 TCGA-OE-A75W 
       15.12        36.26         2.01        17.00         8.78 

$`RANBP9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RANBP9 MUTATED RANBP9 WILD-TYPE 
            2.01             0.23 
  RANBP9 MUTATED RANBP9 WILD-TYPE 
           36.26            90.12 
  RANBP9 MUTATED RANBP9 WILD-TYPE 
           15.12            15.27 
[1] "2.0 - 36.3 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D350V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RANBP9 MUTATED         0        0        1         1         3         0
  RANBP9 WILD-TYPE       1        3       11        18        79         4
                  vv
clus               STAGE IV
  RANBP9 MUTATED          0
  RANBP9 WILD-TYPE        3
D350V3, multiclass
           clus
vv          RANBP9 MUTATED RANBP9 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RANBP9 MUTATED    0  1     4
  RANBP9 WILD-TYPE  5 16    98
D350V4, multiclass
       clus
vv      RANBP9 MUTATED RANBP9 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V5, binary
                  cls
clus                0  1
  RANBP9 MUTATED    2  3
  RANBP9 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP9 MUTATED      2    3
  RANBP9 WILD-TYPE   33   86
   clus
vv  RANBP9 MUTATED RANBP9 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D350V6, binary
                  cls
clus                0  1
  RANBP9 MUTATED    3  0
  RANBP9 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP9 MUTATED      3    0
  RANBP9 WILD-TYPE   54    3
   clus
vv  RANBP9 MUTATED RANBP9 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D350V7, binary
                  cls
clus                0  1
  RANBP9 MUTATED    3  2
  RANBP9 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP9 MUTATED      3    2
  RANBP9 WILD-TYPE   48   73
        clus
vv       RANBP9 MUTATED RANBP9 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D350V8, binary
                  cls
clus                0  1
  RANBP9 MUTATED    3  2
  RANBP9 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP9 MUTATED      3    2
  RANBP9 WILD-TYPE   85   28
     clus
vv    RANBP9 MUTATED RANBP9 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RANBP9 MUTATED                                     4
  RANBP9 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RANBP9 MUTATED                                       1
  RANBP9 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RANBP9 MUTATED                                                  0
  RANBP9 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RANBP9 MUTATED                                     0
  RANBP9 WILD-TYPE                                   1
D350V9, multiclass
                                                  clus
vv                                                 RANBP9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RANBP9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V10, continuous
[1] "Remove cluster labels:" "RANBP9 MUTATED"        
clus
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-LB-A7SX 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-XN-A8T5 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-YY-A8LH 
"RANBP9 WILD-TYPE" 
D350V11, continuous
[1] "Remove cluster labels:" "RANBP9 MUTATED"        
clus
  RANBP9 MUTATED RANBP9 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-LB-A7SX 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" "RANBP9 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RANBP9 MUTATED    5  0  0  0
  RANBP9 WILD-TYPE 75 35  4  2
D350V12, multiclass
    clus
vv   RANBP9 MUTATED RANBP9 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RANBP9 MUTATED       0                         1     4
  RANBP9 WILD-TYPE     6                         4   110
D350V14, multiclass
                           clus
vv                          RANBP9 MUTATED RANBP9 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V15, binary
                  cls
clus                0  1
  RANBP9 MUTATED    1  4
  RANBP9 WILD-TYPE  4 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP9 MUTATED      1    4
  RANBP9 WILD-TYPE    4   87
                        clus
vv                       RANBP9 MUTATED RANBP9 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(351) Variable = RASAL2 MUTATION ANALYSIS
D351V1, survival
                  sevent
clus2               0  1
  RASAL2 MUTATED    2  3
  RASAL2 WILD-TYPE 61 59
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5              120 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               3               59 
$`RASAL2 MUTATED`
TCGA-3A-A9IC TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A6UG TCGA-YH-A8SY 
       24.26        32.15        19.82         1.35        12.76 

$`RASAL2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
            1.35             0.23 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           32.15            90.12 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
          19.820           15.205 
[1] "1.4 - 32.1 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D351V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RASAL2 MUTATED         0        0        0         0         4         1
  RASAL2 WILD-TYPE       1        3       12        19        78         3
                  vv
clus               STAGE IV
  RASAL2 MUTATED          0
  RASAL2 WILD-TYPE        3
D351V3, multiclass
           clus
vv          RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RASAL2 MUTATED    0  0     5
  RASAL2 WILD-TYPE  5 17    97
D351V4, multiclass
       clus
vv      RASAL2 MUTATED RASAL2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V5, binary
                  cls
clus                0  1
  RASAL2 MUTATED    0  5
  RASAL2 WILD-TYPE 35 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      0    5
  RASAL2 WILD-TYPE   35   84
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0              0               35
  1              5               84
[1] 2 2
[1] FALSE
D351V6, binary
                  cls
clus                0  1
  RASAL2 MUTATED    3  0
  RASAL2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      3    0
  RASAL2 WILD-TYPE   54    3
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D351V7, binary
                  cls
clus                0  1
  RASAL2 MUTATED    3  2
  RASAL2 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      3    2
  RASAL2 WILD-TYPE   48   73
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D351V8, binary
                  cls
clus                0  1
  RASAL2 MUTATED    2  3
  RASAL2 WILD-TYPE 86 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      2    3
  RASAL2 WILD-TYPE   86   27
     clus
vv    RASAL2 MUTATED RASAL2 WILD-TYPE
  NO               2               86
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RASAL2 MUTATED                                     3
  RASAL2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RASAL2 MUTATED                                       1
  RASAL2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RASAL2 MUTATED                                                  0
  RASAL2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RASAL2 MUTATED                                     0
  RASAL2 WILD-TYPE                                   1
D351V9, multiclass
                                                  clus
vv                                                 RASAL2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RASAL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V10, continuous
[1] "Remove cluster labels:" "RASAL2 MUTATED"        
clus
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-YY-A8LH 
"RASAL2 WILD-TYPE" 
D351V11, continuous
[1] "Remove cluster labels:" "RASAL2 MUTATED"        
clus
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" "RASAL2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RASAL2 MUTATED    3  1  0  0
  RASAL2 WILD-TYPE 77 34  4  2
D351V12, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASAL2 MUTATED       1                         0     4
  RASAL2 WILD-TYPE     5                         5   110
D351V14, multiclass
                           clus
vv                          RASAL2 MUTATED RASAL2 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V15, binary
                  cls
clus                0  1
  RASAL2 MUTATED    0  4
  RASAL2 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      0    4
  RASAL2 WILD-TYPE    5   87
                        clus
vv                       RASAL2 MUTATED RASAL2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(352) Variable = CD86 MUTATION ANALYSIS
D352V1, survival
                sevent
clus2             0  1
  CD86 MUTATED    2  2
  CD86 WILD-TYPE 61 60
  CD86 MUTATED CD86 WILD-TYPE 
             4            121 
  CD86 MUTATED CD86 WILD-TYPE 
             2             60 
$`CD86 MUTATED`
TCGA-3A-A9IC TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-AAUU 
       24.26        17.00        19.82         8.05 

$`CD86 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CD86 MUTATED CD86 WILD-TYPE 
          8.05           0.23 
  CD86 MUTATED CD86 WILD-TYPE 
         24.26          90.12 
  CD86 MUTATED CD86 WILD-TYPE 
         18.41          15.19 
[1] "8.1 - 24.3 (18.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D352V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CD86 MUTATED         0        0        0         1         3         0
  CD86 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  CD86 MUTATED          0
  CD86 WILD-TYPE        3
D352V3, multiclass
           clus
vv          CD86 MUTATED CD86 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CD86 MUTATED    0  0     4
  CD86 WILD-TYPE  5 17    98
D352V4, multiclass
       clus
vv      CD86 MUTATED CD86 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V5, binary
                cls
clus              0  1
  CD86 MUTATED    1  3
  CD86 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      1    3
  CD86 WILD-TYPE   34   86
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D352V6, binary
                cls
clus              0  1
  CD86 MUTATED    3  0
  CD86 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      3    0
  CD86 WILD-TYPE   54    3
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D352V7, binary
                cls
clus              0  1
  CD86 MUTATED    2  2
  CD86 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      2    2
  CD86 WILD-TYPE   49   73
        clus
vv       CD86 MUTATED CD86 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D352V8, binary
                cls
clus              0  1
  CD86 MUTATED    3  1
  CD86 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      3    1
  CD86 WILD-TYPE   85   29
     clus
vv    CD86 MUTATED CD86 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD86 MUTATED                                     4
  CD86 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD86 MUTATED                                       0
  CD86 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD86 MUTATED                                                  0
  CD86 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CD86 MUTATED                                     0
  CD86 WILD-TYPE                                   1
D352V9, multiclass
                                                  clus
vv                                                 CD86 MUTATED CD86 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V10, continuous
D352V11, continuous
[1] "Remove cluster labels:" "CD86 MUTATED"          
clus
  CD86 MUTATED CD86 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" "CD86 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CD86 MUTATED    3  1  0  0
  CD86 WILD-TYPE 77 34  4  2
D352V12, multiclass
    clus
vv   CD86 MUTATED CD86 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD86 MUTATED       0                         0     4
  CD86 WILD-TYPE     6                         5   110
D352V14, multiclass
                           clus
vv                          CD86 MUTATED CD86 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V15, binary
                cls
clus              0  1
  CD86 MUTATED    0  4
  CD86 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      0    4
  CD86 WILD-TYPE    5   87
                        clus
vv                       CD86 MUTATED CD86 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(353) Variable = OR1N2 MUTATION ANALYSIS
D353V1, survival
                 sevent
clus2              0  1
  OR1N2 MUTATED    1  5
  OR1N2 WILD-TYPE 62 57
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              6             119 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              5              57 
$`OR1N2 MUTATED`
TCGA-3A-A9IC TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-IB-7651 TCGA-IB-AAUO TCGA-XN-A8T5 
       24.26        71.74         3.12        19.82         7.86        23.67 

$`OR1N2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        11.51        12.76        66.28        15.35 

  OR1N2 MUTATED OR1N2 WILD-TYPE 
           3.12            0.23 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
          71.74           90.12 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
         21.745          15.190 
[1] "3.1 - 71.7 (21.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D353V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR1N2 MUTATED         0        0        1         1         4         0
  OR1N2 WILD-TYPE       1        3       11        18        78         4
                 vv
clus              STAGE IV
  OR1N2 MUTATED          0
  OR1N2 WILD-TYPE        3
D353V3, multiclass
           clus
vv          OR1N2 MUTATED OR1N2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OR1N2 MUTATED    0  1     5
  OR1N2 WILD-TYPE  5 16    97
D353V4, multiclass
       clus
vv      OR1N2 MUTATED OR1N2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V5, binary
                 cls
clus               0  1
  OR1N2 MUTATED    2  4
  OR1N2 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      2    4
  OR1N2 WILD-TYPE   33   85
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D353V6, binary
                 cls
clus               0  1
  OR1N2 MUTATED    4  0
  OR1N2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      4    0
  OR1N2 WILD-TYPE   53    3
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D353V7, binary
                 cls
clus               0  1
  OR1N2 MUTATED    4  2
  OR1N2 WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      4    2
  OR1N2 WILD-TYPE   47   73
        clus
vv       OR1N2 MUTATED OR1N2 WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D353V8, binary
                 cls
clus               0  1
  OR1N2 MUTATED    3  2
  OR1N2 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      3    2
  OR1N2 WILD-TYPE   85   28
     clus
vv    OR1N2 MUTATED OR1N2 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR1N2 MUTATED                                     5
  OR1N2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR1N2 MUTATED                                       1
  OR1N2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR1N2 MUTATED                                                  0
  OR1N2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR1N2 MUTATED                                     0
  OR1N2 WILD-TYPE                                   1
D353V9, multiclass
                                                  clus
vv                                                 OR1N2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 OR1N2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V10, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-YY-A8LH 
"OR1N2 WILD-TYPE" 
D353V11, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-YY-A8LH 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR1N2 MUTATED    2  3  0  0
  OR1N2 WILD-TYPE 78 32  4  2
D353V12, multiclass
    clus
vv   OR1N2 MUTATED OR1N2 WILD-TYPE
  R0             2              78
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR1N2 MUTATED       0                         0     6
  OR1N2 WILD-TYPE     6                         5   108
D353V14, multiclass
                           clus
vv                          OR1N2 MUTATED OR1N2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V15, binary
                 cls
clus               0  1
  OR1N2 MUTATED    2  3
  OR1N2 WILD-TYPE  3 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      2    3
  OR1N2 WILD-TYPE    3   88
                        clus
vv                       OR1N2 MUTATED OR1N2 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(354) Variable = KIAA0408 MUTATION ANALYSIS
D354V1, survival
                    sevent
clus2                 0  1
  KIAA0408 MUTATED    1  5
  KIAA0408 WILD-TYPE 62 57
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                 6                119 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
                 5                 57 
$`KIAA0408 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-IB-7651 TCGA-US-A77J TCGA-YY-A8LH 
        4.70        12.95         7.36        19.82        18.67        66.28 

$`KIAA0408 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
              4.70               0.23 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
             66.28              90.12 
  KIAA0408 MUTATED KIAA0408 WILD-TYPE 
             15.81              15.22 
[1] "4.7 - 66.3 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D354V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA0408 MUTATED         0        0        0         0         5         1
  KIAA0408 WILD-TYPE       1        3       12        19        77         3
                    vv
clus                 STAGE IV
  KIAA0408 MUTATED          0
  KIAA0408 WILD-TYPE        3
D354V3, multiclass
           clus
vv          KIAA0408 MUTATED KIAA0408 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA0408 MUTATED    0  0     6
  KIAA0408 WILD-TYPE  5 17    96
D354V4, multiclass
       clus
vv      KIAA0408 MUTATED KIAA0408 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V5, binary
                    cls
clus                  0  1
  KIAA0408 MUTATED    1  5
  KIAA0408 WILD-TYPE 34 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      1    5
  KIAA0408 WILD-TYPE   34   84
   clus
vv  KIAA0408 MUTATED KIAA0408 WILD-TYPE
  0                1                 34
  1                5                 84
[1] 2 2
[1] FALSE
D354V6, binary
                    cls
clus                  0  1
  KIAA0408 MUTATED    1  0
  KIAA0408 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      1    0
  KIAA0408 WILD-TYPE   56    3
   clus
vv  KIAA0408 MUTATED KIAA0408 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D354V7, binary
                    cls
clus                  0  1
  KIAA0408 MUTATED    5  1
  KIAA0408 WILD-TYPE 46 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      5    1
  KIAA0408 WILD-TYPE   46   74
        clus
vv       KIAA0408 MUTATED KIAA0408 WILD-TYPE
  FEMALE                5                 46
  MALE                  1                 74
[1] 2 2
[1] FALSE
D354V8, binary
                    cls
clus                  0  1
  KIAA0408 MUTATED    4  1
  KIAA0408 WILD-TYPE 84 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      4    1
  KIAA0408 WILD-TYPE   84   29
     clus
vv    KIAA0408 MUTATED KIAA0408 WILD-TYPE
  NO                 4                 84
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0408 MUTATED                                     6
  KIAA0408 WILD-TYPE                                  99
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0408 MUTATED                                       0
  KIAA0408 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0408 MUTATED                                                  0
  KIAA0408 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA0408 MUTATED                                     0
  KIAA0408 WILD-TYPE                                   1
D354V9, multiclass
                                                  clus
vv                                                 KIAA0408 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA0408 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V10, continuous
D354V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA0408 MUTATED    4  2  0  0
  KIAA0408 WILD-TYPE 76 33  4  2
D354V12, multiclass
    clus
vv   KIAA0408 MUTATED KIAA0408 WILD-TYPE
  R0                4                 76
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0408 MUTATED       0                         0     6
  KIAA0408 WILD-TYPE     6                         5   108
D354V14, multiclass
                           clus
vv                          KIAA0408 MUTATED KIAA0408 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    6                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V15, binary
                    cls
clus                  0  1
  KIAA0408 MUTATED    0  4
  KIAA0408 WILD-TYPE  5 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0408 MUTATED      0    4
  KIAA0408 WILD-TYPE    5   87
                        clus
vv                       KIAA0408 MUTATED KIAA0408 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(355) Variable = GPRIN2 MUTATION ANALYSIS
D355V1, survival
                  sevent
clus2               0  1
  GPRIN2 MUTATED    2  2
  GPRIN2 WILD-TYPE 61 60
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               4              121 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               2               60 
$`GPRIN2 MUTATED`
TCGA-2J-AAB4 TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-IB-AAUU 
       23.97         5.03        19.82         8.05 

$`GPRIN2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
            5.03             0.23 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
           23.97            90.12 
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
          13.935           15.220 
[1] "5.0 - 24.0 (13.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D355V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GPRIN2 MUTATED         0        0        0         0         4         0
  GPRIN2 WILD-TYPE       1        3       12        19        78         4
                  vv
clus               STAGE IV
  GPRIN2 MUTATED          0
  GPRIN2 WILD-TYPE        3
D355V3, multiclass
           clus
vv          GPRIN2 MUTATED GPRIN2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GPRIN2 MUTATED    0  1     3
  GPRIN2 WILD-TYPE  5 16    99
D355V4, multiclass
       clus
vv      GPRIN2 MUTATED GPRIN2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V5, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    0  4
  GPRIN2 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      0    4
  GPRIN2 WILD-TYPE   35   85
   clus
vv  GPRIN2 MUTATED GPRIN2 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D355V6, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    3  0
  GPRIN2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      3    0
  GPRIN2 WILD-TYPE   54    3
   clus
vv  GPRIN2 MUTATED GPRIN2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D355V7, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    2  2
  GPRIN2 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      2    2
  GPRIN2 WILD-TYPE   49   73
        clus
vv       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D355V8, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    4  0
  GPRIN2 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      4    0
  GPRIN2 WILD-TYPE   84   30
     clus
vv    GPRIN2 MUTATED GPRIN2 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPRIN2 MUTATED                                     3
  GPRIN2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPRIN2 MUTATED                                       1
  GPRIN2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPRIN2 MUTATED                                                  0
  GPRIN2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GPRIN2 MUTATED                                     0
  GPRIN2 WILD-TYPE                                   1
D355V9, multiclass
                                                  clus
vv                                                 GPRIN2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GPRIN2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V10, continuous
[1] "Remove cluster labels:" "GPRIN2 MUTATED"        
clus
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-YY-A8LH 
"GPRIN2 WILD-TYPE" 
D355V11, continuous
[1] "Remove cluster labels:" "GPRIN2 MUTATED"        
clus
  GPRIN2 MUTATED GPRIN2 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" "GPRIN2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GPRIN2 MUTATED    3  1  0  0
  GPRIN2 WILD-TYPE 77 34  4  2
D355V12, multiclass
    clus
vv   GPRIN2 MUTATED GPRIN2 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPRIN2 MUTATED       0                         0     4
  GPRIN2 WILD-TYPE     6                         5   110
D355V14, multiclass
                           clus
vv                          GPRIN2 MUTATED GPRIN2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V15, binary
                  cls
clus                0  1
  GPRIN2 MUTATED    0  3
  GPRIN2 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN2 MUTATED      0    3
  GPRIN2 WILD-TYPE    5   88
                        clus
vv                       GPRIN2 MUTATED GPRIN2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(356) Variable = HSP90AA1 MUTATION ANALYSIS
D356V1, survival
                    sevent
clus2                 0  1
  HSP90AA1 MUTATED    3  1
  HSP90AA1 WILD-TYPE 60 61
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 4                121 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 1                 61 
$`HSP90AA1 MUTATED`
TCGA-2L-AAQM TCGA-3A-A9IV TCGA-IB-7651 TCGA-YB-A89D 
       45.47        36.26        19.82        11.51 

$`HSP90AA1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95         9.60        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             11.51               0.23 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             45.47              90.12 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             28.04              15.19 
[1] "11.5 - 45.5 (28.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3"  
D356V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HSP90AA1 MUTATED         0        0        1         0         3         0
  HSP90AA1 WILD-TYPE       1        3       11        19        79         4
                    vv
clus                 STAGE IV
  HSP90AA1 MUTATED          0
  HSP90AA1 WILD-TYPE        3
D356V3, multiclass
           clus
vv          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                0                 19
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  HSP90AA1 MUTATED    0  1     3
  HSP90AA1 WILD-TYPE  5 16    99
D356V4, multiclass
       clus
vv      HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V5, binary
                    cls
clus                  0  1
  HSP90AA1 MUTATED    1  3
  HSP90AA1 WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      1    3
  HSP90AA1 WILD-TYPE   34   86
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D356V6, binary
                    cls
clus                  0  1
  HSP90AA1 MUTATED    1  0
  HSP90AA1 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      1    0
  HSP90AA1 WILD-TYPE   56    3
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D356V7, binary
                    cls
clus                  0  1
  HSP90AA1 MUTATED    2  2
  HSP90AA1 WILD-TYPE 49 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      2    2
  HSP90AA1 WILD-TYPE   49   73
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  FEMALE                2                 49
  MALE                  2                 73
[1] 2 2
[1] FALSE
D356V8, binary
                    cls
clus                  0  1
  HSP90AA1 MUTATED    3  1
  HSP90AA1 WILD-TYPE 85 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      3    1
  HSP90AA1 WILD-TYPE   85   29
     clus
vv    HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  NO                 3                 85
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HSP90AA1 MUTATED                                     2
  HSP90AA1 WILD-TYPE                                 103
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HSP90AA1 MUTATED                                       2
  HSP90AA1 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HSP90AA1 MUTATED                                                  0
  HSP90AA1 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  HSP90AA1 MUTATED                                     0
  HSP90AA1 WILD-TYPE                                   1
D356V9, multiclass
                                                  clus
vv                                                 HSP90AA1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 HSP90AA1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V10, continuous
[1] "Remove cluster labels:" "HSP90AA1 MUTATED"      
clus
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
D356V11, continuous
[1] "Remove cluster labels:" "HSP90AA1 MUTATED"      
clus
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"HSP90AA1 WILD-TYPE" "HSP90AA1 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  HSP90AA1 MUTATED    3  1  0  0
  HSP90AA1 WILD-TYPE 77 34  4  2
D356V12, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  R0                3                 77
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSP90AA1 MUTATED       0                         0     4
  HSP90AA1 WILD-TYPE     6                         5   110
D356V14, multiclass
                           clus
vv                          HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V15, binary
                    cls
clus                  0  1
  HSP90AA1 MUTATED    0  3
  HSP90AA1 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      0    3
  HSP90AA1 WILD-TYPE    5   88
                        clus
vv                       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(357) Variable = SHPRH MUTATION ANALYSIS
D357V1, survival
                 sevent
clus2              0  1
  SHPRH MUTATED    3  2
  SHPRH WILD-TYPE 60 60
  SHPRH MUTATED SHPRH WILD-TYPE 
              5             120 
  SHPRH MUTATED SHPRH WILD-TYPE 
              2              60 
$`SHPRH MUTATED`
TCGA-F2-A44G TCGA-XD-AAUL TCGA-2J-AABP TCGA-HV-A7OP TCGA-IB-7651 
        7.66        16.37        15.22        32.15        19.82 

$`SHPRH WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SHPRH MUTATED SHPRH WILD-TYPE 
           7.66            0.23 
  SHPRH MUTATED SHPRH WILD-TYPE 
          32.15           90.12 
  SHPRH MUTATED SHPRH WILD-TYPE 
         16.370          15.155 
[1] "7.7 - 32.1 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D357V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SHPRH MUTATED         0        0        0         1         4         0
  SHPRH WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  SHPRH MUTATED          0
  SHPRH WILD-TYPE        3
D357V3, multiclass
           clus
vv          SHPRH MUTATED SHPRH WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SHPRH MUTATED    0  0     5
  SHPRH WILD-TYPE  5 17    97
D357V4, multiclass
       clus
vv      SHPRH MUTATED SHPRH WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V5, binary
                 cls
clus               0  1
  SHPRH MUTATED    1  4
  SHPRH WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHPRH MUTATED      1    4
  SHPRH WILD-TYPE   34   85
   clus
vv  SHPRH MUTATED SHPRH WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D357V6, binary
                 cls
clus               0  1
  SHPRH MUTATED    4  0
  SHPRH WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHPRH MUTATED      4    0
  SHPRH WILD-TYPE   53    3
   clus
vv  SHPRH MUTATED SHPRH WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D357V7, binary
                 cls
clus               0  1
  SHPRH MUTATED    3  2
  SHPRH WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHPRH MUTATED      3    2
  SHPRH WILD-TYPE   48   73
        clus
vv       SHPRH MUTATED SHPRH WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D357V8, binary
                 cls
clus               0  1
  SHPRH MUTATED    3  2
  SHPRH WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHPRH MUTATED      3    2
  SHPRH WILD-TYPE   85   28
     clus
vv    SHPRH MUTATED SHPRH WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SHPRH MUTATED                                     3
  SHPRH WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SHPRH MUTATED                                       1
  SHPRH WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SHPRH MUTATED                                                  0
  SHPRH WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SHPRH MUTATED                                     1
  SHPRH WILD-TYPE                                   0
D357V9, multiclass
                                                  clus
vv                                                 SHPRH MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 SHPRH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V10, continuous
[1] "Remove cluster labels:" "SHPRH MUTATED"         
clus
  SHPRH MUTATED SHPRH WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-YY-A8LH 
"SHPRH WILD-TYPE" 
D357V11, continuous
[1] "Remove cluster labels:" "SHPRH MUTATED"         
clus
  SHPRH MUTATED SHPRH WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SHPRH WILD-TYPE" "SHPRH WILD-TYPE" "SHPRH WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SHPRH MUTATED    4  1  0  0
  SHPRH WILD-TYPE 76 34  4  2
D357V12, multiclass
    clus
vv   SHPRH MUTATED SHPRH WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SHPRH MUTATED       1                         0     4
  SHPRH WILD-TYPE     5                         5   110
D357V14, multiclass
                           clus
vv                          SHPRH MUTATED SHPRH WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V15, binary
                 cls
clus               0  1
  SHPRH MUTATED    0  3
  SHPRH WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SHPRH MUTATED      0    3
  SHPRH WILD-TYPE    5   88
                        clus
vv                       SHPRH MUTATED SHPRH WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(358) Variable = CCKAR MUTATION ANALYSIS
D358V1, survival
                 sevent
clus2              0  1
  CCKAR MUTATED    1  3
  CCKAR WILD-TYPE 62 59
  CCKAR MUTATED CCKAR WILD-TYPE 
              4             121 
  CCKAR MUTATED CCKAR WILD-TYPE 
              3              59 
$`CCKAR MUTATED`
TCGA-3A-A9IV TCGA-FZ-5923 TCGA-HZ-8637 TCGA-IB-7651 
       36.26        20.35        17.00        19.82 

$`CCKAR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CCKAR MUTATED CCKAR WILD-TYPE 
          17.00            0.23 
  CCKAR MUTATED CCKAR WILD-TYPE 
          36.26           90.12 
  CCKAR MUTATED CCKAR WILD-TYPE 
         20.085          15.120 
[1] "17.0 - 36.3 (20.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.1"
D358V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCKAR MUTATED         0        0        1         0         2         0
  CCKAR WILD-TYPE       1        3       11        19        80         4
                 vv
clus              STAGE IV
  CCKAR MUTATED          1
  CCKAR WILD-TYPE        2
D358V3, multiclass
           clus
vv          CCKAR MUTATED CCKAR WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CCKAR MUTATED    0  1     3
  CCKAR WILD-TYPE  5 16    99
D358V4, multiclass
       clus
vv      CCKAR MUTATED CCKAR WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V5, binary
                 cls
clus               0  1
  CCKAR MUTATED    1  3
  CCKAR WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      1    3
  CCKAR WILD-TYPE   34   86
   clus
vv  CCKAR MUTATED CCKAR WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D358V6, binary
                 cls
clus               0  1
  CCKAR MUTATED    1  1
  CCKAR WILD-TYPE 56  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      1    1
  CCKAR WILD-TYPE   56    2
   clus
vv  CCKAR MUTATED CCKAR WILD-TYPE
  0             1              56
  1             1               2
[1] 2 2
[1] FALSE
D358V7, binary
                 cls
clus               0  1
  CCKAR MUTATED    3  1
  CCKAR WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      3    1
  CCKAR WILD-TYPE   48   74
        clus
vv       CCKAR MUTATED CCKAR WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D358V8, binary
                 cls
clus               0  1
  CCKAR MUTATED    3  1
  CCKAR WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      3    1
  CCKAR WILD-TYPE   85   29
     clus
vv    CCKAR MUTATED CCKAR WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCKAR MUTATED                                     3
  CCKAR WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCKAR MUTATED                                       1
  CCKAR WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCKAR MUTATED                                                  0
  CCKAR WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCKAR MUTATED                                     0
  CCKAR WILD-TYPE                                   1
D358V9, multiclass
                                                  clus
vv                                                 CCKAR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CCKAR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V10, continuous
[1] "Remove cluster labels:" "CCKAR MUTATED"         
clus
  CCKAR MUTATED CCKAR WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
D358V11, continuous
[1] "Remove cluster labels:" "CCKAR MUTATED"         
clus
  CCKAR MUTATED CCKAR WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CCKAR MUTATED    4  0  0  0
  CCKAR WILD-TYPE 76 35  4  2
D358V12, multiclass
    clus
vv   CCKAR MUTATED CCKAR WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCKAR MUTATED       0                         0     4
  CCKAR WILD-TYPE     6                         5   110
D358V14, multiclass
                           clus
vv                          CCKAR MUTATED CCKAR WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V15, binary
                 cls
clus               0  1
  CCKAR MUTATED    1  3
  CCKAR WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      1    3
  CCKAR WILD-TYPE    4   88
                        clus
vv                       CCKAR MUTATED CCKAR WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(359) Variable = CHRNA9 MUTATION ANALYSIS
D359V1, survival
                  sevent
clus2               0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 62 59
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              121 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               3               59 
$`CHRNA9 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQL TCGA-3A-A9IB TCGA-IB-A6UF 
        4.70         9.60         7.36        21.90 

$`CHRNA9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
       12.95        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
            4.70             0.23 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
           21.90            90.12 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
            8.48            15.32 
[1] "4.7 - 21.9 (8.5)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.5"
D359V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CHRNA9 MUTATED         0        0        0         0         4         0
  CHRNA9 WILD-TYPE       1        3       12        19        78         4
                  vv
clus               STAGE IV
  CHRNA9 MUTATED          0
  CHRNA9 WILD-TYPE        3
D359V3, multiclass
           clus
vv          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CHRNA9 MUTATED    0  0     4
  CHRNA9 WILD-TYPE  5 17    98
D359V4, multiclass
       clus
vv      CHRNA9 MUTATED CHRNA9 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V5, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    0  4
  CHRNA9 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    4
  CHRNA9 WILD-TYPE   35   85
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D359V6, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  0
  CHRNA9 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    0
  CHRNA9 WILD-TYPE   56    3
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D359V7, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    3
  CHRNA9 WILD-TYPE   50   72
        clus
vv       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D359V8, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    4  0
  CHRNA9 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      4    0
  CHRNA9 WILD-TYPE   84   30
     clus
vv    CHRNA9 MUTATED CHRNA9 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHRNA9 MUTATED                                     4
  CHRNA9 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHRNA9 MUTATED                                       0
  CHRNA9 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHRNA9 MUTATED                                                  0
  CHRNA9 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CHRNA9 MUTATED                                     0
  CHRNA9 WILD-TYPE                                   1
D359V9, multiclass
                                                  clus
vv                                                 CHRNA9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CHRNA9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V10, continuous
D359V11, continuous
[1] "Remove cluster labels:" "CHRNA9 MUTATED"        
clus
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IR       TCGA-3A-A9IX 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CHRNA9 MUTATED    1  2  0  1
  CHRNA9 WILD-TYPE 79 33  4  1
D359V12, multiclass
    clus
vv   CHRNA9 MUTATED CHRNA9 WILD-TYPE
  R0              1               79
  R1              2               33
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHRNA9 MUTATED       0                         0     4
  CHRNA9 WILD-TYPE     6                         5   110
D359V14, multiclass
                           clus
vv                          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V15, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    0  2
  CHRNA9 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    2
  CHRNA9 WILD-TYPE    5   89
                        clus
vv                       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(360) Variable = SH2D2A MUTATION ANALYSIS
D360V1, survival
                  sevent
clus2               0  1
  SH2D2A MUTATED    2  3
  SH2D2A WILD-TYPE 61 59
  SH2D2A MUTATED SH2D2A WILD-TYPE 
               5              120 
  SH2D2A MUTATED SH2D2A WILD-TYPE 
               3               59 
$`SH2D2A MUTATED`
TCGA-IB-A5SS TCGA-2J-AABE TCGA-2J-AABP TCGA-3A-A9IZ TCGA-IB-7651 
       15.12        22.22        15.22        10.13        19.82 

$`SH2D2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       19.96        22.72        42.31        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SH2D2A MUTATED SH2D2A WILD-TYPE 
           10.13             0.23 
  SH2D2A MUTATED SH2D2A WILD-TYPE 
           22.22            90.12 
  SH2D2A MUTATED SH2D2A WILD-TYPE 
          15.220           15.255 
[1] "10.1 - 22.2 (15.2)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.2"
D360V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SH2D2A MUTATED         0        0        0         1         4         0
  SH2D2A WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  SH2D2A MUTATED          0
  SH2D2A WILD-TYPE        3
D360V3, multiclass
           clus
vv          SH2D2A MUTATED SH2D2A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SH2D2A MUTATED    0  0     5
  SH2D2A WILD-TYPE  5 17    97
D360V4, multiclass
       clus
vv      SH2D2A MUTATED SH2D2A WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V5, binary
                  cls
clus                0  1
  SH2D2A MUTATED    1  4
  SH2D2A WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH2D2A MUTATED      1    4
  SH2D2A WILD-TYPE   34   85
   clus
vv  SH2D2A MUTATED SH2D2A WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D360V6, binary
                  cls
clus                0  1
  SH2D2A MUTATED    4  0
  SH2D2A WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH2D2A MUTATED      4    0
  SH2D2A WILD-TYPE   53    3
   clus
vv  SH2D2A MUTATED SH2D2A WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D360V7, binary
                  cls
clus                0  1
  SH2D2A MUTATED    3  2
  SH2D2A WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH2D2A MUTATED      3    2
  SH2D2A WILD-TYPE   48   73
        clus
vv       SH2D2A MUTATED SH2D2A WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D360V8, binary
                  cls
clus                0  1
  SH2D2A MUTATED    4  1
  SH2D2A WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH2D2A MUTATED      4    1
  SH2D2A WILD-TYPE   84   29
     clus
vv    SH2D2A MUTATED SH2D2A WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SH2D2A MUTATED                                     4
  SH2D2A WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SH2D2A MUTATED                                       0
  SH2D2A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SH2D2A MUTATED                                                  0
  SH2D2A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SH2D2A MUTATED                                     1
  SH2D2A WILD-TYPE                                   0
D360V9, multiclass
                                                  clus
vv                                                 SH2D2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 SH2D2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V10, continuous
D360V11, continuous
                  vv
clus               R0 R1 R2 RX
  SH2D2A MUTATED    4  1  0  0
  SH2D2A WILD-TYPE 76 34  4  2
D360V12, multiclass
    clus
vv   SH2D2A MUTATED SH2D2A WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SH2D2A MUTATED       0                         0     5
  SH2D2A WILD-TYPE     6                         5   109
D360V14, multiclass
                           clus
vv                          SH2D2A MUTATED SH2D2A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V15, binary
                  cls
clus                0  1
  SH2D2A MUTATED    1  2
  SH2D2A WILD-TYPE  4 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH2D2A MUTATED      1    2
  SH2D2A WILD-TYPE    4   89
                        clus
vv                       SH2D2A MUTATED SH2D2A WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(361) Variable = SLC9A11 MUTATION ANALYSIS
D361V1, survival
                   sevent
clus2                0  1
  SLC9A11 MUTATED    3  2
  SLC9A11 WILD-TYPE 60 60
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                5               120 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                2                60 
$`SLC9A11 MUTATED`
TCGA-S4-A8RO TCGA-2L-AAQL TCGA-IB-7651 TCGA-IB-A6UF TCGA-LB-A8F3 
       17.26         9.60        19.82        21.90        12.46 

$`SLC9A11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
             9.60              0.23 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            21.90             90.12 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
           17.260            15.205 
[1] "9.6 - 21.9 (17.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D361V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC9A11 MUTATED         0        0        0         1         4         0
  SLC9A11 WILD-TYPE       1        3       12        18        78         4
                   vv
clus                STAGE IV
  SLC9A11 MUTATED          0
  SLC9A11 WILD-TYPE        3
D361V3, multiclass
           clus
vv          SLC9A11 MUTATED SLC9A11 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC9A11 MUTATED    0  0     5
  SLC9A11 WILD-TYPE  5 17    97
D361V4, multiclass
       clus
vv      SLC9A11 MUTATED SLC9A11 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V5, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    1  4
  SLC9A11 WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      1    4
  SLC9A11 WILD-TYPE   34   85
   clus
vv  SLC9A11 MUTATED SLC9A11 WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D361V6, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    2  0
  SLC9A11 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      2    0
  SLC9A11 WILD-TYPE   55    3
   clus
vv  SLC9A11 MUTATED SLC9A11 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D361V7, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    3  2
  SLC9A11 WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      3    2
  SLC9A11 WILD-TYPE   48   73
        clus
vv       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  FEMALE               3                48
  MALE                 2                73
[1] 2 2
[1] FALSE
D361V8, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    3  2
  SLC9A11 WILD-TYPE 85 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      3    2
  SLC9A11 WILD-TYPE   85   28
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  NO                3                85
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC9A11 MUTATED                                     5
  SLC9A11 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC9A11 MUTATED                                       0
  SLC9A11 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC9A11 MUTATED                                                  0
  SLC9A11 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC9A11 MUTATED                                     0
  SLC9A11 WILD-TYPE                                   1
D361V9, multiclass
                                                  clus
vv                                                 SLC9A11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC9A11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V10, continuous
[1] "Remove cluster labels:" "SLC9A11 MUTATED"       
clus
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UG 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC9A11 WILD-TYPE" 
D361V11, continuous
[1] "Remove cluster labels:" "SLC9A11 MUTATED"       
clus
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC9A11 MUTATED    2  2  0  1
  SLC9A11 WILD-TYPE 78 33  4  1
D361V12, multiclass
    clus
vv   SLC9A11 MUTATED SLC9A11 WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC9A11 MUTATED       0                         1     4
  SLC9A11 WILD-TYPE     6                         4   110
D361V14, multiclass
                           clus
vv                          SLC9A11 MUTATED SLC9A11 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V15, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    0  4
  SLC9A11 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      0    4
  SLC9A11 WILD-TYPE    5   87
                        clus
vv                       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(362) Variable = P2RY1 MUTATION ANALYSIS
D362V1, survival
                 sevent
clus2              0  1
  P2RY1 MUTATED    2  4
  P2RY1 WILD-TYPE 61 58
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              6             119 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              4              58 
$`P2RY1 MUTATED`
TCGA-XD-AAUL TCGA-2L-AAQA TCGA-3A-A9IB TCGA-F2-A8YN TCGA-IB-7651 TCGA-OE-A75W 
       16.37         4.70         7.36        17.00        19.82         8.78 

$`P2RY1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        8.05        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  P2RY1 MUTATED P2RY1 WILD-TYPE 
           4.70            0.23 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
          19.82           90.12 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
         12.575          15.220 
[1] "4.7 - 19.8 (12.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D362V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  P2RY1 MUTATED         0        0        0         3         3         0
  P2RY1 WILD-TYPE       1        3       12        16        79         4
                 vv
clus              STAGE IV
  P2RY1 MUTATED          0
  P2RY1 WILD-TYPE        3
D362V3, multiclass
           clus
vv          P2RY1 MUTATED P2RY1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             3              16
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  P2RY1 MUTATED    0  0     6
  P2RY1 WILD-TYPE  5 17    96
D362V4, multiclass
       clus
vv      P2RY1 MUTATED P2RY1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V5, binary
                 cls
clus               0  1
  P2RY1 MUTATED    3  3
  P2RY1 WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    3
  P2RY1 WILD-TYPE   32   86
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D362V6, binary
                 cls
clus               0  1
  P2RY1 MUTATED    3  0
  P2RY1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    0
  P2RY1 WILD-TYPE   54    3
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D362V7, binary
                 cls
clus               0  1
  P2RY1 MUTATED    2  4
  P2RY1 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      2    4
  P2RY1 WILD-TYPE   49   71
        clus
vv       P2RY1 MUTATED P2RY1 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D362V8, binary
                 cls
clus               0  1
  P2RY1 MUTATED    5  1
  P2RY1 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      5    1
  P2RY1 WILD-TYPE   83   29
     clus
vv    P2RY1 MUTATED P2RY1 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  P2RY1 MUTATED                                     6
  P2RY1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  P2RY1 MUTATED                                       0
  P2RY1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  P2RY1 MUTATED                                                  0
  P2RY1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  P2RY1 MUTATED                                     0
  P2RY1 WILD-TYPE                                   1
D362V9, multiclass
                                                  clus
vv                                                 P2RY1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 P2RY1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V10, continuous
D362V11, continuous
                 vv
clus              R0 R1 R2 RX
  P2RY1 MUTATED    4  2  0  0
  P2RY1 WILD-TYPE 76 33  4  2
D362V12, multiclass
    clus
vv   P2RY1 MUTATED P2RY1 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  P2RY1 MUTATED       0                         0     6
  P2RY1 WILD-TYPE     6                         5   108
D362V14, multiclass
                           clus
vv                          P2RY1 MUTATED P2RY1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V15, binary
                 cls
clus               0  1
  P2RY1 MUTATED    0  5
  P2RY1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      0    5
  P2RY1 WILD-TYPE    5   86
                        clus
vv                       P2RY1 MUTATED P2RY1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(363) Variable = SCYL3 MUTATION ANALYSIS
D363V1, survival
                 sevent
clus2              0  1
  SCYL3 MUTATED    0  4
  SCYL3 WILD-TYPE 63 58
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              4             121 
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              4              58 
$`SCYL3 MUTATED`
TCGA-3A-A9IC TCGA-FB-AAPQ TCGA-IB-7651 TCGA-RB-A7B8 
       24.26        37.15        19.82        15.32 

$`SCYL3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SCYL3 MUTATED SCYL3 WILD-TYPE 
          15.32            0.23 
  SCYL3 MUTATED SCYL3 WILD-TYPE 
          37.15           90.12 
  SCYL3 MUTATED SCYL3 WILD-TYPE 
          22.04           15.12 
[1] "15.3 - 37.1 (22.0)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.4"
D363V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SCYL3 MUTATED         0        0        0         0         4         0
  SCYL3 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  SCYL3 MUTATED          0
  SCYL3 WILD-TYPE        3
D363V3, multiclass
           clus
vv          SCYL3 MUTATED SCYL3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SCYL3 MUTATED    0  0     4
  SCYL3 WILD-TYPE  5 17    98
D363V4, multiclass
       clus
vv      SCYL3 MUTATED SCYL3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V5, binary
                 cls
clus               0  1
  SCYL3 MUTATED    0  4
  SCYL3 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL3 MUTATED      0    4
  SCYL3 WILD-TYPE   35   85
   clus
vv  SCYL3 MUTATED SCYL3 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D363V6, binary
                 cls
clus               0  1
  SCYL3 MUTATED    1  0
  SCYL3 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL3 MUTATED      1    0
  SCYL3 WILD-TYPE   56    3
   clus
vv  SCYL3 MUTATED SCYL3 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D363V7, binary
                 cls
clus               0  1
  SCYL3 MUTATED    3  1
  SCYL3 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL3 MUTATED      3    1
  SCYL3 WILD-TYPE   48   74
        clus
vv       SCYL3 MUTATED SCYL3 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D363V8, binary
                 cls
clus               0  1
  SCYL3 MUTATED    3  1
  SCYL3 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL3 MUTATED      3    1
  SCYL3 WILD-TYPE   85   29
     clus
vv    SCYL3 MUTATED SCYL3 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SCYL3 MUTATED                                     3
  SCYL3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SCYL3 MUTATED                                       1
  SCYL3 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SCYL3 MUTATED                                                  0
  SCYL3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SCYL3 MUTATED                                     0
  SCYL3 WILD-TYPE                                   1
D363V9, multiclass
                                                  clus
vv                                                 SCYL3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SCYL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V10, continuous
[1] "Remove cluster labels:" "SCYL3 MUTATED"         
clus
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-YY-A8LH 
"SCYL3 WILD-TYPE" 
D363V11, continuous
[1] "Remove cluster labels:" "SCYL3 MUTATED"         
clus
  SCYL3 MUTATED SCYL3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" "SCYL3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SCYL3 MUTATED    4  0  0  0
  SCYL3 WILD-TYPE 76 35  4  2
D363V12, multiclass
    clus
vv   SCYL3 MUTATED SCYL3 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCYL3 MUTATED       0                         0     4
  SCYL3 WILD-TYPE     6                         5   110
D363V14, multiclass
                           clus
vv                          SCYL3 MUTATED SCYL3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V15, binary
                 cls
clus               0  1
  SCYL3 MUTATED    0  4
  SCYL3 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL3 MUTATED      0    4
  SCYL3 WILD-TYPE    5   87
                        clus
vv                       SCYL3 MUTATED SCYL3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(364) Variable = INTS5 MUTATION ANALYSIS
D364V1, survival
                 sevent
clus2              0  1
  INTS5 MUTATED    0  3
  INTS5 WILD-TYPE 63 59
  INTS5 MUTATED INTS5 WILD-TYPE 
              3             122 
  INTS5 MUTATED INTS5 WILD-TYPE 
              3              59 
$`INTS5 MUTATED`
TCGA-2J-AAB6 TCGA-IB-7651 TCGA-LB-A9Q5 
        9.63        19.82        10.29 

$`INTS5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  INTS5 MUTATED INTS5 WILD-TYPE 
           9.63            0.23 
  INTS5 MUTATED INTS5 WILD-TYPE 
          19.82           90.12 
  INTS5 MUTATED INTS5 WILD-TYPE 
          10.29           15.27 
[1] "9.6 - 19.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.8"
D364V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  INTS5 MUTATED         0        0        0         1         2         0
  INTS5 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  INTS5 MUTATED          0
  INTS5 WILD-TYPE        3
D364V3, multiclass
           clus
vv          INTS5 MUTATED INTS5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  INTS5 MUTATED    0  0     3
  INTS5 WILD-TYPE  5 17    99
D364V4, multiclass
       clus
vv      INTS5 MUTATED INTS5 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V5, binary
                 cls
clus               0  1
  INTS5 MUTATED    1  2
  INTS5 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS5 MUTATED      1    2
  INTS5 WILD-TYPE   34   87
   clus
vv  INTS5 MUTATED INTS5 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D364V6, binary
                 cls
clus               0  1
  INTS5 MUTATED    2  0
  INTS5 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS5 MUTATED      2    0
  INTS5 WILD-TYPE   55    3
   clus
vv  INTS5 MUTATED INTS5 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D364V7, binary
                 cls
clus               0  1
  INTS5 MUTATED    2  1
  INTS5 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS5 MUTATED      2    1
  INTS5 WILD-TYPE   49   74
        clus
vv       INTS5 MUTATED INTS5 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D364V8, binary
                 cls
clus               0  1
  INTS5 MUTATED    2  1
  INTS5 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS5 MUTATED      2    1
  INTS5 WILD-TYPE   86   29
     clus
vv    INTS5 MUTATED INTS5 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  INTS5 MUTATED                                     3
  INTS5 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  INTS5 MUTATED                                       0
  INTS5 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  INTS5 MUTATED                                                  0
  INTS5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  INTS5 MUTATED                                     0
  INTS5 WILD-TYPE                                   1
D364V9, multiclass
                                                  clus
vv                                                 INTS5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 INTS5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V10, continuous
[1] "Remove cluster labels:" "INTS5 MUTATED"         
clus
  INTS5 MUTATED INTS5 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-OE-A75W      TCGA-XN-A8T5 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-YY-A8LH 
"INTS5 WILD-TYPE" 
D364V11, continuous
[1] "Remove cluster labels:" "INTS5 MUTATED"         
clus
  INTS5 MUTATED INTS5 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-OE-A75W 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"INTS5 WILD-TYPE" "INTS5 WILD-TYPE" "INTS5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  INTS5 MUTATED    3  0  0  0
  INTS5 WILD-TYPE 77 35  4  2
D364V12, multiclass
    clus
vv   INTS5 MUTATED INTS5 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INTS5 MUTATED       0                         0     3
  INTS5 WILD-TYPE     6                         5   111
D364V14, multiclass
                           clus
vv                          INTS5 MUTATED INTS5 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V15, binary
                 cls
clus               0  1
  INTS5 MUTATED    0  2
  INTS5 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS5 MUTATED      0    2
  INTS5 WILD-TYPE    5   89
                        clus
vv                       INTS5 MUTATED INTS5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(365) Variable = DAAM1 MUTATION ANALYSIS
D365V1, survival
                 sevent
clus2              0  1
  DAAM1 MUTATED    1  5
  DAAM1 WILD-TYPE 62 57
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             119 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              5              57 
$`DAAM1 MUTATED`
TCGA-FB-AAQ6 TCGA-LB-A7SX TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-AAUQ 
        8.02        12.92        15.55        19.82        36.69         6.02 

$`DAAM1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73         7.86        14.17        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  DAAM1 MUTATED DAAM1 WILD-TYPE 
           6.02            0.23 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
          36.69           90.12 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
         14.235          15.220 
[1] "6.0 - 36.7 (14.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D365V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DAAM1 MUTATED         0        1        0         1         4         0
  DAAM1 WILD-TYPE       1        2       12        18        78         4
                 vv
clus              STAGE IV
  DAAM1 MUTATED          0
  DAAM1 WILD-TYPE        3
D365V3, multiclass
           clus
vv          DAAM1 MUTATED DAAM1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DAAM1 MUTATED    1  0     5
  DAAM1 WILD-TYPE  4 17    97
D365V4, multiclass
       clus
vv      DAAM1 MUTATED DAAM1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V5, binary
                 cls
clus               0  1
  DAAM1 MUTATED    2  4
  DAAM1 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      2    4
  DAAM1 WILD-TYPE   33   85
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D365V6, binary
                 cls
clus               0  1
  DAAM1 MUTATED    3  0
  DAAM1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      3    0
  DAAM1 WILD-TYPE   54    3
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D365V7, binary
                 cls
clus               0  1
  DAAM1 MUTATED    3  3
  DAAM1 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      3    3
  DAAM1 WILD-TYPE   48   72
        clus
vv       DAAM1 MUTATED DAAM1 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D365V8, binary
                 cls
clus               0  1
  DAAM1 MUTATED    6  0
  DAAM1 WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      6    0
  DAAM1 WILD-TYPE   82   30
     clus
vv    DAAM1 MUTATED DAAM1 WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DAAM1 MUTATED                                     6
  DAAM1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DAAM1 MUTATED                                       0
  DAAM1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DAAM1 MUTATED                                                  0
  DAAM1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DAAM1 MUTATED                                     0
  DAAM1 WILD-TYPE                                   1
D365V9, multiclass
                                                  clus
vv                                                 DAAM1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DAAM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V10, continuous
D365V11, continuous
                 vv
clus              R0 R1 R2 RX
  DAAM1 MUTATED    3  3  0  0
  DAAM1 WILD-TYPE 77 32  4  2
D365V12, multiclass
    clus
vv   DAAM1 MUTATED DAAM1 WILD-TYPE
  R0             3              77
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAAM1 MUTATED       1                         1     4
  DAAM1 WILD-TYPE     5                         4   110
D365V14, multiclass
                           clus
vv                          DAAM1 MUTATED DAAM1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V15, binary
                 cls
clus               0  1
  DAAM1 MUTATED    0  6
  DAAM1 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      0    6
  DAAM1 WILD-TYPE    5   85
                        clus
vv                       DAAM1 MUTATED DAAM1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(366) Variable = RERE MUTATION ANALYSIS
D366V1, survival
                sevent
clus2             0  1
  RERE MUTATED    2  4
  RERE WILD-TYPE 61 58
  RERE MUTATED RERE WILD-TYPE 
             6            119 
  RERE MUTATED RERE WILD-TYPE 
             4             58 
$`RERE MUTATED`
TCGA-US-A77E TCGA-FB-AAQ3 TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-7885 TCGA-XN-A8T3 
       14.14         1.02        17.49        19.82        41.33        31.27 

$`RERE WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 
       17.79        22.06         8.28        32.15        30.25        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  RERE MUTATED RERE WILD-TYPE 
          1.02           0.23 
  RERE MUTATED RERE WILD-TYPE 
         41.33          90.12 
  RERE MUTATED RERE WILD-TYPE 
        18.655         15.190 
[1] "1.0 - 41.3 (18.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D366V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RERE MUTATED         0        0        1         0         5         0
  RERE WILD-TYPE       1        3       11        19        77         4
                vv
clus             STAGE IV
  RERE MUTATED          0
  RERE WILD-TYPE        3
D366V3, multiclass
           clus
vv          RERE MUTATED RERE WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RERE MUTATED    0  2     4
  RERE WILD-TYPE  5 15    98
D366V4, multiclass
       clus
vv      RERE MUTATED RERE WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V5, binary
                cls
clus              0  1
  RERE MUTATED    1  5
  RERE WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      1    5
  RERE WILD-TYPE   34   84
   clus
vv  RERE MUTATED RERE WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D366V6, binary
                cls
clus              0  1
  RERE MUTATED    3  0
  RERE WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      3    0
  RERE WILD-TYPE   54    3
   clus
vv  RERE MUTATED RERE WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D366V7, binary
                cls
clus              0  1
  RERE MUTATED    4  2
  RERE WILD-TYPE 47 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      4    2
  RERE WILD-TYPE   47   73
        clus
vv       RERE MUTATED RERE WILD-TYPE
  FEMALE            4             47
  MALE              2             73
[1] 2 2
[1] FALSE
D366V8, binary
                cls
clus              0  1
  RERE MUTATED    5  1
  RERE WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      5    1
  RERE WILD-TYPE   83   29
     clus
vv    RERE MUTATED RERE WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RERE MUTATED                                     5
  RERE WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RERE MUTATED                                       1
  RERE WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RERE MUTATED                                                  0
  RERE WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RERE MUTATED                                     0
  RERE WILD-TYPE                                   1
D366V9, multiclass
                                                  clus
vv                                                 RERE MUTATED RERE WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V10, continuous
[1] "Remove cluster labels:" "RERE MUTATED"          
clus
  RERE MUTATED RERE WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-YY-A8LH 
"RERE WILD-TYPE" 
D366V11, continuous
[1] "Remove cluster labels:" "RERE MUTATED"          
clus
  RERE MUTATED RERE WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-8126 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"RERE WILD-TYPE" "RERE WILD-TYPE" "RERE WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RERE MUTATED    3  2  1  0
  RERE WILD-TYPE 77 33  3  2
D366V12, multiclass
    clus
vv   RERE MUTATED RERE WILD-TYPE
  R0            3             77
  R1            2             33
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RERE MUTATED       1                         0     5
  RERE WILD-TYPE     5                         5   109
D366V14, multiclass
                           clus
vv                          RERE MUTATED RERE WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V15, binary
                cls
clus              0  1
  RERE MUTATED    1  4
  RERE WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  RERE MUTATED      1    4
  RERE WILD-TYPE    4   87
                        clus
vv                       RERE MUTATED RERE WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(367) Variable = CUX2 MUTATION ANALYSIS
D367V1, survival
                sevent
clus2             0  1
  CUX2 MUTATED    4  1
  CUX2 WILD-TYPE 59 61
  CUX2 MUTATED CUX2 WILD-TYPE 
             5            120 
  CUX2 MUTATED CUX2 WILD-TYPE 
             1             61 
$`CUX2 MUTATED`
TCGA-FB-AAPZ TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-A5ST 
       23.54        22.06         8.28        19.82        20.88 

$`CUX2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       20.35        17.79        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CUX2 MUTATED CUX2 WILD-TYPE 
          8.28           0.23 
  CUX2 MUTATED CUX2 WILD-TYPE 
         23.54          90.12 
  CUX2 MUTATED CUX2 WILD-TYPE 
        20.880         15.155 
[1] "8.3 - 23.5 (20.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.3"
D367V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CUX2 MUTATED         0        0        0         2         3         0
  CUX2 WILD-TYPE       1        3       12        17        79         4
                vv
clus             STAGE IV
  CUX2 MUTATED          0
  CUX2 WILD-TYPE        3
D367V3, multiclass
           clus
vv          CUX2 MUTATED CUX2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CUX2 MUTATED    0  1     4
  CUX2 WILD-TYPE  5 16    98
D367V4, multiclass
       clus
vv      CUX2 MUTATED CUX2 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V5, binary
                cls
clus              0  1
  CUX2 MUTATED    2  3
  CUX2 WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX2 MUTATED      2    3
  CUX2 WILD-TYPE   33   86
   clus
vv  CUX2 MUTATED CUX2 WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D367V6, binary
                cls
clus              0  1
  CUX2 MUTATED    2  0
  CUX2 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX2 MUTATED      2    0
  CUX2 WILD-TYPE   55    3
   clus
vv  CUX2 MUTATED CUX2 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D367V7, binary
                cls
clus              0  1
  CUX2 MUTATED    2  3
  CUX2 WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX2 MUTATED      2    3
  CUX2 WILD-TYPE   49   72
        clus
vv       CUX2 MUTATED CUX2 WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D367V8, binary
                cls
clus              0  1
  CUX2 MUTATED    5  0
  CUX2 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX2 MUTATED      5    0
  CUX2 WILD-TYPE   83   30
     clus
vv    CUX2 MUTATED CUX2 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CUX2 MUTATED                                     4
  CUX2 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CUX2 MUTATED                                       1
  CUX2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CUX2 MUTATED                                                  0
  CUX2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CUX2 MUTATED                                     0
  CUX2 WILD-TYPE                                   1
D367V9, multiclass
                                                  clus
vv                                                 CUX2 MUTATED CUX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V10, continuous
[1] "Remove cluster labels:" "CUX2 MUTATED"          
clus
  CUX2 MUTATED CUX2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-YY-A8LH 
"CUX2 WILD-TYPE" 
D367V11, continuous
[1] "Remove cluster labels:" "CUX2 MUTATED"          
clus
  CUX2 MUTATED CUX2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CUX2 WILD-TYPE" "CUX2 WILD-TYPE" "CUX2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CUX2 MUTATED    4  0  1  0
  CUX2 WILD-TYPE 76 35  3  2
D367V12, multiclass
    clus
vv   CUX2 MUTATED CUX2 WILD-TYPE
  R0            4             76
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUX2 MUTATED       1                         0     4
  CUX2 WILD-TYPE     5                         5   110
D367V14, multiclass
                           clus
vv                          CUX2 MUTATED CUX2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V15, binary
                cls
clus              0  1
  CUX2 MUTATED    0  4
  CUX2 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX2 MUTATED      0    4
  CUX2 WILD-TYPE    5   87
                        clus
vv                       CUX2 MUTATED CUX2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(368) Variable = RPTN MUTATION ANALYSIS
D368V1, survival
                sevent
clus2             0  1
  RPTN MUTATED    5  5
  RPTN WILD-TYPE 58 57
  RPTN MUTATED RPTN WILD-TYPE 
            10            115 
  RPTN MUTATED RPTN WILD-TYPE 
             5             57 
$`RPTN MUTATED`
TCGA-3A-A9IJ TCGA-XD-AAUL TCGA-2J-AAB6 TCGA-3A-A9I9 TCGA-FB-AAPU TCGA-IB-7651 
       60.95        16.37         9.63        20.84        12.53        19.82 
TCGA-IB-A6UG TCGA-RB-AA9M TCGA-XD-AAUH TCGA-XN-A8T3 
        1.35         9.40        12.99        31.27 

$`RPTN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ 
       16.37        12.33        15.95        37.15         7.50        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.03        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RPTN MUTATED RPTN WILD-TYPE 
          1.35           0.23 
  RPTN MUTATED RPTN WILD-TYPE 
         60.95          90.12 
  RPTN MUTATED RPTN WILD-TYPE 
         14.68          15.22 
[1] "1.4 - 61.0 (14.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D368V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RPTN MUTATED         0        0        2         4         5         0
  RPTN WILD-TYPE       1        3       10        15        77         4
                vv
clus             STAGE IV
  RPTN MUTATED          0
  RPTN WILD-TYPE        3
D368V3, multiclass
           clus
vv          RPTN MUTATED RPTN WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            4             15
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RPTN MUTATED    1  2     8
  RPTN WILD-TYPE  4 15    94
D368V4, multiclass
       clus
vv      RPTN MUTATED RPTN WILD-TYPE
  T1               1              4
  T2               2             15
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V5, binary
                cls
clus              0  1
  RPTN MUTATED    6  5
  RPTN WILD-TYPE 29 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      6    5
  RPTN WILD-TYPE   29   84
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            6             29
  1            5             84
[1] 2 2
[1] FALSE
D368V6, binary
                cls
clus              0  1
  RPTN MUTATED    5  0
  RPTN WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      5    0
  RPTN WILD-TYPE   52    3
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D368V7, binary
                cls
clus              0  1
  RPTN MUTATED    3  8
  RPTN WILD-TYPE 48 67
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      3    8
  RPTN WILD-TYPE   48   67
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            3             48
  MALE              8             67
[1] 2 2
[1] FALSE
D368V8, binary
                cls
clus              0  1
  RPTN MUTATED    6  4
  RPTN WILD-TYPE 82 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      6    4
  RPTN WILD-TYPE   82   26
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO             6             82
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RPTN MUTATED                                    10
  RPTN WILD-TYPE                                  95
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RPTN MUTATED                                       1
  RPTN WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RPTN MUTATED                                                  0
  RPTN WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RPTN MUTATED                                     0
  RPTN WILD-TYPE                                   1
D368V9, multiclass
                                                  clus
vv                                                 RPTN MUTATED RPTN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        10             95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V10, continuous
D368V11, continuous
                vv
clus             R0 R1 R2 RX
  RPTN MUTATED    7  3  1  0
  RPTN WILD-TYPE 73 32  3  2
D368V12, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            7             73
  R1            3             32
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       1                         0    10
  RPTN WILD-TYPE     5                         5   104
D368V14, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               10            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V15, binary
                cls
clus              0  1
  RPTN MUTATED    1  9
  RPTN WILD-TYPE  4 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      1    9
  RPTN WILD-TYPE    4   82
                        clus
vv                       RPTN MUTATED RPTN WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            9             82
[1] 2 2
[1] FALSE

Clustering(369) Variable = HIST1H2BJ MUTATION ANALYSIS
D369V1, survival
                     sevent
clus2                  0  1
  HIST1H2BJ MUTATED    2  2
  HIST1H2BJ WILD-TYPE 61 60
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  4                 121 
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  2                  60 
$`HIST1H2BJ MUTATED`
TCGA-3A-A9IV TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-RB-AA9M 
       36.26         5.03        19.82         9.40 

$`HIST1H2BJ WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
               5.03                0.23 
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
              36.26               90.12 
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
              14.61               15.22 
[1] "5.0 - 36.3 (14.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D369V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIST1H2BJ MUTATED         0        0        1         0         3         0
  HIST1H2BJ WILD-TYPE       1        3       11        19        79         4
                     vv
clus                  STAGE IV
  HIST1H2BJ MUTATED          0
  HIST1H2BJ WILD-TYPE        3
D369V3, multiclass
           clus
vv          HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  0                   3
  STAGE IB                  1                  11
  STAGE IIA                 0                  19
  STAGE IIB                 3                  79
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2 T3+T4
  HIST1H2BJ MUTATED     1   1     2
  HIST1H2BJ WILD-TYPE   4  16   100
D369V4, multiclass
       clus
vv      HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  T1                    1                   4
  T2                    1                  16
  T3+T4                 2                 100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V5, binary
                     cls
clus                   0  1
  HIST1H2BJ MUTATED    1  3
  HIST1H2BJ WILD-TYPE 34 86
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BJ MUTATED      1    3
  HIST1H2BJ WILD-TYPE   34   86
   clus
vv  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  0                 1                  34
  1                 3                  86
[1] 2 2
[1] FALSE
D369V6, binary
                     cls
clus                   0  1
  HIST1H2BJ MUTATED    1  0
  HIST1H2BJ WILD-TYPE 56  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BJ MUTATED      1    0
  HIST1H2BJ WILD-TYPE   56    3
   clus
vv  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  0                 1                  56
  1                 0                   3
[1] 2 2
[1] FALSE
D369V7, binary
                     cls
clus                   0  1
  HIST1H2BJ MUTATED    3  1
  HIST1H2BJ WILD-TYPE 48 74
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BJ MUTATED      3    1
  HIST1H2BJ WILD-TYPE   48   74
        clus
vv       HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  FEMALE                 3                  48
  MALE                   1                  74
[1] 2 2
[1] FALSE
D369V8, binary
                     cls
clus                   0  1
  HIST1H2BJ MUTATED    3  1
  HIST1H2BJ WILD-TYPE 85 29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BJ MUTATED      3    1
  HIST1H2BJ WILD-TYPE   85   29
     clus
vv    HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  NO                  3                  85
  YES                 1                  29
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H2BJ MUTATED                                     3
  HIST1H2BJ WILD-TYPE                                 102
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H2BJ MUTATED                                       1
  HIST1H2BJ WILD-TYPE                                    17
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H2BJ MUTATED                                                  0
  HIST1H2BJ WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIST1H2BJ MUTATED                                     0
  HIST1H2BJ WILD-TYPE                                   1
D369V9, multiclass
                                                  clus
vv                                                 HIST1H2BJ MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 HIST1H2BJ WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V10, continuous
[1] "Remove cluster labels:" "HIST1H2BJ MUTATED"     
clus
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  1                  38 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2J-AABV 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-2L-AAQA          TCGA-2L-AAQE          TCGA-3A-A9I9 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IX          TCGA-F2-A8YN 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-FB-A5VM          TCGA-FB-A78T          TCGA-FB-AAPQ 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-H8-A6C1          TCGA-HV-AA8V 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUU 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-AAUV          TCGA-LB-A9Q5          TCGA-OE-A75W 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
D369V11, continuous
[1] "Remove cluster labels:" "HIST1H2BJ MUTATED"     
clus
  HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE 
                  1                  32 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABE          TCGA-2J-AABF 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-2J-AABO          TCGA-3A-A9IB          TCGA-3A-A9IR 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-FB-A5VM          TCGA-FB-A78T 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-FB-AAPQ          TCGA-FB-AAPS          TCGA-H8-A6C1 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XD-AAUI 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"HIST1H2BJ WILD-TYPE" "HIST1H2BJ WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  HIST1H2BJ MUTATED    3  1  0  0
  HIST1H2BJ WILD-TYPE 77 34  4  2
D369V12, multiclass
    clus
vv   HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  R0                 3                  77
  R1                 1                  34
  R2                 0                   4
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BJ MUTATED       0                         0     4
  HIST1H2BJ WILD-TYPE     6                         5   110
D369V14, multiclass
                           clus
vv                          HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     4                 110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V15, binary
                     cls
clus                   0  1
  HIST1H2BJ MUTATED    0  4
  HIST1H2BJ WILD-TYPE  5 87
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BJ MUTATED      0    4
  HIST1H2BJ WILD-TYPE    5   87
                        clus
vv                       HIST1H2BJ MUTATED HIST1H2BJ WILD-TYPE
  HISPANIC OR LATINO                     0                   5
  NOT HISPANIC OR LATINO                 4                  87
[1] 2 2
[1] FALSE

Clustering(370) Variable = SLCO2A1 MUTATION ANALYSIS
D370V1, survival
                   sevent
clus2                0  1
  SLCO2A1 MUTATED    2  2
  SLCO2A1 WILD-TYPE 61 60
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                4               121 
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                2                60 
$`SLCO2A1 MUTATED`
TCGA-2J-AAB6 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-XN-A8T3 
        9.63        19.82        19.82        31.27 

$`SLCO2A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85         0.23        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
             9.63              0.23 
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
            31.27             90.12 
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
            19.82             15.19 
[1] "9.6 - 31.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D370V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLCO2A1 MUTATED         0        0        1         1         1         0
  SLCO2A1 WILD-TYPE       1        3       11        18        81         4
                   vv
clus                STAGE IV
  SLCO2A1 MUTATED          1
  SLCO2A1 WILD-TYPE        2
D370V3, multiclass
           clus
vv          SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               1                81
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLCO2A1 MUTATED    0  1     3
  SLCO2A1 WILD-TYPE  5 16    99
D370V4, multiclass
       clus
vv      SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V5, binary
                   cls
clus                 0  1
  SLCO2A1 MUTATED    3  1
  SLCO2A1 WILD-TYPE 32 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO2A1 MUTATED      3    1
  SLCO2A1 WILD-TYPE   32   88
   clus
vv  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  0               3                32
  1               1                88
[1] 2 2
[1] FALSE
D370V6, binary
                   cls
clus                 0  1
  SLCO2A1 MUTATED    3  1
  SLCO2A1 WILD-TYPE 54  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO2A1 MUTATED      3    1
  SLCO2A1 WILD-TYPE   54    2
   clus
vv  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  0               3                54
  1               1                 2
[1] 2 2
[1] FALSE
D370V7, binary
                   cls
clus                 0  1
  SLCO2A1 MUTATED    1  3
  SLCO2A1 WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO2A1 MUTATED      1    3
  SLCO2A1 WILD-TYPE   50   72
        clus
vv       SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D370V8, binary
                   cls
clus                 0  1
  SLCO2A1 MUTATED    3  1
  SLCO2A1 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO2A1 MUTATED      3    1
  SLCO2A1 WILD-TYPE   85   29
     clus
vv    SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLCO2A1 MUTATED                                     3
  SLCO2A1 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLCO2A1 MUTATED                                       1
  SLCO2A1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLCO2A1 MUTATED                                                  0
  SLCO2A1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLCO2A1 MUTATED                                     0
  SLCO2A1 WILD-TYPE                                   1
D370V9, multiclass
                                                  clus
vv                                                 SLCO2A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLCO2A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V10, continuous
[1] "Remove cluster labels:" "SLCO2A1 MUTATED"       
clus
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
D370V11, continuous
[1] "Remove cluster labels:" "SLCO2A1 MUTATED"       
clus
  SLCO2A1 MUTATED SLCO2A1 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" "SLCO2A1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLCO2A1 MUTATED    3  1  0  0
  SLCO2A1 WILD-TYPE 77 34  4  2
D370V12, multiclass
    clus
vv   SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLCO2A1 MUTATED       0                         0     4
  SLCO2A1 WILD-TYPE     6                         5   110
D370V14, multiclass
                           clus
vv                          SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V15, binary
                   cls
clus                 0  1
  SLCO2A1 MUTATED    1  2
  SLCO2A1 WILD-TYPE  4 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO2A1 MUTATED      1    2
  SLCO2A1 WILD-TYPE    4   89
                        clus
vv                       SLCO2A1 MUTATED SLCO2A1 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(371) Variable = TULP1 MUTATION ANALYSIS
D371V1, survival
                 sevent
clus2              0  1
  TULP1 MUTATED    3  0
  TULP1 WILD-TYPE 60 62
  TULP1 MUTATED TULP1 WILD-TYPE 
              3             122 
  TULP1 MUTATED TULP1 WILD-TYPE 
              0              62 
$`TULP1 MUTATED`
TCGA-2J-AABE TCGA-IB-AAUM TCGA-IB-AAUP 
       22.22         0.26        14.17 

$`TULP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ 
        1.35         8.22        15.88         4.73         7.86         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TULP1 MUTATED TULP1 WILD-TYPE 
           0.26            0.23 
  TULP1 MUTATED TULP1 WILD-TYPE 
          22.22           90.12 
  TULP1 MUTATED TULP1 WILD-TYPE 
          14.17           15.27 
[1] "0.3 - 22.2 (14.2)" "0.2 - 90.1 (15.3)"
[1] "hr="     "9200000"
D371V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TULP1 MUTATED         0        0        0         1         2         0
  TULP1 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  TULP1 MUTATED          0
  TULP1 WILD-TYPE        3
D371V3, multiclass
           clus
vv          TULP1 MUTATED TULP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  TULP1 MUTATED     0   1     2
  TULP1 WILD-TYPE   5  16   100
D371V4, multiclass
       clus
vv      TULP1 MUTATED TULP1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V5, binary
                 cls
clus               0  1
  TULP1 MUTATED    1  2
  TULP1 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP1 MUTATED      1    2
  TULP1 WILD-TYPE   34   87
   clus
vv  TULP1 MUTATED TULP1 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D371V6, binary
                 cls
clus               0  1
  TULP1 MUTATED    3  0
  TULP1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP1 MUTATED      3    0
  TULP1 WILD-TYPE   54    3
   clus
vv  TULP1 MUTATED TULP1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D371V7, binary
                 cls
clus               0  1
  TULP1 MUTATED    0  3
  TULP1 WILD-TYPE 51 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP1 MUTATED      0    3
  TULP1 WILD-TYPE   51   72
        clus
vv       TULP1 MUTATED TULP1 WILD-TYPE
  FEMALE             0              51
  MALE               3              72
[1] 2 2
[1] FALSE
D371V8, binary
                 cls
clus               0  1
  TULP1 MUTATED    2  1
  TULP1 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP1 MUTATED      2    1
  TULP1 WILD-TYPE   86   29
     clus
vv    TULP1 MUTATED TULP1 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TULP1 MUTATED                                     3
  TULP1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TULP1 MUTATED                                       0
  TULP1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TULP1 MUTATED                                                  0
  TULP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TULP1 MUTATED                                     0
  TULP1 WILD-TYPE                                   1
D371V9, multiclass
                                                  clus
vv                                                 TULP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TULP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V10, continuous
[1] "Remove cluster labels:" "TULP1 MUTATED"         
clus
  TULP1 MUTATED TULP1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
D371V11, continuous
[1] "Remove cluster labels:" "TULP1 MUTATED"         
clus
  TULP1 MUTATED TULP1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABF 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" "TULP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TULP1 MUTATED    2  1  0  0
  TULP1 WILD-TYPE 78 34  4  2
D371V12, multiclass
    clus
vv   TULP1 MUTATED TULP1 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TULP1 MUTATED       0                         0     3
  TULP1 WILD-TYPE     6                         5   111
D371V14, multiclass
                           clus
vv                          TULP1 MUTATED TULP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V15, binary
                 cls
clus               0  1
  TULP1 MUTATED    0  2
  TULP1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TULP1 MUTATED      0    2
  TULP1 WILD-TYPE    5   89
                        clus
vv                       TULP1 MUTATED TULP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(372) Variable = C14ORF21 MUTATION ANALYSIS
D372V1, survival
                    sevent
clus2                 0  1
  C14ORF21 MUTATED    2  4
  C14ORF21 WILD-TYPE 61 58
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 6                119 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 4                 58 
$`C14ORF21 MUTATED`
TCGA-3A-A9IL TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-IB-7651 TCGA-IB-A6UF 
       90.12         9.11         4.70        22.49        19.82        21.90 

$`C14ORF21 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
       15.22        21.44         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
              4.70               0.23 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
             90.12              75.12 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
             20.86              15.19 
[1] "4.7 - 90.1 (20.9)" "0.2 - 75.1 (15.2)"
[1] "hr=" "1"  
D372V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C14ORF21 MUTATED         1        0        0         0         5         0
  C14ORF21 WILD-TYPE       0        3       12        19        77         4
                    vv
clus                 STAGE IV
  C14ORF21 MUTATED          0
  C14ORF21 WILD-TYPE        3
D372V3, multiclass
           clus
vv          C14ORF21 MUTATED C14ORF21 WILD-TYPE
  STAGE I                  1                  0
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C14ORF21 MUTATED    1  0     5
  C14ORF21 WILD-TYPE  4 17    97
D372V4, multiclass
       clus
vv      C14ORF21 MUTATED C14ORF21 WILD-TYPE
  T1                   1                  4
  T2                   0                 17
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V5, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    0  5
  C14ORF21 WILD-TYPE 35 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      0    5
  C14ORF21 WILD-TYPE   35   84
   clus
vv  C14ORF21 MUTATED C14ORF21 WILD-TYPE
  0                0                 35
  1                5                 84
[1] 2 2
[1] FALSE
D372V6, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    4  0
  C14ORF21 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      4    0
  C14ORF21 WILD-TYPE   53    3
   clus
vv  C14ORF21 MUTATED C14ORF21 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D372V7, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    2  4
  C14ORF21 WILD-TYPE 49 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      2    4
  C14ORF21 WILD-TYPE   49   71
        clus
vv       C14ORF21 MUTATED C14ORF21 WILD-TYPE
  FEMALE                2                 49
  MALE                  4                 71
[1] 2 2
[1] FALSE
D372V8, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    6  0
  C14ORF21 WILD-TYPE 82 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      6    0
  C14ORF21 WILD-TYPE   82   30
     clus
vv    C14ORF21 MUTATED C14ORF21 WILD-TYPE
  NO                 6                 82
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C14ORF21 MUTATED                                     5
  C14ORF21 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C14ORF21 MUTATED                                       1
  C14ORF21 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C14ORF21 MUTATED                                                  0
  C14ORF21 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C14ORF21 MUTATED                                     0
  C14ORF21 WILD-TYPE                                   1
D372V9, multiclass
                                                  clus
vv                                                 C14ORF21 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C14ORF21 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V10, continuous
D372V11, continuous
[1] "Remove cluster labels:" "C14ORF21 MUTATED"      
clus
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-YY-A8LH 
"C14ORF21 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C14ORF21 MUTATED    4  2  0  0
  C14ORF21 WILD-TYPE 76 33  4  2
D372V12, multiclass
    clus
vv   C14ORF21 MUTATED C14ORF21 WILD-TYPE
  R0                4                 76
  R1                2                 33
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF21 MUTATED       0                         0     6
  C14ORF21 WILD-TYPE     6                         5   108
D372V14, multiclass
                           clus
vv                          C14ORF21 MUTATED C14ORF21 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    6                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V15, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    0  3
  C14ORF21 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      0    3
  C14ORF21 WILD-TYPE    5   88
                        clus
vv                       C14ORF21 MUTATED C14ORF21 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(373) Variable = PPIG MUTATION ANALYSIS
D373V1, survival
                sevent
clus2             0  1
  PPIG MUTATED    1  3
  PPIG WILD-TYPE 62 59
  PPIG MUTATED PPIG WILD-TYPE 
             4            121 
  PPIG MUTATED PPIG WILD-TYPE 
             3             59 
$`PPIG MUTATED`
TCGA-F2-7273 TCGA-FZ-5922 TCGA-IB-7651 TCGA-YB-A89D 
       19.46        36.20        19.82        11.51 

$`PPIG WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PPIG MUTATED PPIG WILD-TYPE 
         11.51           0.23 
  PPIG MUTATED PPIG WILD-TYPE 
         36.20          90.12 
  PPIG MUTATED PPIG WILD-TYPE 
         19.64          15.19 
[1] "11.5 - 36.2 (19.6)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D373V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPIG MUTATED         0        0        0         1         3         0
  PPIG WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  PPIG MUTATED          0
  PPIG WILD-TYPE        3
D373V3, multiclass
           clus
vv          PPIG MUTATED PPIG WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PPIG MUTATED    0  0     4
  PPIG WILD-TYPE  5 17    98
D373V4, multiclass
       clus
vv      PPIG MUTATED PPIG WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V5, binary
                cls
clus              0  1
  PPIG MUTATED    1  3
  PPIG WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      1    3
  PPIG WILD-TYPE   34   86
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D373V6, binary
                cls
clus              0  1
  PPIG MUTATED    3  0
  PPIG WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      3    0
  PPIG WILD-TYPE   54    3
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D373V7, binary
                cls
clus              0  1
  PPIG MUTATED    1  3
  PPIG WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      1    3
  PPIG WILD-TYPE   50   72
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D373V8, binary
                cls
clus              0  1
  PPIG MUTATED    2  2
  PPIG WILD-TYPE 86 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      2    2
  PPIG WILD-TYPE   86   28
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO             2             86
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPIG MUTATED                                     4
  PPIG WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPIG MUTATED                                       0
  PPIG WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPIG MUTATED                                                  0
  PPIG WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPIG MUTATED                                     0
  PPIG WILD-TYPE                                   1
D373V9, multiclass
                                                  clus
vv                                                 PPIG MUTATED PPIG WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V10, continuous
[1] "Remove cluster labels:" "PPIG MUTATED"          
clus
  PPIG MUTATED PPIG WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" 
D373V11, continuous
[1] "Remove cluster labels:" "PPIG MUTATED"          
clus
  PPIG MUTATED PPIG WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PPIG MUTATED    3  1  0  0
  PPIG WILD-TYPE 77 34  4  2
D373V12, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPIG MUTATED       0                         1     3
  PPIG WILD-TYPE     6                         4   111
D373V14, multiclass
                           clus
vv                          PPIG MUTATED PPIG WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V15, binary
                cls
clus              0  1
  PPIG MUTATED    0  4
  PPIG WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      0    4
  PPIG WILD-TYPE    5   87
                        clus
vv                       PPIG MUTATED PPIG WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(374) Variable = SLC39A4 MUTATION ANALYSIS
D374V1, survival
                   sevent
clus2                0  1
  SLC39A4 MUTATED    2  2
  SLC39A4 WILD-TYPE 61 60
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                4               121 
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                2                60 
$`SLC39A4 MUTATED`
TCGA-IB-7651 TCGA-IB-A7M4 TCGA-US-A776 TCGA-US-A77G 
       19.82        15.88        39.98         0.39 

$`SLC39A4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        9.40         0.30        16.80        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
             0.39              0.23 
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
            39.98             90.12 
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
            17.85             15.19 
[1] "0.4 - 40.0 (17.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D374V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC39A4 MUTATED         0        0        0         1         3         0
  SLC39A4 WILD-TYPE       1        3       12        18        79         4
                   vv
clus                STAGE IV
  SLC39A4 MUTATED          0
  SLC39A4 WILD-TYPE        3
D374V3, multiclass
           clus
vv          SLC39A4 MUTATED SLC39A4 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC39A4 MUTATED    0  0     4
  SLC39A4 WILD-TYPE  5 17    98
D374V4, multiclass
       clus
vv      SLC39A4 MUTATED SLC39A4 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V5, binary
                   cls
clus                 0  1
  SLC39A4 MUTATED    1  3
  SLC39A4 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A4 MUTATED      1    3
  SLC39A4 WILD-TYPE   34   86
   clus
vv  SLC39A4 MUTATED SLC39A4 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D374V6, binary
                   cls
clus                 0  1
  SLC39A4 MUTATED    1  0
  SLC39A4 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A4 MUTATED      1    0
  SLC39A4 WILD-TYPE   56    3
   clus
vv  SLC39A4 MUTATED SLC39A4 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D374V7, binary
                   cls
clus                 0  1
  SLC39A4 MUTATED    1  3
  SLC39A4 WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A4 MUTATED      1    3
  SLC39A4 WILD-TYPE   50   72
        clus
vv       SLC39A4 MUTATED SLC39A4 WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D374V8, binary
                   cls
clus                 0  1
  SLC39A4 MUTATED    4  0
  SLC39A4 WILD-TYPE 84 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A4 MUTATED      4    0
  SLC39A4 WILD-TYPE   84   30
     clus
vv    SLC39A4 MUTATED SLC39A4 WILD-TYPE
  NO                4                84
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC39A4 MUTATED                                     3
  SLC39A4 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC39A4 MUTATED                                       0
  SLC39A4 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC39A4 MUTATED                                                  1
  SLC39A4 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC39A4 MUTATED                                     0
  SLC39A4 WILD-TYPE                                   1
D374V9, multiclass
                                                  clus
vv                                                 SLC39A4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC39A4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V10, continuous
[1] "Remove cluster labels:" "SLC39A4 MUTATED"       
clus
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC39A4 WILD-TYPE" 
D374V11, continuous
[1] "Remove cluster labels:" "SLC39A4 MUTATED"       
clus
  SLC39A4 MUTATED SLC39A4 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-AAUQ 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" "SLC39A4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC39A4 MUTATED    4  0  0  0
  SLC39A4 WILD-TYPE 76 35  4  2
D374V12, multiclass
    clus
vv   SLC39A4 MUTATED SLC39A4 WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC39A4 MUTATED       0                         0     4
  SLC39A4 WILD-TYPE     6                         5   110
D374V14, multiclass
                           clus
vv                          SLC39A4 MUTATED SLC39A4 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V15, binary
                   cls
clus                 0  1
  SLC39A4 MUTATED    0  4
  SLC39A4 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A4 MUTATED      0    4
  SLC39A4 WILD-TYPE    5   87
                        clus
vv                       SLC39A4 MUTATED SLC39A4 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(375) Variable = CBLL1 MUTATION ANALYSIS
D375V1, survival
                 sevent
clus2              0  1
  CBLL1 MUTATED    2  2
  CBLL1 WILD-TYPE 61 60
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              4             121 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              2              60 
$`CBLL1 MUTATED`
TCGA-2L-AAQA TCGA-3A-A9IO TCGA-IB-7651 TCGA-IB-AAUV 
        4.70        63.85        19.82        13.28 

$`CBLL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           4.70            0.23 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          63.85           90.12 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          16.55           15.22 
[1] "4.7 - 63.9 (16.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D375V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CBLL1 MUTATED         0        0        0         0         3         0
  CBLL1 WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  CBLL1 MUTATED          0
  CBLL1 WILD-TYPE        3
D375V3, multiclass
           clus
vv          CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CBLL1 MUTATED    0  0     3
  CBLL1 WILD-TYPE  5 17    99
D375V4, multiclass
       clus
vv      CBLL1 MUTATED CBLL1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V5, binary
                 cls
clus               0  1
  CBLL1 MUTATED    0  3
  CBLL1 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    3
  CBLL1 WILD-TYPE   35   86
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D375V6, binary
                 cls
clus               0  1
  CBLL1 MUTATED    2  0
  CBLL1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      2    0
  CBLL1 WILD-TYPE   55    3
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D375V7, binary
                 cls
clus               0  1
  CBLL1 MUTATED    1  3
  CBLL1 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      1    3
  CBLL1 WILD-TYPE   50   72
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D375V8, binary
                 cls
clus               0  1
  CBLL1 MUTATED    4  0
  CBLL1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      4    0
  CBLL1 WILD-TYPE   84   30
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CBLL1 MUTATED                                     3
  CBLL1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CBLL1 MUTATED                                       1
  CBLL1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CBLL1 MUTATED                                                  0
  CBLL1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CBLL1 MUTATED                                     0
  CBLL1 WILD-TYPE                                   1
D375V9, multiclass
                                                  clus
vv                                                 CBLL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CBLL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V10, continuous
D375V11, continuous
[1] "Remove cluster labels:" "CBLL1 MUTATED"         
clus
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" "CBLL1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CBLL1 MUTATED    3  1  0  0
  CBLL1 WILD-TYPE 77 34  4  2
D375V12, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBLL1 MUTATED       0                         0     4
  CBLL1 WILD-TYPE     6                         5   110
D375V14, multiclass
                           clus
vv                          CBLL1 MUTATED CBLL1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V15, binary
                 cls
clus               0  1
  CBLL1 MUTATED    0  3
  CBLL1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      0    3
  CBLL1 WILD-TYPE    5   88
                        clus
vv                       CBLL1 MUTATED CBLL1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(376) Variable = FCGBP MUTATION ANALYSIS
D376V1, survival
                 sevent
clus2              0  1
  FCGBP MUTATED    4  8
  FCGBP WILD-TYPE 59 54
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             113 
  FCGBP MUTATED FCGBP WILD-TYPE 
              8              54 
$`FCGBP MUTATED`
TCGA-3A-A9I5 TCGA-LB-A7SX TCGA-2J-AAB6 TCGA-2L-AAQI TCGA-2L-AAQL TCGA-FB-AAQ1 
       58.98        12.92         9.63         3.39         9.60         4.04 
TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUM TCGA-IB-AAUQ TCGA-XD-AAUH 
       32.15        19.82        12.00         0.26         6.02        12.99 

$`FCGBP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 
       21.44         4.70        22.49        12.95        45.47        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR 
       20.84         7.36        24.26        33.57        63.85        50.70 
TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 
       32.81        15.06        36.26        34.09        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
       15.55         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
       15.88         4.73         7.86        14.17        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  FCGBP MUTATED FCGBP WILD-TYPE 
           0.26            0.23 
  FCGBP MUTATED FCGBP WILD-TYPE 
          58.98           90.12 
  FCGBP MUTATED FCGBP WILD-TYPE 
         10.815          15.550 
[1] "0.3 - 59.0 (10.8)" "0.2 - 90.1 (15.6)"
[1] "hr=" "2"  
D376V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FCGBP MUTATED         0        0        0         1        10         0
  FCGBP WILD-TYPE       1        3       12        18        72         4
                 vv
clus              STAGE IV
  FCGBP MUTATED          0
  FCGBP WILD-TYPE        3
D376V3, multiclass
           clus
vv          FCGBP MUTATED FCGBP WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB            10              72
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FCGBP MUTATED    0  1    10
  FCGBP WILD-TYPE  5 16    92
D376V4, multiclass
       clus
vv      FCGBP MUTATED FCGBP WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V5, binary
                 cls
clus               0  1
  FCGBP MUTATED    2 10
  FCGBP WILD-TYPE 33 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2   10
  FCGBP WILD-TYPE   33   79
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             2              33
  1            10              79
[1] 2 2
[1] FALSE
D376V6, binary
                 cls
clus               0  1
  FCGBP MUTATED    7  0
  FCGBP WILD-TYPE 50  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      7    0
  FCGBP WILD-TYPE   50    3
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             7              50
  1             0               3
[1] 2 2
[1] FALSE
D376V7, binary
                 cls
clus               0  1
  FCGBP MUTATED    3  9
  FCGBP WILD-TYPE 48 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      3    9
  FCGBP WILD-TYPE   48   66
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  FEMALE             3              48
  MALE               9              66
[1] 2 2
[1] FALSE
D376V8, binary
                 cls
clus               0  1
  FCGBP MUTATED    9  3
  FCGBP WILD-TYPE 79 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      9    3
  FCGBP WILD-TYPE   79   27
     clus
vv    FCGBP MUTATED FCGBP WILD-TYPE
  NO              9              79
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FCGBP MUTATED                                    11
  FCGBP WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FCGBP MUTATED                                       1
  FCGBP WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FCGBP MUTATED                                                  0
  FCGBP WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FCGBP MUTATED                                     0
  FCGBP WILD-TYPE                                   1
D376V9, multiclass
                                                  clus
vv                                                 FCGBP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FCGBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V10, continuous
D376V11, continuous
                 vv
clus              R0 R1 R2 RX
  FCGBP MUTATED    6  4  1  1
  FCGBP WILD-TYPE 74 31  3  1
D376V12, multiclass
    clus
vv   FCGBP MUTATED FCGBP WILD-TYPE
  R0             6              74
  R1             4              31
  R2             1               3
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FCGBP MUTATED       1                         1    10
  FCGBP WILD-TYPE     5                         4   104
D376V14, multiclass
                           clus
vv                          FCGBP MUTATED FCGBP WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V15, binary
                 cls
clus               0  1
  FCGBP MUTATED    0  7
  FCGBP WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      0    7
  FCGBP WILD-TYPE    5   84
                        clus
vv                       FCGBP MUTATED FCGBP WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(377) Variable = MAMSTR MUTATION ANALYSIS
D377V1, survival
                  sevent
clus2               0  1
  MAMSTR MUTATED    1  2
  MAMSTR WILD-TYPE 62 60
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               3              122 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
               2               60 
$`MAMSTR MUTATED`
TCGA-US-A77G TCGA-US-A77J TCGA-YB-A89D 
        0.39        18.67        11.51 

$`MAMSTR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MAMSTR MUTATED MAMSTR WILD-TYPE 
            0.39             0.23 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
           18.67            90.12 
  MAMSTR MUTATED MAMSTR WILD-TYPE 
           11.51            15.27 
[1] "0.4 - 18.7 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D377V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAMSTR MUTATED         0        0        0         0         3         0
  MAMSTR WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  MAMSTR MUTATED          0
  MAMSTR WILD-TYPE        3
D377V3, multiclass
           clus
vv          MAMSTR MUTATED MAMSTR WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MAMSTR MUTATED    0  0     3
  MAMSTR WILD-TYPE  5 17    99
D377V4, multiclass
       clus
vv      MAMSTR MUTATED MAMSTR WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V5, binary
                  cls
clus                0  1
  MAMSTR MUTATED    0  3
  MAMSTR WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      0    3
  MAMSTR WILD-TYPE   35   86
   clus
vv  MAMSTR MUTATED MAMSTR WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D377V6, binary
                  cls
clus                0  1
  MAMSTR MUTATED    0  0
  MAMSTR WILD-TYPE 57  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      0    0
  MAMSTR WILD-TYPE   57    3
D377V7, binary
                  cls
clus                0  1
  MAMSTR MUTATED    1  2
  MAMSTR WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      1    2
  MAMSTR WILD-TYPE   50   73
        clus
vv       MAMSTR MUTATED MAMSTR WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D377V8, binary
                  cls
clus                0  1
  MAMSTR MUTATED    1  1
  MAMSTR WILD-TYPE 87 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      1    1
  MAMSTR WILD-TYPE   87   29
     clus
vv    MAMSTR MUTATED MAMSTR WILD-TYPE
  NO               1               87
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAMSTR MUTATED                                     3
  MAMSTR WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAMSTR MUTATED                                       0
  MAMSTR WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAMSTR MUTATED                                                  0
  MAMSTR WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAMSTR MUTATED                                     0
  MAMSTR WILD-TYPE                                   1
D377V9, multiclass
                                                  clus
vv                                                 MAMSTR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MAMSTR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V10, continuous
D377V11, continuous
                  vv
clus               R0 R1 R2 RX
  MAMSTR MUTATED    3  0  0  0
  MAMSTR WILD-TYPE 77 35  4  2
D377V12, multiclass
    clus
vv   MAMSTR MUTATED MAMSTR WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMSTR MUTATED       0                         0     3
  MAMSTR WILD-TYPE     6                         5   111
D377V14, multiclass
                           clus
vv                          MAMSTR MUTATED MAMSTR WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V15, binary
                  cls
clus                0  1
  MAMSTR MUTATED    0  3
  MAMSTR WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMSTR MUTATED      0    3
  MAMSTR WILD-TYPE    5   88
                        clus
vv                       MAMSTR MUTATED MAMSTR WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(378) Variable = OR2T33 MUTATION ANALYSIS
D378V1, survival
                  sevent
clus2               0  1
  OR2T33 MUTATED    2  1
  OR2T33 WILD-TYPE 61 61
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               3              122 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               1               61 
$`OR2T33 MUTATED`
TCGA-XD-AAUL TCGA-HV-A7OP TCGA-IB-7651 
       16.37        32.15        19.82 

$`OR2T33 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  OR2T33 MUTATED OR2T33 WILD-TYPE 
           16.37             0.23 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
           32.15            90.12 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
          19.820           15.155 
[1] "16.4 - 32.1 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.1"
D378V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR2T33 MUTATED         0        0        0         1         3         0
  OR2T33 WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  OR2T33 MUTATED          0
  OR2T33 WILD-TYPE        3
D378V3, multiclass
           clus
vv          OR2T33 MUTATED OR2T33 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  OR2T33 MUTATED    0  0     4
  OR2T33 WILD-TYPE  5 17    98
D378V4, multiclass
       clus
vv      OR2T33 MUTATED OR2T33 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V5, binary
                  cls
clus                0  1
  OR2T33 MUTATED    1  3
  OR2T33 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      1    3
  OR2T33 WILD-TYPE   34   86
   clus
vv  OR2T33 MUTATED OR2T33 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D378V6, binary
                  cls
clus                0  1
  OR2T33 MUTATED    2  0
  OR2T33 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      2    0
  OR2T33 WILD-TYPE   55    3
   clus
vv  OR2T33 MUTATED OR2T33 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D378V7, binary
                  cls
clus                0  1
  OR2T33 MUTATED    1  3
  OR2T33 WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      1    3
  OR2T33 WILD-TYPE   50   72
        clus
vv       OR2T33 MUTATED OR2T33 WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D378V8, binary
                  cls
clus                0  1
  OR2T33 MUTATED    2  1
  OR2T33 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      2    1
  OR2T33 WILD-TYPE   86   29
     clus
vv    OR2T33 MUTATED OR2T33 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR2T33 MUTATED                                     3
  OR2T33 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR2T33 MUTATED                                       1
  OR2T33 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR2T33 MUTATED                                                  0
  OR2T33 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR2T33 MUTATED                                     0
  OR2T33 WILD-TYPE                                   1
D378V9, multiclass
                                                  clus
vv                                                 OR2T33 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 OR2T33 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V10, continuous
D378V11, continuous
                  vv
clus               R0 R1 R2 RX
  OR2T33 MUTATED    4  0  0  0
  OR2T33 WILD-TYPE 76 35  4  2
D378V12, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2T33 MUTATED       1                         0     3
  OR2T33 WILD-TYPE     5                         5   111
D378V14, multiclass
                           clus
vv                          OR2T33 MUTATED OR2T33 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V15, binary
                  cls
clus                0  1
  OR2T33 MUTATED    0  3
  OR2T33 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED      0    3
  OR2T33 WILD-TYPE    5   88
                        clus
vv                       OR2T33 MUTATED OR2T33 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(379) Variable = KCNB1 MUTATION ANALYSIS
D379V1, survival
                 sevent
clus2              0  1
  KCNB1 MUTATED    1  4
  KCNB1 WILD-TYPE 62 58
  KCNB1 MUTATED KCNB1 WILD-TYPE 
              5             120 
  KCNB1 MUTATED KCNB1 WILD-TYPE 
              4              58 
$`KCNB1 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-A6UG TCGA-LB-A9Q5 
       10.85        19.82         7.20         1.35        10.29 

$`KCNB1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       12.00        15.85        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KCNB1 MUTATED KCNB1 WILD-TYPE 
           1.35            0.23 
  KCNB1 MUTATED KCNB1 WILD-TYPE 
          19.82           90.12 
  KCNB1 MUTATED KCNB1 WILD-TYPE 
         10.290          15.335 
[1] "1.4 - 19.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "3.2"
D379V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KCNB1 MUTATED         0        0        1         0         4         0
  KCNB1 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  KCNB1 MUTATED          0
  KCNB1 WILD-TYPE        3
D379V3, multiclass
           clus
vv          KCNB1 MUTATED KCNB1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KCNB1 MUTATED    0  1     4
  KCNB1 WILD-TYPE  5 16    98
D379V4, multiclass
       clus
vv      KCNB1 MUTATED KCNB1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V5, binary
                 cls
clus               0  1
  KCNB1 MUTATED    1  4
  KCNB1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB1 MUTATED      1    4
  KCNB1 WILD-TYPE   34   85
   clus
vv  KCNB1 MUTATED KCNB1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D379V6, binary
                 cls
clus               0  1
  KCNB1 MUTATED    3  0
  KCNB1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB1 MUTATED      3    0
  KCNB1 WILD-TYPE   54    3
   clus
vv  KCNB1 MUTATED KCNB1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D379V7, binary
                 cls
clus               0  1
  KCNB1 MUTATED    3  2
  KCNB1 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB1 MUTATED      3    2
  KCNB1 WILD-TYPE   48   73
        clus
vv       KCNB1 MUTATED KCNB1 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D379V8, binary
                 cls
clus               0  1
  KCNB1 MUTATED    4  1
  KCNB1 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB1 MUTATED      4    1
  KCNB1 WILD-TYPE   84   29
     clus
vv    KCNB1 MUTATED KCNB1 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNB1 MUTATED                                     4
  KCNB1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNB1 MUTATED                                       1
  KCNB1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNB1 MUTATED                                                  0
  KCNB1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KCNB1 MUTATED                                     0
  KCNB1 WILD-TYPE                                   1
D379V9, multiclass
                                                  clus
vv                                                 KCNB1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KCNB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V10, continuous
D379V11, continuous
                 vv
clus              R0 R1 R2 RX
  KCNB1 MUTATED    4  1  0  0
  KCNB1 WILD-TYPE 76 34  4  2
D379V12, multiclass
    clus
vv   KCNB1 MUTATED KCNB1 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNB1 MUTATED       0                         0     5
  KCNB1 WILD-TYPE     6                         5   109
D379V14, multiclass
                           clus
vv                          KCNB1 MUTATED KCNB1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V15, binary
                 cls
clus               0  1
  KCNB1 MUTATED    0  5
  KCNB1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNB1 MUTATED      0    5
  KCNB1 WILD-TYPE    5   86
                        clus
vv                       KCNB1 MUTATED KCNB1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(380) Variable = RREB1 MUTATION ANALYSIS
D380V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    5  5
  RREB1 WILD-TYPE 58 57
  RREB1 MUTATED RREB1 WILD-TYPE 
             10             115 
  RREB1 MUTATED RREB1 WILD-TYPE 
              5              57 
$`RREB1 MUTATED`
TCGA-FB-AAQ6 TCGA-2J-AABA TCGA-3A-A9I9 TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-A5SP 
        8.02        19.96        20.84         7.50        19.82        15.85 
TCGA-OE-A75W TCGA-RL-AAAS TCGA-XN-A8T5 TCGA-YB-A89D 
        8.78         0.30        23.67        11.51 

$`RREB1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        15.19        12.00         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH 
       13.81        12.99        12.03        31.27        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RREB1 MUTATED RREB1 WILD-TYPE 
           0.30            0.23 
  RREB1 MUTATED RREB1 WILD-TYPE 
          23.67           90.12 
  RREB1 MUTATED RREB1 WILD-TYPE 
          13.68           15.22 
[1] "0.3 - 23.7 (13.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D380V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RREB1 MUTATED         0        1        2         3         4         0
  RREB1 WILD-TYPE       1        2       10        16        78         4
                 vv
clus              STAGE IV
  RREB1 MUTATED          0
  RREB1 WILD-TYPE        3
D380V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              2              10
  STAGE IIA             3              16
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RREB1 MUTATED    1  3     6
  RREB1 WILD-TYPE  4 14    96
D380V4, multiclass
       clus
vv      RREB1 MUTATED RREB1 WILD-TYPE
  T1                1               4
  T2                3              14
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V5, binary
                 cls
clus               0  1
  RREB1 MUTATED    6  4
  RREB1 WILD-TYPE 29 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      6    4
  RREB1 WILD-TYPE   29   85
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             6              29
  1             4              85
[1] 2 2
[1] FALSE
D380V6, binary
                 cls
clus               0  1
  RREB1 MUTATED    6  0
  RREB1 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      6    0
  RREB1 WILD-TYPE   51    3
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D380V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    4  6
  RREB1 WILD-TYPE 47 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      4    6
  RREB1 WILD-TYPE   47   69
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             4              47
  MALE               6              69
[1] 2 2
[1] FALSE
D380V8, binary
                 cls
clus               0  1
  RREB1 MUTATED    5  5
  RREB1 WILD-TYPE 83 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      5    5
  RREB1 WILD-TYPE   83   25
     clus
vv    RREB1 MUTATED RREB1 WILD-TYPE
  NO              5              83
  YES             5              25
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RREB1 MUTATED                                     9
  RREB1 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RREB1 MUTATED                                       1
  RREB1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RREB1 MUTATED                                                  0
  RREB1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RREB1 MUTATED                                     0
  RREB1 WILD-TYPE                                   1
D380V9, multiclass
                                                  clus
vv                                                 RREB1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RREB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V10, continuous
D380V11, continuous
                 vv
clus              R0 R1 R2 RX
  RREB1 MUTATED    7  3  0  0
  RREB1 WILD-TYPE 73 32  4  2
D380V12, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  R0             7              73
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RREB1 MUTATED       0                         0    10
  RREB1 WILD-TYPE     6                         5   104
D380V14, multiclass
                           clus
vv                          RREB1 MUTATED RREB1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V15, binary
                 cls
clus               0  1
  RREB1 MUTATED    1  7
  RREB1 WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      1    7
  RREB1 WILD-TYPE    4   84
                        clus
vv                       RREB1 MUTATED RREB1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(381) Variable = CANT1 MUTATION ANALYSIS
D381V1, survival
                 sevent
clus2              0  1
  CANT1 MUTATED    2  1
  CANT1 WILD-TYPE 61 61
  CANT1 MUTATED CANT1 WILD-TYPE 
              3             122 
  CANT1 MUTATED CANT1 WILD-TYPE 
              1              61 
$`CANT1 MUTATED`
TCGA-XD-AAUL TCGA-HV-AA8X TCGA-RB-AA9M 
       16.37        17.49         9.40 

$`CANT1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CANT1 MUTATED CANT1 WILD-TYPE 
           9.40            0.23 
  CANT1 MUTATED CANT1 WILD-TYPE 
          17.49           90.12 
  CANT1 MUTATED CANT1 WILD-TYPE 
         16.370          15.205 
[1] "9.4 - 17.5 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D381V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CANT1 MUTATED         0        0        0         1         2         0
  CANT1 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  CANT1 MUTATED          0
  CANT1 WILD-TYPE        3
D381V3, multiclass
           clus
vv          CANT1 MUTATED CANT1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CANT1 MUTATED     1   1     1
  CANT1 WILD-TYPE   4  16   101
D381V4, multiclass
       clus
vv      CANT1 MUTATED CANT1 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             1             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V5, binary
                 cls
clus               0  1
  CANT1 MUTATED    1  2
  CANT1 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CANT1 MUTATED      1    2
  CANT1 WILD-TYPE   34   87
   clus
vv  CANT1 MUTATED CANT1 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D381V6, binary
                 cls
clus               0  1
  CANT1 MUTATED    0  0
  CANT1 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CANT1 MUTATED      0    0
  CANT1 WILD-TYPE   57    3
D381V7, binary
                 cls
clus               0  1
  CANT1 MUTATED    1  2
  CANT1 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CANT1 MUTATED      1    2
  CANT1 WILD-TYPE   50   73
        clus
vv       CANT1 MUTATED CANT1 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D381V8, binary
                 cls
clus               0  1
  CANT1 MUTATED    2  1
  CANT1 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CANT1 MUTATED      2    1
  CANT1 WILD-TYPE   86   29
     clus
vv    CANT1 MUTATED CANT1 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CANT1 MUTATED                                     3
  CANT1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CANT1 MUTATED                                       0
  CANT1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CANT1 MUTATED                                                  0
  CANT1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CANT1 MUTATED                                     0
  CANT1 WILD-TYPE                                   1
D381V9, multiclass
                                                  clus
vv                                                 CANT1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CANT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V10, continuous
[1] "Remove cluster labels:" "CANT1 MUTATED"         
clus
  CANT1 MUTATED CANT1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
D381V11, continuous
[1] "Remove cluster labels:" "CANT1 MUTATED"         
clus
  CANT1 MUTATED CANT1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" "CANT1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CANT1 MUTATED    2  0  1  0
  CANT1 WILD-TYPE 78 35  3  2
D381V12, multiclass
    clus
vv   CANT1 MUTATED CANT1 WILD-TYPE
  R0             2              78
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CANT1 MUTATED       1                         0     2
  CANT1 WILD-TYPE     5                         5   112
D381V14, multiclass
                           clus
vv                          CANT1 MUTATED CANT1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V15, binary
                 cls
clus               0  1
  CANT1 MUTATED    0  2
  CANT1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CANT1 MUTATED      0    2
  CANT1 WILD-TYPE    5   89
                        clus
vv                       CANT1 MUTATED CANT1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(382) Variable = SMARCA2 MUTATION ANALYSIS
D382V1, survival
                   sevent
clus2                0  1
  SMARCA2 MUTATED    2  2
  SMARCA2 WILD-TYPE 61 60
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4               121 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                60 
$`SMARCA2 MUTATED`
TCGA-3A-A9IH TCGA-3E-AAAY TCGA-FB-A5VM TCGA-IB-7651 
       33.57        75.12        16.37        19.82 

$`SMARCA2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        24.43        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
            16.37              0.23 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
            75.12             90.12 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
           26.695            15.120 
[1] "16.4 - 75.1 (26.7)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.8"
D382V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMARCA2 MUTATED         0        1        1         0         2         0
  SMARCA2 WILD-TYPE       1        2       11        19        80         4
                   vv
clus                STAGE IV
  SMARCA2 MUTATED          0
  SMARCA2 WILD-TYPE        3
D382V3, multiclass
           clus
vv          SMARCA2 MUTATED SMARCA2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               2                80
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SMARCA2 MUTATED     1   1     2
  SMARCA2 WILD-TYPE   4  16   100
D382V4, multiclass
       clus
vv      SMARCA2 MUTATED SMARCA2 WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V5, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    2  2
  SMARCA2 WILD-TYPE 33 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      2    2
  SMARCA2 WILD-TYPE   33   87
   clus
vv  SMARCA2 MUTATED SMARCA2 WILD-TYPE
  0               2                33
  1               2                87
[1] 2 2
[1] FALSE
D382V6, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    2  0
  SMARCA2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      2    0
  SMARCA2 WILD-TYPE   55    3
   clus
vv  SMARCA2 MUTATED SMARCA2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D382V7, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    2  2
  SMARCA2 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      2    2
  SMARCA2 WILD-TYPE   49   73
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D382V8, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    4  0
  SMARCA2 WILD-TYPE 84 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      4    0
  SMARCA2 WILD-TYPE   84   30
     clus
vv    SMARCA2 MUTATED SMARCA2 WILD-TYPE
  NO                4                84
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMARCA2 MUTATED                                     4
  SMARCA2 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMARCA2 MUTATED                                       0
  SMARCA2 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMARCA2 MUTATED                                                  0
  SMARCA2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMARCA2 MUTATED                                     0
  SMARCA2 WILD-TYPE                                   1
D382V9, multiclass
                                                  clus
vv                                                 SMARCA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SMARCA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V10, continuous
[1] "Remove cluster labels:" "SMARCA2 MUTATED"       
clus
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-YY-A8LH 
"SMARCA2 WILD-TYPE" 
D382V11, continuous
[1] "Remove cluster labels:" "SMARCA2 MUTATED"       
clus
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SMARCA2 MUTATED    3  0  0  0
  SMARCA2 WILD-TYPE 77 35  4  2
D382V12, multiclass
    clus
vv   SMARCA2 MUTATED SMARCA2 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCA2 MUTATED       0                         0     4
  SMARCA2 WILD-TYPE     6                         5   110
D382V14, multiclass
                           clus
vv                          SMARCA2 MUTATED SMARCA2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V15, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    0  4
  SMARCA2 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      0    4
  SMARCA2 WILD-TYPE    5   87
                        clus
vv                       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(383) Variable = GIGYF2 MUTATION ANALYSIS
D383V1, survival
                  sevent
clus2               0  1
  GIGYF2 MUTATED    3  1
  GIGYF2 WILD-TYPE 60 61
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4              121 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               1               61 
$`GIGYF2 MUTATED`
TCGA-3A-A9IV TCGA-3E-AAAZ TCGA-IB-A5ST TCGA-YY-A8LH 
       36.26        71.74        20.88        66.28 

$`GIGYF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       15.06        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           20.88             0.23 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           71.74            90.12 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
           51.27            15.12 
[1] "20.9 - 71.7 (51.3)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "4.5"
D383V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GIGYF2 MUTATED         0        0        1         1         2         0
  GIGYF2 WILD-TYPE       1        3       11        18        80         4
                  vv
clus               STAGE IV
  GIGYF2 MUTATED          0
  GIGYF2 WILD-TYPE        3
D383V3, multiclass
           clus
vv          GIGYF2 MUTATED GIGYF2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GIGYF2 MUTATED    0  1     3
  GIGYF2 WILD-TYPE  5 16    99
D383V4, multiclass
       clus
vv      GIGYF2 MUTATED GIGYF2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V5, binary
                  cls
clus                0  1
  GIGYF2 MUTATED    2  2
  GIGYF2 WILD-TYPE 33 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      2    2
  GIGYF2 WILD-TYPE   33   87
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0              2               33
  1              2               87
[1] 2 2
[1] FALSE
D383V6, binary
                  cls
clus                0  1
  GIGYF2 MUTATED    1  0
  GIGYF2 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      1    0
  GIGYF2 WILD-TYPE   56    3
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D383V7, binary
                  cls
clus                0  1
  GIGYF2 MUTATED    3  1
  GIGYF2 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      3    1
  GIGYF2 WILD-TYPE   48   74
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D383V8, binary
                  cls
clus                0  1
  GIGYF2 MUTATED    2  1
  GIGYF2 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      2    1
  GIGYF2 WILD-TYPE   86   29
     clus
vv    GIGYF2 MUTATED GIGYF2 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GIGYF2 MUTATED                                     3
  GIGYF2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GIGYF2 MUTATED                                       1
  GIGYF2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GIGYF2 MUTATED                                                  0
  GIGYF2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GIGYF2 MUTATED                                     0
  GIGYF2 WILD-TYPE                                   1
D383V9, multiclass
                                                  clus
vv                                                 GIGYF2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GIGYF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V10, continuous
[1] "Remove cluster labels:" "GIGYF2 MUTATED"        
clus
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XN-A8T5 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
D383V11, continuous
[1] "Remove cluster labels:" "GIGYF2 MUTATED"        
clus
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5 
"GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" "GIGYF2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GIGYF2 MUTATED    3  0  0  0
  GIGYF2 WILD-TYPE 77 35  4  2
D383V12, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GIGYF2 MUTATED       0                         0     4
  GIGYF2 WILD-TYPE     6                         5   110
D383V14, multiclass
                           clus
vv                          GIGYF2 MUTATED GIGYF2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V15, binary
                  cls
clus                0  1
  GIGYF2 MUTATED    1  3
  GIGYF2 WILD-TYPE  4 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED      1    3
  GIGYF2 WILD-TYPE    4   88
                        clus
vv                       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(384) Variable = PPP2R5C MUTATION ANALYSIS
D384V1, survival
                   sevent
clus2                0  1
  PPP2R5C MUTATED    4  1
  PPP2R5C WILD-TYPE 59 61
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
                5               120 
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
                1                61 
$`PPP2R5C MUTATED`
TCGA-S4-A8RO TCGA-2J-AABK TCGA-IB-7651 TCGA-IB-A6UF TCGA-IB-A7M4 
       17.26        15.91        19.82        21.90        15.88 

$`PPP2R5C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
       15.85         7.20        20.88         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
            15.88              0.23 
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
            21.90             90.12 
  PPP2R5C MUTATED PPP2R5C WILD-TYPE 
            17.26             15.09 
[1] "15.9 - 21.9 (17.3)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "2.9"
D384V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPP2R5C MUTATED         0        0        0         0         5         0
  PPP2R5C WILD-TYPE       1        3       12        19        77         4
                   vv
clus                STAGE IV
  PPP2R5C MUTATED          0
  PPP2R5C WILD-TYPE        3
D384V3, multiclass
           clus
vv          PPP2R5C MUTATED PPP2R5C WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  PPP2R5C MUTATED    0  0     5
  PPP2R5C WILD-TYPE  5 17    97
D384V4, multiclass
       clus
vv      PPP2R5C MUTATED PPP2R5C WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V5, binary
                   cls
clus                 0  1
  PPP2R5C MUTATED    0  5
  PPP2R5C WILD-TYPE 35 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5C MUTATED      0    5
  PPP2R5C WILD-TYPE   35   84
   clus
vv  PPP2R5C MUTATED PPP2R5C WILD-TYPE
  0               0                35
  1               5                84
[1] 2 2
[1] FALSE
D384V6, binary
                   cls
clus                 0  1
  PPP2R5C MUTATED    3  0
  PPP2R5C WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5C MUTATED      3    0
  PPP2R5C WILD-TYPE   54    3
   clus
vv  PPP2R5C MUTATED PPP2R5C WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D384V7, binary
                   cls
clus                 0  1
  PPP2R5C MUTATED    2  3
  PPP2R5C WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5C MUTATED      2    3
  PPP2R5C WILD-TYPE   49   72
        clus
vv       PPP2R5C MUTATED PPP2R5C WILD-TYPE
  FEMALE               2                49
  MALE                 3                72
[1] 2 2
[1] FALSE
D384V8, binary
                   cls
clus                 0  1
  PPP2R5C MUTATED    3  2
  PPP2R5C WILD-TYPE 85 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5C MUTATED      3    2
  PPP2R5C WILD-TYPE   85   28
     clus
vv    PPP2R5C MUTATED PPP2R5C WILD-TYPE
  NO                3                85
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPP2R5C MUTATED                                     5
  PPP2R5C WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPP2R5C MUTATED                                       0
  PPP2R5C WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPP2R5C MUTATED                                                  0
  PPP2R5C WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPP2R5C MUTATED                                     0
  PPP2R5C WILD-TYPE                                   1
D384V9, multiclass
                                                  clus
vv                                                 PPP2R5C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PPP2R5C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V10, continuous
D384V11, continuous
                   vv
clus                R0 R1 R2 RX
  PPP2R5C MUTATED    2  3  0  0
  PPP2R5C WILD-TYPE 78 32  4  2
D384V12, multiclass
    clus
vv   PPP2R5C MUTATED PPP2R5C WILD-TYPE
  R0               2                78
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP2R5C MUTATED       0                         0     5
  PPP2R5C WILD-TYPE     6                         5   109
D384V14, multiclass
                           clus
vv                          PPP2R5C MUTATED PPP2R5C WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V15, binary
                   cls
clus                 0  1
  PPP2R5C MUTATED    0  4
  PPP2R5C WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5C MUTATED      0    4
  PPP2R5C WILD-TYPE    5   87
                        clus
vv                       PPP2R5C MUTATED PPP2R5C WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(385) Variable = COPA MUTATION ANALYSIS
D385V1, survival
                sevent
clus2             0  1
  COPA MUTATED    3  2
  COPA WILD-TYPE 60 60
  COPA MUTATED COPA WILD-TYPE 
             5            120 
  COPA MUTATED COPA WILD-TYPE 
             2             60 
$`COPA MUTATED`
TCGA-LB-A7SX TCGA-IB-7651 TCGA-IB-A6UF TCGA-LB-A8F3 TCGA-YH-A8SY 
       12.92        19.82        21.90        12.46        12.76 

$`COPA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  COPA MUTATED COPA WILD-TYPE 
         12.46           0.23 
  COPA MUTATED COPA WILD-TYPE 
         21.90          90.12 
  COPA MUTATED COPA WILD-TYPE 
         12.92          15.27 
[1] "12.5 - 21.9 (12.9)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.2"
D385V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  COPA MUTATED         0        0        0         1         3         1
  COPA WILD-TYPE       1        3       12        18        79         3
                vv
clus             STAGE IV
  COPA MUTATED          0
  COPA WILD-TYPE        3
D385V3, multiclass
           clus
vv          COPA MUTATED COPA WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  COPA MUTATED    0  0     5
  COPA WILD-TYPE  5 17    97
D385V4, multiclass
       clus
vv      COPA MUTATED COPA WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V5, binary
                cls
clus              0  1
  COPA MUTATED    1  4
  COPA WILD-TYPE 34 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  COPA MUTATED      1    4
  COPA WILD-TYPE   34   85
   clus
vv  COPA MUTATED COPA WILD-TYPE
  0            1             34
  1            4             85
[1] 2 2
[1] FALSE
D385V6, binary
                cls
clus              0  1
  COPA MUTATED    2  0
  COPA WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  COPA MUTATED      2    0
  COPA WILD-TYPE   55    3
   clus
vv  COPA MUTATED COPA WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D385V7, binary
                cls
clus              0  1
  COPA MUTATED    4  1
  COPA WILD-TYPE 47 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  COPA MUTATED      4    1
  COPA WILD-TYPE   47   74
        clus
vv       COPA MUTATED COPA WILD-TYPE
  FEMALE            4             47
  MALE              1             74
[1] 2 2
[1] FALSE
D385V8, binary
                cls
clus              0  1
  COPA MUTATED    3  2
  COPA WILD-TYPE 85 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  COPA MUTATED      3    2
  COPA WILD-TYPE   85   28
     clus
vv    COPA MUTATED COPA WILD-TYPE
  NO             3             85
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COPA MUTATED                                     4
  COPA WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COPA MUTATED                                       0
  COPA WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COPA MUTATED                                                  0
  COPA WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  COPA MUTATED                                     0
  COPA WILD-TYPE                                   1
D385V9, multiclass
                                                  clus
vv                                                 COPA MUTATED COPA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V10, continuous
D385V11, continuous
                vv
clus             R0 R1 R2 RX
  COPA MUTATED    2  2  0  0
  COPA WILD-TYPE 78 33  4  2
D385V12, multiclass
    clus
vv   COPA MUTATED COPA WILD-TYPE
  R0            2             78
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COPA MUTATED       0                         2     3
  COPA WILD-TYPE     6                         3   111
D385V14, multiclass
                           clus
vv                          COPA MUTATED COPA WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V15, binary
                cls
clus              0  1
  COPA MUTATED    0  5
  COPA WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  COPA MUTATED      0    5
  COPA WILD-TYPE    5   86
                        clus
vv                       COPA MUTATED COPA WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(386) Variable = RCOR1 MUTATION ANALYSIS
D386V1, survival
                 sevent
clus2              0  1
  RCOR1 MUTATED    1  4
  RCOR1 WILD-TYPE 62 58
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              5             120 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              4              58 
$`RCOR1 MUTATED`
TCGA-XD-AAUL TCGA-3A-A9IZ TCGA-FB-AAQ3 TCGA-IB-7651 TCGA-LB-A9Q5 
       16.37        10.13         1.02        19.82        10.29 

$`RCOR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RCOR1 MUTATED RCOR1 WILD-TYPE 
           1.02            0.23 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
          19.82           90.12 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
          10.29           15.27 
[1] "1.0 - 19.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.6"
D386V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RCOR1 MUTATED         0        0        0         1         4         0
  RCOR1 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  RCOR1 MUTATED          0
  RCOR1 WILD-TYPE        3
D386V3, multiclass
           clus
vv          RCOR1 MUTATED RCOR1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RCOR1 MUTATED    0  0     5
  RCOR1 WILD-TYPE  5 17    97
D386V4, multiclass
       clus
vv      RCOR1 MUTATED RCOR1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V5, binary
                 cls
clus               0  1
  RCOR1 MUTATED    1  4
  RCOR1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      1    4
  RCOR1 WILD-TYPE   34   85
   clus
vv  RCOR1 MUTATED RCOR1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D386V6, binary
                 cls
clus               0  1
  RCOR1 MUTATED    1  0
  RCOR1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      1    0
  RCOR1 WILD-TYPE   56    3
   clus
vv  RCOR1 MUTATED RCOR1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D386V7, binary
                 cls
clus               0  1
  RCOR1 MUTATED    3  2
  RCOR1 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      3    2
  RCOR1 WILD-TYPE   48   73
        clus
vv       RCOR1 MUTATED RCOR1 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D386V8, binary
                 cls
clus               0  1
  RCOR1 MUTATED    4  1
  RCOR1 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      4    1
  RCOR1 WILD-TYPE   84   29
     clus
vv    RCOR1 MUTATED RCOR1 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RCOR1 MUTATED                                     5
  RCOR1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RCOR1 MUTATED                                       0
  RCOR1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RCOR1 MUTATED                                                  0
  RCOR1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RCOR1 MUTATED                                     0
  RCOR1 WILD-TYPE                                   1
D386V9, multiclass
                                                  clus
vv                                                 RCOR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RCOR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V10, continuous
D386V11, continuous
                 vv
clus              R0 R1 R2 RX
  RCOR1 MUTATED    4  1  0  0
  RCOR1 WILD-TYPE 76 34  4  2
D386V12, multiclass
    clus
vv   RCOR1 MUTATED RCOR1 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RCOR1 MUTATED       0                         0     5
  RCOR1 WILD-TYPE     6                         5   109
D386V14, multiclass
                           clus
vv                          RCOR1 MUTATED RCOR1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V15, binary
                 cls
clus               0  1
  RCOR1 MUTATED    1  4
  RCOR1 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      1    4
  RCOR1 WILD-TYPE    4   87
                        clus
vv                       RCOR1 MUTATED RCOR1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(387) Variable = PTCD1 MUTATION ANALYSIS
D387V1, survival
                 sevent
clus2              0  1
  PTCD1 MUTATED    1  2
  PTCD1 WILD-TYPE 62 60
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              3             122 
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              2              60 
$`PTCD1 MUTATED`
TCGA-FB-AAPU TCGA-FB-AAQ2 TCGA-IB-A7M4 
       12.53         5.03        15.88 

$`PTCD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PTCD1 MUTATED PTCD1 WILD-TYPE 
           5.03            0.23 
  PTCD1 MUTATED PTCD1 WILD-TYPE 
          15.88           90.12 
  PTCD1 MUTATED PTCD1 WILD-TYPE 
          12.53           15.27 
[1] "5.0 - 15.9 (12.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D387V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PTCD1 MUTATED         0        0        0         1         2         0
  PTCD1 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  PTCD1 MUTATED          0
  PTCD1 WILD-TYPE        3
D387V3, multiclass
           clus
vv          PTCD1 MUTATED PTCD1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PTCD1 MUTATED    0  0     3
  PTCD1 WILD-TYPE  5 17    99
D387V4, multiclass
       clus
vv      PTCD1 MUTATED PTCD1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V5, binary
                 cls
clus               0  1
  PTCD1 MUTATED    1  2
  PTCD1 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCD1 MUTATED      1    2
  PTCD1 WILD-TYPE   34   87
   clus
vv  PTCD1 MUTATED PTCD1 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D387V6, binary
                 cls
clus               0  1
  PTCD1 MUTATED    0  0
  PTCD1 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCD1 MUTATED      0    0
  PTCD1 WILD-TYPE   57    3
D387V7, binary
                 cls
clus               0  1
  PTCD1 MUTATED    2  1
  PTCD1 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCD1 MUTATED      2    1
  PTCD1 WILD-TYPE   49   74
        clus
vv       PTCD1 MUTATED PTCD1 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D387V8, binary
                 cls
clus               0  1
  PTCD1 MUTATED    3  0
  PTCD1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCD1 MUTATED      3    0
  PTCD1 WILD-TYPE   85   30
     clus
vv    PTCD1 MUTATED PTCD1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTCD1 MUTATED                                     3
  PTCD1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTCD1 MUTATED                                       0
  PTCD1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTCD1 MUTATED                                                  0
  PTCD1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PTCD1 MUTATED                                     0
  PTCD1 WILD-TYPE                                   1
D387V9, multiclass
                                                  clus
vv                                                 PTCD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PTCD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V10, continuous
[1] "Remove cluster labels:" "PTCD1 MUTATED"         
clus
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
D387V11, continuous
[1] "Remove cluster labels:" "PTCD1 MUTATED"         
clus
  PTCD1 MUTATED PTCD1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" "PTCD1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PTCD1 MUTATED    1  2  0  0
  PTCD1 WILD-TYPE 79 33  4  2
D387V12, multiclass
    clus
vv   PTCD1 MUTATED PTCD1 WILD-TYPE
  R0             1              79
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTCD1 MUTATED       1                         0     2
  PTCD1 WILD-TYPE     5                         5   112
D387V14, multiclass
                           clus
vv                          PTCD1 MUTATED PTCD1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V15, binary
                 cls
clus               0  1
  PTCD1 MUTATED    0  3
  PTCD1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCD1 MUTATED      0    3
  PTCD1 WILD-TYPE    5   88
                        clus
vv                       PTCD1 MUTATED PTCD1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(388) Variable = SOS1 MUTATION ANALYSIS
D388V1, survival
                sevent
clus2             0  1
  SOS1 MUTATED    1  4
  SOS1 WILD-TYPE 62 58
  SOS1 MUTATED SOS1 WILD-TYPE 
             5            120 
  SOS1 MUTATED SOS1 WILD-TYPE 
             4             58 
$`SOS1 MUTATED`
TCGA-3A-A9IB TCGA-FB-A5VM TCGA-FZ-5920 TCGA-IB-7651 TCGA-RB-AA9M 
        7.36        16.37         2.01        19.82         9.40 

$`SOS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SOS1 MUTATED SOS1 WILD-TYPE 
          2.01           0.23 
  SOS1 MUTATED SOS1 WILD-TYPE 
         19.82          90.12 
  SOS1 MUTATED SOS1 WILD-TYPE 
          9.40          15.27 
[1] "2.0 - 19.8 (9.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.8"
D388V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SOS1 MUTATED         0        0        1         0         4         0
  SOS1 WILD-TYPE       1        3       11        19        78         4
                vv
clus             STAGE IV
  SOS1 MUTATED          0
  SOS1 WILD-TYPE        3
D388V3, multiclass
           clus
vv          SOS1 MUTATED SOS1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  SOS1 MUTATED    1  1     3
  SOS1 WILD-TYPE  4 16    99
D388V4, multiclass
       clus
vv      SOS1 MUTATED SOS1 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V5, binary
                cls
clus              0  1
  SOS1 MUTATED    1  4
  SOS1 WILD-TYPE 34 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      1    4
  SOS1 WILD-TYPE   34   85
   clus
vv  SOS1 MUTATED SOS1 WILD-TYPE
  0            1             34
  1            4             85
[1] 2 2
[1] FALSE
D388V6, binary
                cls
clus              0  1
  SOS1 MUTATED    3  0
  SOS1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      3    0
  SOS1 WILD-TYPE   54    3
   clus
vv  SOS1 MUTATED SOS1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D388V7, binary
                cls
clus              0  1
  SOS1 MUTATED    2  3
  SOS1 WILD-TYPE 49 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      2    3
  SOS1 WILD-TYPE   49   72
        clus
vv       SOS1 MUTATED SOS1 WILD-TYPE
  FEMALE            2             49
  MALE              3             72
[1] 2 2
[1] FALSE
D388V8, binary
                cls
clus              0  1
  SOS1 MUTATED    4  1
  SOS1 WILD-TYPE 84 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      4    1
  SOS1 WILD-TYPE   84   29
     clus
vv    SOS1 MUTATED SOS1 WILD-TYPE
  NO             4             84
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SOS1 MUTATED                                     5
  SOS1 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SOS1 MUTATED                                       0
  SOS1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SOS1 MUTATED                                                  0
  SOS1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  SOS1 MUTATED                                     0
  SOS1 WILD-TYPE                                   1
D388V9, multiclass
                                                  clus
vv                                                 SOS1 MUTATED SOS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V10, continuous
D388V11, continuous
                vv
clus             R0 R1 R2 RX
  SOS1 MUTATED    5  0  0  0
  SOS1 WILD-TYPE 75 35  4  2
D388V12, multiclass
    clus
vv   SOS1 MUTATED SOS1 WILD-TYPE
  R0            5             75
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SOS1 MUTATED       0                         1     4
  SOS1 WILD-TYPE     6                         4   110
D388V14, multiclass
                           clus
vv                          SOS1 MUTATED SOS1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V15, binary
                cls
clus              0  1
  SOS1 MUTATED    0  5
  SOS1 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOS1 MUTATED      0    5
  SOS1 WILD-TYPE    5   86
                        clus
vv                       SOS1 MUTATED SOS1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(389) Variable = IPO4 MUTATION ANALYSIS
D389V1, survival
                sevent
clus2             0  1
  IPO4 MUTATED    0  3
  IPO4 WILD-TYPE 63 59
  IPO4 MUTATED IPO4 WILD-TYPE 
             3            122 
  IPO4 MUTATED IPO4 WILD-TYPE 
             3             59 
$`IPO4 MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9I9 TCGA-IB-7651 
       12.95        20.84        19.82 

$`IPO4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  IPO4 MUTATED IPO4 WILD-TYPE 
         12.95           0.23 
  IPO4 MUTATED IPO4 WILD-TYPE 
         20.84          90.12 
  IPO4 MUTATED IPO4 WILD-TYPE 
        19.820         15.205 
[1] "12.9 - 20.8 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.8"
D389V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IPO4 MUTATED         0        0        0         1         1         1
  IPO4 WILD-TYPE       1        3       12        18        81         3
                vv
clus             STAGE IV
  IPO4 MUTATED          0
  IPO4 WILD-TYPE        3
D389V3, multiclass
           clus
vv          IPO4 MUTATED IPO4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            1             81
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  IPO4 MUTATED    0  0     3
  IPO4 WILD-TYPE  5 17    99
D389V4, multiclass
       clus
vv      IPO4 MUTATED IPO4 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V5, binary
                cls
clus              0  1
  IPO4 MUTATED    2  1
  IPO4 WILD-TYPE 33 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO4 MUTATED      2    1
  IPO4 WILD-TYPE   33   88
   clus
vv  IPO4 MUTATED IPO4 WILD-TYPE
  0            2             33
  1            1             88
[1] 2 2
[1] FALSE
D389V6, binary
                cls
clus              0  1
  IPO4 MUTATED    1  0
  IPO4 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO4 MUTATED      1    0
  IPO4 WILD-TYPE   56    3
   clus
vv  IPO4 MUTATED IPO4 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D389V7, binary
                cls
clus              0  1
  IPO4 MUTATED    2  1
  IPO4 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO4 MUTATED      2    1
  IPO4 WILD-TYPE   49   74
        clus
vv       IPO4 MUTATED IPO4 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D389V8, binary
                cls
clus              0  1
  IPO4 MUTATED    2  1
  IPO4 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO4 MUTATED      2    1
  IPO4 WILD-TYPE   86   29
     clus
vv    IPO4 MUTATED IPO4 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IPO4 MUTATED                                     3
  IPO4 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IPO4 MUTATED                                       0
  IPO4 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IPO4 MUTATED                                                  0
  IPO4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  IPO4 MUTATED                                     0
  IPO4 WILD-TYPE                                   1
D389V9, multiclass
                                                  clus
vv                                                 IPO4 MUTATED IPO4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V10, continuous
[1] "Remove cluster labels:" "IPO4 MUTATED"          
clus
  IPO4 MUTATED IPO4 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9IB     TCGA-3A-A9IX 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-YY-A8LH 
"IPO4 WILD-TYPE" 
D389V11, continuous
[1] "Remove cluster labels:" "IPO4 MUTATED"          
clus
  IPO4 MUTATED IPO4 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" "IPO4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  IPO4 MUTATED    2  1  0  0
  IPO4 WILD-TYPE 78 34  4  2
D389V12, multiclass
    clus
vv   IPO4 MUTATED IPO4 WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPO4 MUTATED       0                         0     3
  IPO4 WILD-TYPE     6                         5   111
D389V14, multiclass
                           clus
vv                          IPO4 MUTATED IPO4 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V15, binary
                cls
clus              0  1
  IPO4 MUTATED    0  2
  IPO4 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPO4 MUTATED      0    2
  IPO4 WILD-TYPE    5   89
                        clus
vv                       IPO4 MUTATED IPO4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(390) Variable = KCNA4 MUTATION ANALYSIS
D390V1, survival
                 sevent
clus2              0  1
  KCNA4 MUTATED    6  4
  KCNA4 WILD-TYPE 57 58
  KCNA4 MUTATED KCNA4 WILD-TYPE 
             10             115 
  KCNA4 MUTATED KCNA4 WILD-TYPE 
              4              58 
$`KCNA4 MUTATED`
TCGA-2J-AABT TCGA-3A-A9IJ TCGA-2J-AAB8 TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       10.49        60.95         2.63        15.06        34.09        10.13 
TCGA-IB-7651 TCGA-OE-A75W TCGA-XD-AAUG TCGA-XN-A8T3 
       19.82         8.78        13.81        31.27 

$`KCNA4 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        58.98        90.12         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-3E-AAAY 
       63.85        50.70        32.81        36.26        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KCNA4 MUTATED KCNA4 WILD-TYPE 
           2.63            0.23 
  KCNA4 MUTATED KCNA4 WILD-TYPE 
          60.95           90.12 
  KCNA4 MUTATED KCNA4 WILD-TYPE 
         14.435          15.320 
[1] "2.6 - 61.0 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D390V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KCNA4 MUTATED         0        1        2         1         5         0
  KCNA4 WILD-TYPE       1        2       10        18        77         4
                 vv
clus              STAGE IV
  KCNA4 MUTATED          1
  KCNA4 WILD-TYPE        2
D390V3, multiclass
           clus
vv          KCNA4 MUTATED KCNA4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KCNA4 MUTATED    1  2     7
  KCNA4 WILD-TYPE  4 15    95
D390V4, multiclass
       clus
vv      KCNA4 MUTATED KCNA4 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V5, binary
                 cls
clus               0  1
  KCNA4 MUTATED    4  6
  KCNA4 WILD-TYPE 31 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA4 MUTATED      4    6
  KCNA4 WILD-TYPE   31   83
   clus
vv  KCNA4 MUTATED KCNA4 WILD-TYPE
  0             4              31
  1             6              83
[1] 2 2
[1] FALSE
D390V6, binary
                 cls
clus               0  1
  KCNA4 MUTATED    5  1
  KCNA4 WILD-TYPE 52  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA4 MUTATED      5    1
  KCNA4 WILD-TYPE   52    2
   clus
vv  KCNA4 MUTATED KCNA4 WILD-TYPE
  0             5              52
  1             1               2
[1] 2 2
[1] FALSE
D390V7, binary
                 cls
clus               0  1
  KCNA4 MUTATED    3  7
  KCNA4 WILD-TYPE 48 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA4 MUTATED      3    7
  KCNA4 WILD-TYPE   48   68
        clus
vv       KCNA4 MUTATED KCNA4 WILD-TYPE
  FEMALE             3              48
  MALE               7              68
[1] 2 2
[1] FALSE
D390V8, binary
                 cls
clus               0  1
  KCNA4 MUTATED    5  3
  KCNA4 WILD-TYPE 83 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA4 MUTATED      5    3
  KCNA4 WILD-TYPE   83   27
     clus
vv    KCNA4 MUTATED KCNA4 WILD-TYPE
  NO              5              83
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNA4 MUTATED                                     9
  KCNA4 WILD-TYPE                                  96
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNA4 MUTATED                                       1
  KCNA4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNA4 MUTATED                                                  0
  KCNA4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KCNA4 MUTATED                                     0
  KCNA4 WILD-TYPE                                   1
D390V9, multiclass
                                                  clus
vv                                                 KCNA4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KCNA4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           96
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V10, continuous
D390V11, continuous
                 vv
clus              R0 R1 R2 RX
  KCNA4 MUTATED    7  3  0  0
  KCNA4 WILD-TYPE 73 32  4  2
D390V12, multiclass
    clus
vv   KCNA4 MUTATED KCNA4 WILD-TYPE
  R0             7              73
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNA4 MUTATED       0                         0    10
  KCNA4 WILD-TYPE     6                         5   104
D390V14, multiclass
                           clus
vv                          KCNA4 MUTATED KCNA4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V15, binary
                 cls
clus               0  1
  KCNA4 MUTATED    2  6
  KCNA4 WILD-TYPE  3 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA4 MUTATED      2    6
  KCNA4 WILD-TYPE    3   85
                        clus
vv                       KCNA4 MUTATED KCNA4 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(391) Variable = ZNF644 MUTATION ANALYSIS
D391V1, survival
                  sevent
clus2               0  1
  ZNF644 MUTATED    2  3
  ZNF644 WILD-TYPE 61 59
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               5              120 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               3               59 
$`ZNF644 MUTATED`
TCGA-2L-AAQA TCGA-HV-A7OL TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-AAUU 
        4.70         8.28        17.00        19.82         8.05 

$`ZNF644 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ZNF644 MUTATED ZNF644 WILD-TYPE 
            4.70             0.23 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
           19.82            90.12 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
            8.28            15.27 
[1] "4.7 - 19.8 (8.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D391V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF644 MUTATED         0        0        0         1         4         0
  ZNF644 WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  ZNF644 MUTATED          0
  ZNF644 WILD-TYPE        3
D391V3, multiclass
           clus
vv          ZNF644 MUTATED ZNF644 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF644 MUTATED    0  0     5
  ZNF644 WILD-TYPE  5 17    97
D391V4, multiclass
       clus
vv      ZNF644 MUTATED ZNF644 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V5, binary
                  cls
clus                0  1
  ZNF644 MUTATED    1  4
  ZNF644 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      1    4
  ZNF644 WILD-TYPE   34   85
   clus
vv  ZNF644 MUTATED ZNF644 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D391V6, binary
                  cls
clus                0  1
  ZNF644 MUTATED    2  0
  ZNF644 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      2    0
  ZNF644 WILD-TYPE   55    3
   clus
vv  ZNF644 MUTATED ZNF644 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D391V7, binary
                  cls
clus                0  1
  ZNF644 MUTATED    2  3
  ZNF644 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      2    3
  ZNF644 WILD-TYPE   49   72
        clus
vv       ZNF644 MUTATED ZNF644 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D391V8, binary
                  cls
clus                0  1
  ZNF644 MUTATED    4  1
  ZNF644 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      4    1
  ZNF644 WILD-TYPE   84   29
     clus
vv    ZNF644 MUTATED ZNF644 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF644 MUTATED                                     5
  ZNF644 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF644 MUTATED                                       0
  ZNF644 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF644 MUTATED                                                  0
  ZNF644 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF644 MUTATED                                     0
  ZNF644 WILD-TYPE                                   1
D391V9, multiclass
                                                  clus
vv                                                 ZNF644 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF644 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V10, continuous
D391V11, continuous
[1] "Remove cluster labels:" "ZNF644 MUTATED"        
clus
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" "ZNF644 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF644 MUTATED    3  1  1  0
  ZNF644 WILD-TYPE 77 34  3  2
D391V12, multiclass
    clus
vv   ZNF644 MUTATED ZNF644 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF644 MUTATED       1                         0     4
  ZNF644 WILD-TYPE     5                         5   110
D391V14, multiclass
                           clus
vv                          ZNF644 MUTATED ZNF644 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V15, binary
                  cls
clus                0  1
  ZNF644 MUTATED    1  2
  ZNF644 WILD-TYPE  4 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      1    2
  ZNF644 WILD-TYPE    4   89
                        clus
vv                       ZNF644 MUTATED ZNF644 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(392) Variable = TEP1 MUTATION ANALYSIS
D392V1, survival
                sevent
clus2             0  1
  TEP1 MUTATED    3  6
  TEP1 WILD-TYPE 60 56
  TEP1 MUTATED TEP1 WILD-TYPE 
             9            116 
  TEP1 MUTATED TEP1 WILD-TYPE 
             6             56 
$`TEP1 MUTATED`
TCGA-IB-A5SS TCGA-2L-AAQL TCGA-3A-A9IR TCGA-3A-A9IX TCGA-HZ-A77O TCGA-IB-7651 
       15.12         9.60        50.70        34.09         5.26        19.82 
TCGA-IB-A6UF TCGA-OE-A75W TCGA-US-A77J 
       21.90         8.78        18.67 

$`TEP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ 
       33.57        63.85        32.81        15.06        36.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
        9.40         0.30        39.98        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TEP1 MUTATED TEP1 WILD-TYPE 
          5.26           0.23 
  TEP1 MUTATED TEP1 WILD-TYPE 
         50.70          90.12 
  TEP1 MUTATED TEP1 WILD-TYPE 
        18.670         15.205 
[1] "5.3 - 50.7 (18.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D392V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TEP1 MUTATED         0        1        1         1         6         0
  TEP1 WILD-TYPE       1        2       11        18        76         4
                vv
clus             STAGE IV
  TEP1 MUTATED          0
  TEP1 WILD-TYPE        3
D392V3, multiclass
           clus
vv          TEP1 MUTATED TEP1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TEP1 MUTATED    1  2     6
  TEP1 WILD-TYPE  4 15    96
D392V4, multiclass
       clus
vv      TEP1 MUTATED TEP1 WILD-TYPE
  T1               1              4
  T2               2             15
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V5, binary
                cls
clus              0  1
  TEP1 MUTATED    3  6
  TEP1 WILD-TYPE 32 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEP1 MUTATED      3    6
  TEP1 WILD-TYPE   32   83
   clus
vv  TEP1 MUTATED TEP1 WILD-TYPE
  0            3             32
  1            6             83
[1] 2 2
[1] FALSE
D392V6, binary
                cls
clus              0  1
  TEP1 MUTATED    4  0
  TEP1 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEP1 MUTATED      4    0
  TEP1 WILD-TYPE   53    3
   clus
vv  TEP1 MUTATED TEP1 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D392V7, binary
                cls
clus              0  1
  TEP1 MUTATED    5  4
  TEP1 WILD-TYPE 46 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEP1 MUTATED      5    4
  TEP1 WILD-TYPE   46   71
        clus
vv       TEP1 MUTATED TEP1 WILD-TYPE
  FEMALE            5             46
  MALE              4             71
[1] 2 2
[1] FALSE
D392V8, binary
                cls
clus              0  1
  TEP1 MUTATED    6  2
  TEP1 WILD-TYPE 82 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEP1 MUTATED      6    2
  TEP1 WILD-TYPE   82   28
     clus
vv    TEP1 MUTATED TEP1 WILD-TYPE
  NO             6             82
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEP1 MUTATED                                     8
  TEP1 WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEP1 MUTATED                                       1
  TEP1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEP1 MUTATED                                                  0
  TEP1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TEP1 MUTATED                                     0
  TEP1 WILD-TYPE                                   1
D392V9, multiclass
                                                  clus
vv                                                 TEP1 MUTATED TEP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V10, continuous
D392V11, continuous
                vv
clus             R0 R1 R2 RX
  TEP1 MUTATED    7  1  0  1
  TEP1 WILD-TYPE 73 34  4  1
D392V12, multiclass
    clus
vv   TEP1 MUTATED TEP1 WILD-TYPE
  R0            7             73
  R1            1             34
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEP1 MUTATED       0                         0     9
  TEP1 WILD-TYPE     6                         5   105
D392V14, multiclass
                           clus
vv                          TEP1 MUTATED TEP1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                9            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V15, binary
                cls
clus              0  1
  TEP1 MUTATED    0  8
  TEP1 WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEP1 MUTATED      0    8
  TEP1 WILD-TYPE    5   83
                        clus
vv                       TEP1 MUTATED TEP1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(393) Variable = TMEM184A MUTATION ANALYSIS
D393V1, survival
                    sevent
clus2                 0  1
  TMEM184A MUTATED    1  3
  TMEM184A WILD-TYPE 62 59
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 4                121 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 3                 59 
$`TMEM184A MUTATED`
TCGA-HV-A7OL TCGA-HZ-A77O TCGA-IB-7651 TCGA-US-A779 
        8.28         5.26        19.82        16.80 

$`TMEM184A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TMEM184A MUTATED TMEM184A WILD-TYPE 
              5.26               0.23 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
             19.82              90.12 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
             12.54              15.22 
[1] "5.3 - 19.8 (12.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.2"
D393V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM184A MUTATED         0        0        0         1         3         0
  TMEM184A WILD-TYPE       1        3       12        18        79         4
                    vv
clus                 STAGE IV
  TMEM184A MUTATED          0
  TMEM184A WILD-TYPE        3
D393V3, multiclass
           clus
vv          TMEM184A MUTATED TMEM184A WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  TMEM184A MUTATED    0  1     3
  TMEM184A WILD-TYPE  5 16    99
D393V4, multiclass
       clus
vv      TMEM184A MUTATED TMEM184A WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V5, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    1  3
  TMEM184A WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      1    3
  TMEM184A WILD-TYPE   34   86
   clus
vv  TMEM184A MUTATED TMEM184A WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D393V6, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    1  0
  TMEM184A WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      1    0
  TMEM184A WILD-TYPE   56    3
   clus
vv  TMEM184A MUTATED TMEM184A WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D393V7, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    3  1
  TMEM184A WILD-TYPE 48 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      3    1
  TMEM184A WILD-TYPE   48   74
        clus
vv       TMEM184A MUTATED TMEM184A WILD-TYPE
  FEMALE                3                 48
  MALE                  1                 74
[1] 2 2
[1] FALSE
D393V8, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    3  0
  TMEM184A WILD-TYPE 85 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      3    0
  TMEM184A WILD-TYPE   85   30
     clus
vv    TMEM184A MUTATED TMEM184A WILD-TYPE
  NO                 3                 85
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM184A MUTATED                                     4
  TMEM184A WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM184A MUTATED                                       0
  TMEM184A WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM184A MUTATED                                                  0
  TMEM184A WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM184A MUTATED                                     0
  TMEM184A WILD-TYPE                                   1
D393V9, multiclass
                                                  clus
vv                                                 TMEM184A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 TMEM184A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V10, continuous
[1] "Remove cluster labels:" "TMEM184A MUTATED"      
clus
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
D393V11, continuous
[1] "Remove cluster labels:" "TMEM184A MUTATED"      
clus
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  TMEM184A MUTATED    3  0  1  0
  TMEM184A WILD-TYPE 77 35  3  2
D393V12, multiclass
    clus
vv   TMEM184A MUTATED TMEM184A WILD-TYPE
  R0                3                 77
  R1                0                 35
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM184A MUTATED       1                         0     3
  TMEM184A WILD-TYPE     5                         5   111
D393V14, multiclass
                           clus
vv                          TMEM184A MUTATED TMEM184A WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V15, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    0  3
  TMEM184A WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      0    3
  TMEM184A WILD-TYPE    5   88
                        clus
vv                       TMEM184A MUTATED TMEM184A WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(394) Variable = NBPF9 MUTATION ANALYSIS
D394V1, survival
                 sevent
clus2              0  1
  NBPF9 MUTATED    3  5
  NBPF9 WILD-TYPE 60 57
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              8             117 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              5              57 
$`NBPF9 MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQI TCGA-FB-AAPP TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-AAUO 
       12.92         3.39        15.95        30.25        19.82         7.86 
TCGA-RL-AAAS TCGA-XN-A8T5 
        0.30        23.67 

$`NBPF9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        12.33        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         9.40        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D 
       18.67        13.81        12.99        12.03        31.27        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NBPF9 MUTATED NBPF9 WILD-TYPE 
           0.30            0.23 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
          30.25           90.12 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
         14.435          15.220 
[1] "0.3 - 30.2 (14.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D394V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NBPF9 MUTATED         0        0        2         0         6         0
  NBPF9 WILD-TYPE       1        3       10        19        76         4
                 vv
clus              STAGE IV
  NBPF9 MUTATED          0
  NBPF9 WILD-TYPE        3
D394V3, multiclass
           clus
vv          NBPF9 MUTATED NBPF9 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NBPF9 MUTATED    0  2     6
  NBPF9 WILD-TYPE  5 15    96
D394V4, multiclass
       clus
vv      NBPF9 MUTATED NBPF9 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V5, binary
                 cls
clus               0  1
  NBPF9 MUTATED    2  6
  NBPF9 WILD-TYPE 33 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      2    6
  NBPF9 WILD-TYPE   33   83
   clus
vv  NBPF9 MUTATED NBPF9 WILD-TYPE
  0             2              33
  1             6              83
[1] 2 2
[1] FALSE
D394V6, binary
                 cls
clus               0  1
  NBPF9 MUTATED    4  0
  NBPF9 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      4    0
  NBPF9 WILD-TYPE   53    3
   clus
vv  NBPF9 MUTATED NBPF9 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D394V7, binary
                 cls
clus               0  1
  NBPF9 MUTATED    5  3
  NBPF9 WILD-TYPE 46 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      5    3
  NBPF9 WILD-TYPE   46   72
        clus
vv       NBPF9 MUTATED NBPF9 WILD-TYPE
  FEMALE             5              46
  MALE               3              72
[1] 2 2
[1] FALSE
D394V8, binary
                 cls
clus               0  1
  NBPF9 MUTATED    6  2
  NBPF9 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      6    2
  NBPF9 WILD-TYPE   82   28
     clus
vv    NBPF9 MUTATED NBPF9 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF9 MUTATED                                     7
  NBPF9 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF9 MUTATED                                       1
  NBPF9 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF9 MUTATED                                                  0
  NBPF9 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NBPF9 MUTATED                                     0
  NBPF9 WILD-TYPE                                   1
D394V9, multiclass
                                                  clus
vv                                                 NBPF9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NBPF9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V10, continuous
D394V11, continuous
                 vv
clus              R0 R1 R2 RX
  NBPF9 MUTATED    3  4  1  0
  NBPF9 WILD-TYPE 77 31  3  2
D394V12, multiclass
    clus
vv   NBPF9 MUTATED NBPF9 WILD-TYPE
  R0             3              77
  R1             4              31
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF9 MUTATED       1                         1     6
  NBPF9 WILD-TYPE     5                         4   108
D394V14, multiclass
                           clus
vv                          NBPF9 MUTATED NBPF9 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V15, binary
                 cls
clus               0  1
  NBPF9 MUTATED    1  5
  NBPF9 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      1    5
  NBPF9 WILD-TYPE    4   86
                        clus
vv                       NBPF9 MUTATED NBPF9 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(395) Variable = KIAA1804 MUTATION ANALYSIS
D395V1, survival
                    sevent
clus2                 0  1
  KIAA1804 MUTATED    2  5
  KIAA1804 WILD-TYPE 61 57
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 7                118 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 5                 57 
$`KIAA1804 MUTATED`
TCGA-FB-AAQ6 TCGA-2J-AAB8 TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-FB-AAPQ TCGA-HV-A7OP 
        8.02         2.63         3.39        12.95        37.15        32.15 
TCGA-IB-7651 
       19.82 

$`KIAA1804 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQL TCGA-2L-AAQM 
        9.11        21.44         4.70        22.49         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       16.37        12.33        15.95         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              2.63               0.23 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             37.15              90.12 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             12.95              15.27 
[1] "2.6 - 37.1 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D395V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA1804 MUTATED         0        1        0         0         5         1
  KIAA1804 WILD-TYPE       1        2       12        19        77         3
                    vv
clus                 STAGE IV
  KIAA1804 MUTATED          0
  KIAA1804 WILD-TYPE        3
D395V3, multiclass
           clus
vv          KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  2
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA1804 MUTATED    1  0     6
  KIAA1804 WILD-TYPE  4 17    96
D395V4, multiclass
       clus
vv      KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                   1                  4
  T2                   0                 17
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V5, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    2  5
  KIAA1804 WILD-TYPE 33 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      2    5
  KIAA1804 WILD-TYPE   33   84
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0                2                 33
  1                5                 84
[1] 2 2
[1] FALSE
D395V6, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    3  0
  KIAA1804 WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      3    0
  KIAA1804 WILD-TYPE   54    3
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D395V7, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    2  5
  KIAA1804 WILD-TYPE 49 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      2    5
  KIAA1804 WILD-TYPE   49   70
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE                2                 49
  MALE                  5                 70
[1] 2 2
[1] FALSE
D395V8, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    5  1
  KIAA1804 WILD-TYPE 83 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      5    1
  KIAA1804 WILD-TYPE   83   29
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                 5                 83
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA1804 MUTATED                                     6
  KIAA1804 WILD-TYPE                                  99
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA1804 MUTATED                                       1
  KIAA1804 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA1804 MUTATED                                                  0
  KIAA1804 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA1804 MUTATED                                     0
  KIAA1804 WILD-TYPE                                   1
D395V9, multiclass
                                                  clus
vv                                                 KIAA1804 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA1804 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V10, continuous
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPS 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-YY-A8LH 
"KIAA1804 WILD-TYPE" 
D395V11, continuous
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-YY-A8LH 
"KIAA1804 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  KIAA1804 MUTATED    4  3  0  0
  KIAA1804 WILD-TYPE 76 32  4  2
D395V12, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0                4                 76
  R1                3                 32
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1804 MUTATED       1                         0     6
  KIAA1804 WILD-TYPE     5                         5   108
D395V14, multiclass
                           clus
vv                          KIAA1804 MUTATED KIAA1804 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    6                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V15, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    0  3
  KIAA1804 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      0    3
  KIAA1804 WILD-TYPE    5   88
                        clus
vv                       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(396) Variable = MAML3 MUTATION ANALYSIS
D396V1, survival
                 sevent
clus2              0  1
  MAML3 MUTATED    3  4
  MAML3 WILD-TYPE 60 58
  MAML3 MUTATED MAML3 WILD-TYPE 
              7             118 
  MAML3 MUTATED MAML3 WILD-TYPE 
              4              58 
$`MAML3 MUTATED`
TCGA-HZ-A77Q TCGA-F2-7273 TCGA-FB-A78T TCGA-IB-7651 TCGA-IB-A5SO TCGA-RL-AAAS 
        1.08        19.46        12.33        19.82        12.00         0.30 
TCGA-XN-A8T5 
       23.67 

$`MAML3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        15.19        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         9.40        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  MAML3 MUTATED MAML3 WILD-TYPE 
           0.30            0.23 
  MAML3 MUTATED MAML3 WILD-TYPE 
          23.67           90.12 
  MAML3 MUTATED MAML3 WILD-TYPE 
          12.33           15.27 
[1] "0.3 - 23.7 (12.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D396V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAML3 MUTATED         0        0        2         0         5         0
  MAML3 WILD-TYPE       1        3       10        19        77         4
                 vv
clus              STAGE IV
  MAML3 MUTATED          0
  MAML3 WILD-TYPE        3
D396V3, multiclass
           clus
vv          MAML3 MUTATED MAML3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MAML3 MUTATED    0  2     5
  MAML3 WILD-TYPE  5 15    97
D396V4, multiclass
       clus
vv      MAML3 MUTATED MAML3 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V5, binary
                 cls
clus               0  1
  MAML3 MUTATED    2  5
  MAML3 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAML3 MUTATED      2    5
  MAML3 WILD-TYPE   33   84
   clus
vv  MAML3 MUTATED MAML3 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D396V6, binary
                 cls
clus               0  1
  MAML3 MUTATED    6  0
  MAML3 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAML3 MUTATED      6    0
  MAML3 WILD-TYPE   51    3
   clus
vv  MAML3 MUTATED MAML3 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D396V7, binary
                 cls
clus               0  1
  MAML3 MUTATED    5  2
  MAML3 WILD-TYPE 46 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAML3 MUTATED      5    2
  MAML3 WILD-TYPE   46   73
        clus
vv       MAML3 MUTATED MAML3 WILD-TYPE
  FEMALE             5              46
  MALE               2              73
[1] 2 2
[1] FALSE
D396V8, binary
                 cls
clus               0  1
  MAML3 MUTATED    4  2
  MAML3 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAML3 MUTATED      4    2
  MAML3 WILD-TYPE   84   28
     clus
vv    MAML3 MUTATED MAML3 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAML3 MUTATED                                     5
  MAML3 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAML3 MUTATED                                       2
  MAML3 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAML3 MUTATED                                                  0
  MAML3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAML3 MUTATED                                     0
  MAML3 WILD-TYPE                                   1
D396V9, multiclass
                                                  clus
vv                                                 MAML3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MAML3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V10, continuous
D396V11, continuous
                 vv
clus              R0 R1 R2 RX
  MAML3 MUTATED    5  2  0  0
  MAML3 WILD-TYPE 75 33  4  2
D396V12, multiclass
    clus
vv   MAML3 MUTATED MAML3 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAML3 MUTATED       0                         1     6
  MAML3 WILD-TYPE     6                         4   108
D396V14, multiclass
                           clus
vv                          MAML3 MUTATED MAML3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V15, binary
                 cls
clus               0  1
  MAML3 MUTATED    1  5
  MAML3 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAML3 MUTATED      1    5
  MAML3 WILD-TYPE    4   86
                        clus
vv                       MAML3 MUTATED MAML3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(397) Variable = NBPF3 MUTATION ANALYSIS
D397V1, survival
                 sevent
clus2              0  1
  NBPF3 MUTATED    4  8
  NBPF3 WILD-TYPE 59 54
  NBPF3 MUTATED NBPF3 WILD-TYPE 
             12             113 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              8              54 
$`NBPF3 MUTATED`
TCGA-FB-AAQ6 TCGA-2J-AABA TCGA-2J-AABH TCGA-3A-A9J0 TCGA-FB-AAPQ TCGA-FB-AAPU 
        8.02        19.96        42.31        24.43        37.15        12.53 
TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUO TCGA-Z5-AAPL 
       15.55        19.82         1.35        15.88         7.86        15.35 

$`NBPF3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.22        22.72        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ1 
       16.37        12.33        15.95         7.50        23.54         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        11.51        12.76        66.28 

  NBPF3 MUTATED NBPF3 WILD-TYPE 
           1.35            0.23 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
          42.31           90.12 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
         15.715          15.120 
[1] "1.4 - 42.3 (15.7)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.3"
D397V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NBPF3 MUTATED         0        1        0         4         7         0
  NBPF3 WILD-TYPE       1        2       12        15        75         4
                 vv
clus              STAGE IV
  NBPF3 MUTATED          0
  NBPF3 WILD-TYPE        3
D397V3, multiclass
           clus
vv          NBPF3 MUTATED NBPF3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             4              15
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NBPF3 MUTATED    1  0    11
  NBPF3 WILD-TYPE  4 17    91
D397V4, multiclass
       clus
vv      NBPF3 MUTATED NBPF3 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4            11              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V5, binary
                 cls
clus               0  1
  NBPF3 MUTATED    5  7
  NBPF3 WILD-TYPE 30 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      5    7
  NBPF3 WILD-TYPE   30   82
   clus
vv  NBPF3 MUTATED NBPF3 WILD-TYPE
  0             5              30
  1             7              82
[1] 2 2
[1] FALSE
D397V6, binary
                 cls
clus               0  1
  NBPF3 MUTATED    6  0
  NBPF3 WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      6    0
  NBPF3 WILD-TYPE   51    3
   clus
vv  NBPF3 MUTATED NBPF3 WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D397V7, binary
                 cls
clus               0  1
  NBPF3 MUTATED    4  8
  NBPF3 WILD-TYPE 47 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      4    8
  NBPF3 WILD-TYPE   47   67
        clus
vv       NBPF3 MUTATED NBPF3 WILD-TYPE
  FEMALE             4              47
  MALE               8              67
[1] 2 2
[1] FALSE
D397V8, binary
                 cls
clus               0  1
  NBPF3 MUTATED   12  0
  NBPF3 WILD-TYPE 76 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED     12    0
  NBPF3 WILD-TYPE   76   30
     clus
vv    NBPF3 MUTATED NBPF3 WILD-TYPE
  NO             12              76
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF3 MUTATED                                    11
  NBPF3 WILD-TYPE                                  94
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF3 MUTATED                                       1
  NBPF3 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF3 MUTATED                                                  0
  NBPF3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NBPF3 MUTATED                                     0
  NBPF3 WILD-TYPE                                   1
D397V9, multiclass
                                                  clus
vv                                                 NBPF3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 NBPF3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V10, continuous
D397V11, continuous
                 vv
clus              R0 R1 R2 RX
  NBPF3 MUTATED    8  4  0  0
  NBPF3 WILD-TYPE 72 31  4  2
D397V12, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  R0             8              72
  R1             4              31
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF3 MUTATED       1                         0    11
  NBPF3 WILD-TYPE     5                         5   103
D397V14, multiclass
                           clus
vv                          NBPF3 MUTATED NBPF3 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V15, binary
                 cls
clus               0  1
  NBPF3 MUTATED    0 10
  NBPF3 WILD-TYPE  5 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      0   10
  NBPF3 WILD-TYPE    5   81
                        clus
vv                       NBPF3 MUTATED NBPF3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            10              81
[1] 2 2
[1] FALSE

Clustering(398) Variable = TRAF3IP2 MUTATION ANALYSIS
D398V1, survival
                    sevent
clus2                 0  1
  TRAF3IP2 MUTATED    2  2
  TRAF3IP2 WILD-TYPE 61 60
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 4                121 
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 2                 60 
$`TRAF3IP2 MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IO TCGA-HV-A7OL 
       20.84         7.36        63.85         8.28 

$`TRAF3IP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IC 
        3.39        12.95         9.60        45.47        43.50        24.26 
TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
              7.36               0.23 
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
             63.85              90.12 
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
             14.56              15.22 
[1] "7.4 - 63.9 (14.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D398V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TRAF3IP2 MUTATED         0        0        0         2         1         0
  TRAF3IP2 WILD-TYPE       1        3       12        17        81         4
                    vv
clus                 STAGE IV
  TRAF3IP2 MUTATED          0
  TRAF3IP2 WILD-TYPE        3
D398V3, multiclass
           clus
vv          TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                2                 17
  STAGE IIB                1                 81
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  TRAF3IP2 MUTATED    0  0     3
  TRAF3IP2 WILD-TYPE  5 17    99
D398V4, multiclass
       clus
vv      TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V5, binary
                    cls
clus                  0  1
  TRAF3IP2 MUTATED    2  1
  TRAF3IP2 WILD-TYPE 33 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP2 MUTATED      2    1
  TRAF3IP2 WILD-TYPE   33   88
   clus
vv  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  0                2                 33
  1                1                 88
[1] 2 2
[1] FALSE
D398V6, binary
                    cls
clus                  0  1
  TRAF3IP2 MUTATED    0  0
  TRAF3IP2 WILD-TYPE 57  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP2 MUTATED      0    0
  TRAF3IP2 WILD-TYPE   57    3
D398V7, binary
                    cls
clus                  0  1
  TRAF3IP2 MUTATED    1  3
  TRAF3IP2 WILD-TYPE 50 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP2 MUTATED      1    3
  TRAF3IP2 WILD-TYPE   50   72
        clus
vv       TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  FEMALE                1                 50
  MALE                  3                 72
[1] 2 2
[1] FALSE
D398V8, binary
                    cls
clus                  0  1
  TRAF3IP2 MUTATED    3  1
  TRAF3IP2 WILD-TYPE 85 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP2 MUTATED      3    1
  TRAF3IP2 WILD-TYPE   85   29
     clus
vv    TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  NO                 3                 85
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TRAF3IP2 MUTATED                                     3
  TRAF3IP2 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TRAF3IP2 MUTATED                                       1
  TRAF3IP2 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TRAF3IP2 MUTATED                                                  0
  TRAF3IP2 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  TRAF3IP2 MUTATED                                     0
  TRAF3IP2 WILD-TYPE                                   1
D398V9, multiclass
                                                  clus
vv                                                 TRAF3IP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 TRAF3IP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V10, continuous
[1] "Remove cluster labels:" "TRAF3IP2 MUTATED"      
clus
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9IX 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-F2-A8YN         TCGA-FB-A5VM         TCGA-FB-A78T 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HV-AA8V         TCGA-HZ-A8P1         TCGA-IB-7651 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-YY-A8LH 
"TRAF3IP2 WILD-TYPE" 
D398V11, continuous
[1] "Remove cluster labels:" "TRAF3IP2 MUTATED"      
clus
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IR         TCGA-3A-A9IX 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  TRAF3IP2 MUTATED    3  0  1  0
  TRAF3IP2 WILD-TYPE 77 35  3  2
D398V12, multiclass
    clus
vv   TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  R0                3                 77
  R1                0                 35
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V13, continuous
[1] "Remove cluster labels:" "TRAF3IP2 MUTATED"      
clus
  TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE 
                 2                122 
        TCGA-2J-AABR         TCGA-2J-AABT         TCGA-3A-A9I5 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-3A-A9IJ         TCGA-3A-A9IL         TCGA-F2-A44G 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAQ6         TCGA-FZ-5924         TCGA-HZ-A77Q 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-IB-A5SS         TCGA-LB-A7SX 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-S4-A8RO         TCGA-US-A77E         TCGA-XD-AAUL 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AAB4         TCGA-2J-AAB6 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AAB8         TCGA-2J-AAB9         TCGA-2J-AABA 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABH 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AABK         TCGA-2J-AABO         TCGA-2J-AABP 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2J-AABU         TCGA-2J-AABV         TCGA-2L-AAQA 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-2L-AAQI         TCGA-2L-AAQJ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-2L-AAQL         TCGA-2L-AAQM         TCGA-3A-A9I7 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-3A-A9IC         TCGA-3A-A9IH         TCGA-3A-A9IR 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-3A-A9IS         TCGA-3A-A9IU         TCGA-3A-A9IV 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-3A-A9IZ         TCGA-3A-A9J0 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-3E-AAAY         TCGA-3E-AAAZ         TCGA-F2-7273 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-F2-A7TX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPP         TCGA-FB-AAPQ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPU         TCGA-FB-AAPZ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAQ0         TCGA-FB-AAQ1         TCGA-FB-AAQ2 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FB-AAQ3         TCGA-FZ-5919         TCGA-FZ-5920 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FZ-5921         TCGA-FZ-5922         TCGA-FZ-5923 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-FZ-5926         TCGA-H8-A6C1         TCGA-HV-A7OP 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HV-AA8V         TCGA-HV-AA8X         TCGA-HZ-7918 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HZ-7925         TCGA-HZ-8637         TCGA-HZ-A49I 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HZ-A77O         TCGA-HZ-A77P         TCGA-HZ-A8P1 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-HZ-A9TJ         TCGA-IB-7651         TCGA-IB-7652 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A5SO 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A5SP         TCGA-IB-A5SQ         TCGA-IB-A5ST 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7LX 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-IB-AAUM         TCGA-IB-AAUN 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-AAUO         TCGA-IB-AAUP         TCGA-IB-AAUQ 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-AAUR         TCGA-IB-AAUS         TCGA-IB-AAUU 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-IB-AAUW         TCGA-LB-A8F3 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-Q3-A5QY 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-Q3-AA2A         TCGA-RB-A7B8         TCGA-RB-AA9M 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-RL-AAAS         TCGA-US-A776         TCGA-US-A779 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-US-A77G         TCGA-US-A77J         TCGA-XD-AAUG 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-XD-AAUH         TCGA-XD-AAUI         TCGA-XN-A8T3 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YB-A89D         TCGA-YH-A8SY 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
        TCGA-YY-A8LH         TCGA-Z5-AAPL 
"TRAF3IP2 WILD-TYPE" "TRAF3IP2 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRAF3IP2 MUTATED       1                         0     3
  TRAF3IP2 WILD-TYPE     5                         5   111
D398V14, multiclass
                           clus
vv                          TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V15, binary
                    cls
clus                  0  1
  TRAF3IP2 MUTATED    0  3
  TRAF3IP2 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP2 MUTATED      0    3
  TRAF3IP2 WILD-TYPE    5   88
                        clus
vv                       TRAF3IP2 MUTATED TRAF3IP2 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(399) Variable = SMARCC2 MUTATION ANALYSIS
D399V1, survival
                   sevent
clus2                0  1
  SMARCC2 MUTATED    2  3
  SMARCC2 WILD-TYPE 61 59
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                5               120 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                3                59 
$`SMARCC2 MUTATED`
TCGA-2J-AAB8 TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-IB-7651 TCGA-Z5-AAPL 
        2.63        15.95        37.15        19.82        15.35 

$`SMARCC2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS 
       19.46         3.12        17.00        16.37        12.33         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 

  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
             2.63              0.23 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
            37.15             90.12 
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
           15.950            15.155 
[1] "2.6 - 37.1 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D399V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SMARCC2 MUTATED         0        0        0         1         4         0
  SMARCC2 WILD-TYPE       1        3       12        18        78         4
                   vv
clus                STAGE IV
  SMARCC2 MUTATED          0
  SMARCC2 WILD-TYPE        3
D399V3, multiclass
           clus
vv          SMARCC2 MUTATED SMARCC2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SMARCC2 MUTATED    0  0     5
  SMARCC2 WILD-TYPE  5 17    97
D399V4, multiclass
       clus
vv      SMARCC2 MUTATED SMARCC2 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V5, binary
                   cls
clus                 0  1
  SMARCC2 MUTATED    1  4
  SMARCC2 WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      1    4
  SMARCC2 WILD-TYPE   34   85
   clus
vv  SMARCC2 MUTATED SMARCC2 WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D399V6, binary
                   cls
clus                 0  1
  SMARCC2 MUTATED    3  0
  SMARCC2 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      3    0
  SMARCC2 WILD-TYPE   54    3
   clus
vv  SMARCC2 MUTATED SMARCC2 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D399V7, binary
                   cls
clus                 0  1
  SMARCC2 MUTATED    2  3
  SMARCC2 WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      2    3
  SMARCC2 WILD-TYPE   49   72
        clus
vv       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  FEMALE               2                49
  MALE                 3                72
[1] 2 2
[1] FALSE
D399V8, binary
                   cls
clus                 0  1
  SMARCC2 MUTATED    3  1
  SMARCC2 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      3    1
  SMARCC2 WILD-TYPE   85   29
     clus
vv    SMARCC2 MUTATED SMARCC2 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMARCC2 MUTATED                                     5
  SMARCC2 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMARCC2 MUTATED                                       0
  SMARCC2 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMARCC2 MUTATED                                                  0
  SMARCC2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SMARCC2 MUTATED                                     0
  SMARCC2 WILD-TYPE                                   1
D399V9, multiclass
                                                  clus
vv                                                 SMARCC2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SMARCC2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V10, continuous
[1] "Remove cluster labels:" "SMARCC2 MUTATED"       
clus
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-YY-A8LH 
"SMARCC2 WILD-TYPE" 
D399V11, continuous
[1] "Remove cluster labels:" "SMARCC2 MUTATED"       
clus
  SMARCC2 MUTATED SMARCC2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPS 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" "SMARCC2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SMARCC2 MUTATED    4  1  0  0
  SMARCC2 WILD-TYPE 76 34  4  2
D399V12, multiclass
    clus
vv   SMARCC2 MUTATED SMARCC2 WILD-TYPE
  R0               4                76
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCC2 MUTATED       0                         0     5
  SMARCC2 WILD-TYPE     6                         5   109
D399V14, multiclass
                           clus
vv                          SMARCC2 MUTATED SMARCC2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V15, binary
                   cls
clus                 0  1
  SMARCC2 MUTATED    0  4
  SMARCC2 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCC2 MUTATED      0    4
  SMARCC2 WILD-TYPE    5   87
                        clus
vv                       SMARCC2 MUTATED SMARCC2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(400) Variable = DNAH5 MUTATION ANALYSIS
D400V1, survival
                 sevent
clus2              0  1
  DNAH5 MUTATED    7  4
  DNAH5 WILD-TYPE 56 58
  DNAH5 MUTATED DNAH5 WILD-TYPE 
             11             114 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
              4              58 
$`DNAH5 MUTATED`
TCGA-2J-AABE TCGA-2J-AABP TCGA-F2-A7TX TCGA-FB-AAPQ TCGA-FB-AAQ2 TCGA-IB-7651 
       22.22        15.22         3.12        37.15         5.03        19.82 
TCGA-IB-A6UF TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-YB-A89D 
       21.90        13.81        12.99        31.27        11.51 

$`DNAH5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       18.67        12.03        23.67        12.76        66.28        15.35 

  DNAH5 MUTATED DNAH5 WILD-TYPE 
           3.12            0.23 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
          37.15           90.12 
  DNAH5 MUTATED DNAH5 WILD-TYPE 
         15.220          15.255 
[1] "3.1 - 37.1 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D400V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DNAH5 MUTATED         0        0        1         1         8         0
  DNAH5 WILD-TYPE       1        3       11        18        74         4
                 vv
clus              STAGE IV
  DNAH5 MUTATED          1
  DNAH5 WILD-TYPE        2
D400V3, multiclass
           clus
vv          DNAH5 MUTATED DNAH5 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DNAH5 MUTATED    0  1    10
  DNAH5 WILD-TYPE  5 16    92
D400V4, multiclass
       clus
vv      DNAH5 MUTATED DNAH5 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4            10              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V5, binary
                 cls
clus               0  1
  DNAH5 MUTATED    2  9
  DNAH5 WILD-TYPE 33 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      2    9
  DNAH5 WILD-TYPE   33   80
   clus
vv  DNAH5 MUTATED DNAH5 WILD-TYPE
  0             2              33
  1             9              80
[1] 2 2
[1] FALSE
D400V6, binary
                 cls
clus               0  1
  DNAH5 MUTATED    7  1
  DNAH5 WILD-TYPE 50  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      7    1
  DNAH5 WILD-TYPE   50    2
   clus
vv  DNAH5 MUTATED DNAH5 WILD-TYPE
  0             7              50
  1             1               2
[1] 2 2
[1] FALSE
D400V7, binary
                 cls
clus               0  1
  DNAH5 MUTATED    5  6
  DNAH5 WILD-TYPE 46 69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      5    6
  DNAH5 WILD-TYPE   46   69
        clus
vv       DNAH5 MUTATED DNAH5 WILD-TYPE
  FEMALE             5              46
  MALE               6              69
[1] 2 2
[1] FALSE
D400V8, binary
                 cls
clus               0  1
  DNAH5 MUTATED    7  4
  DNAH5 WILD-TYPE 81 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      7    4
  DNAH5 WILD-TYPE   81   26
     clus
vv    DNAH5 MUTATED DNAH5 WILD-TYPE
  NO              7              81
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DNAH5 MUTATED                                    10
  DNAH5 WILD-TYPE                                  95
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DNAH5 MUTATED                                       0
  DNAH5 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DNAH5 MUTATED                                                  0
  DNAH5 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DNAH5 MUTATED                                     1
  DNAH5 WILD-TYPE                                   0
D400V9, multiclass
                                                  clus
vv                                                 DNAH5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 DNAH5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V10, continuous
D400V11, continuous
                 vv
clus              R0 R1 R2 RX
  DNAH5 MUTATED    6  4  1  0
  DNAH5 WILD-TYPE 74 31  3  2
D400V12, multiclass
    clus
vv   DNAH5 MUTATED DNAH5 WILD-TYPE
  R0             6              74
  R1             4              31
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH5 MUTATED       0                         0    11
  DNAH5 WILD-TYPE     6                         5   103
D400V14, multiclass
                           clus
vv                          DNAH5 MUTATED DNAH5 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                11             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V15, binary
                 cls
clus               0  1
  DNAH5 MUTATED    1  7
  DNAH5 WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH5 MUTATED      1    7
  DNAH5 WILD-TYPE    4   84
                        clus
vv                       DNAH5 MUTATED DNAH5 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(401) Variable = C18ORF19 MUTATION ANALYSIS
D401V1, survival
                    sevent
clus2                 0  1
  C18ORF19 MUTATED    1  2
  C18ORF19 WILD-TYPE 62 60
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 3                122 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 2                 60 
$`C18ORF19 MUTATED`
TCGA-LB-A7SX TCGA-2J-AABO TCGA-FZ-5922 
       12.92        14.47        36.20 

$`C18ORF19 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             12.92               0.23 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             36.20              90.12 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             14.47              15.27 
[1] "12.9 - 36.2 (14.5)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.2"
D401V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C18ORF19 MUTATED         0        0        0         1         2         0
  C18ORF19 WILD-TYPE       1        3       12        18        80         4
                    vv
clus                 STAGE IV
  C18ORF19 MUTATED          0
  C18ORF19 WILD-TYPE        3
D401V3, multiclass
           clus
vv          C18ORF19 MUTATED C18ORF19 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                2                 80
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C18ORF19 MUTATED    0  0     3
  C18ORF19 WILD-TYPE  5 17    99
D401V4, multiclass
       clus
vv      C18ORF19 MUTATED C18ORF19 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V5, binary
                    cls
clus                  0  1
  C18ORF19 MUTATED    1  2
  C18ORF19 WILD-TYPE 34 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      1    2
  C18ORF19 WILD-TYPE   34   87
   clus
vv  C18ORF19 MUTATED C18ORF19 WILD-TYPE
  0                1                 34
  1                2                 87
[1] 2 2
[1] FALSE
D401V6, binary
                    cls
clus                  0  1
  C18ORF19 MUTATED    2  0
  C18ORF19 WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      2    0
  C18ORF19 WILD-TYPE   55    3
   clus
vv  C18ORF19 MUTATED C18ORF19 WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D401V7, binary
                    cls
clus                  0  1
  C18ORF19 MUTATED    1  2
  C18ORF19 WILD-TYPE 50 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      1    2
  C18ORF19 WILD-TYPE   50   73
        clus
vv       C18ORF19 MUTATED C18ORF19 WILD-TYPE
  FEMALE                1                 50
  MALE                  2                 73
[1] 2 2
[1] FALSE
D401V8, binary
                    cls
clus                  0  1
  C18ORF19 MUTATED    2  1
  C18ORF19 WILD-TYPE 86 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      2    1
  C18ORF19 WILD-TYPE   86   29
     clus
vv    C18ORF19 MUTATED C18ORF19 WILD-TYPE
  NO                 2                 86
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C18ORF19 MUTATED                                     3
  C18ORF19 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C18ORF19 MUTATED                                       0
  C18ORF19 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C18ORF19 MUTATED                                                  0
  C18ORF19 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C18ORF19 MUTATED                                     0
  C18ORF19 WILD-TYPE                                   1
D401V9, multiclass
                                                  clus
vv                                                 C18ORF19 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C18ORF19 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V10, continuous
[1] "Remove cluster labels:" "C18ORF19 MUTATED"      
clus
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-2J-AABV         TCGA-2L-AAQA         TCGA-2L-AAQE 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-3A-A9I9         TCGA-3A-A9IB         TCGA-3A-A9IX 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-F2-A8YN         TCGA-FB-A5VM         TCGA-FB-A78T 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-HV-AA8V         TCGA-HZ-A8P1         TCGA-IB-7651 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-YY-A8LH 
"C18ORF19 WILD-TYPE" 
D401V11, continuous
[1] "Remove cluster labels:" "C18ORF19 MUTATED"      
clus
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-3A-A9IB 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-3A-A9IR         TCGA-3A-A9IX         TCGA-FB-A5VM 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A8P1         TCGA-IB-7651 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" "C18ORF19 WILD-TYPE" 
        TCGA-YY-A8LH 
"C18ORF19 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C18ORF19 MUTATED    2  1  0  0
  C18ORF19 WILD-TYPE 78 34  4  2
D401V12, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  R0                2                 78
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C18ORF19 MUTATED       0                         1     2
  C18ORF19 WILD-TYPE     6                         4   112
D401V14, multiclass
                           clus
vv                          C18ORF19 MUTATED C18ORF19 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    2                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V15, binary
                    cls
clus                  0  1
  C18ORF19 MUTATED    0  2
  C18ORF19 WILD-TYPE  5 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      0    2
  C18ORF19 WILD-TYPE    5   89
                        clus
vv                       C18ORF19 MUTATED C18ORF19 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(402) Variable = KIF20B MUTATION ANALYSIS
D402V1, survival
                  sevent
clus2               0  1
  KIF20B MUTATED    3  2
  KIF20B WILD-TYPE 60 60
  KIF20B MUTATED KIF20B WILD-TYPE 
               5              120 
  KIF20B MUTATED KIF20B WILD-TYPE 
               2               60 
$`KIF20B MUTATED`
TCGA-2J-AABV TCGA-3A-A9J0 TCGA-HV-A7OP TCGA-IB-7651 TCGA-Q3-A5QY 
       21.44        24.43        32.15        19.82        13.68 

$`KIF20B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KIF20B MUTATED KIF20B WILD-TYPE 
           13.68             0.23 
  KIF20B MUTATED KIF20B WILD-TYPE 
           32.15            90.12 
  KIF20B MUTATED KIF20B WILD-TYPE 
          21.440           15.155 
[1] "13.7 - 32.1 (21.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.8"
D402V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIF20B MUTATED         0        0        0         0         5         0
  KIF20B WILD-TYPE       1        3       12        19        77         4
                  vv
clus               STAGE IV
  KIF20B MUTATED          0
  KIF20B WILD-TYPE        3
D402V3, multiclass
           clus
vv          KIF20B MUTATED KIF20B WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  KIF20B MUTATED    0  0     5
  KIF20B WILD-TYPE  5 17    97
D402V4, multiclass
       clus
vv      KIF20B MUTATED KIF20B WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V5, binary
                  cls
clus                0  1
  KIF20B MUTATED    0  5
  KIF20B WILD-TYPE 35 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      0    5
  KIF20B WILD-TYPE   35   84
   clus
vv  KIF20B MUTATED KIF20B WILD-TYPE
  0              0               35
  1              5               84
[1] 2 2
[1] FALSE
D402V6, binary
                  cls
clus                0  1
  KIF20B MUTATED    3  0
  KIF20B WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      3    0
  KIF20B WILD-TYPE   54    3
   clus
vv  KIF20B MUTATED KIF20B WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D402V7, binary
                  cls
clus                0  1
  KIF20B MUTATED    1  4
  KIF20B WILD-TYPE 50 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      1    4
  KIF20B WILD-TYPE   50   71
        clus
vv       KIF20B MUTATED KIF20B WILD-TYPE
  FEMALE              1               50
  MALE                4               71
[1] 2 2
[1] FALSE
D402V8, binary
                  cls
clus                0  1
  KIF20B MUTATED    4  1
  KIF20B WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      4    1
  KIF20B WILD-TYPE   84   29
     clus
vv    KIF20B MUTATED KIF20B WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIF20B MUTATED                                     4
  KIF20B WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIF20B MUTATED                                       1
  KIF20B WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIF20B MUTATED                                                  0
  KIF20B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIF20B MUTATED                                     0
  KIF20B WILD-TYPE                                   1
D402V9, multiclass
                                                  clus
vv                                                 KIF20B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 KIF20B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V10, continuous
[1] "Remove cluster labels:" "KIF20B MUTATED"        
clus
  KIF20B MUTATED KIF20B WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2L-AAQA 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-YY-A8LH 
"KIF20B WILD-TYPE" 
D402V11, continuous
[1] "Remove cluster labels:" "KIF20B MUTATED"        
clus
  KIF20B MUTATED KIF20B WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" "KIF20B WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  KIF20B MUTATED    4  1  0  0
  KIF20B WILD-TYPE 76 34  4  2
D402V12, multiclass
    clus
vv   KIF20B MUTATED KIF20B WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF20B MUTATED       1                         0     4
  KIF20B WILD-TYPE     5                         5   110
D402V14, multiclass
                           clus
vv                          KIF20B MUTATED KIF20B WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V15, binary
                  cls
clus                0  1
  KIF20B MUTATED    0  3
  KIF20B WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF20B MUTATED      0    3
  KIF20B WILD-TYPE    5   88
                        clus
vv                       KIF20B MUTATED KIF20B WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(403) Variable = KDM6A MUTATION ANALYSIS
D403V1, survival
                 sevent
clus2              0  1
  KDM6A MUTATED    1  6
  KDM6A WILD-TYPE 62 56
  KDM6A MUTATED KDM6A WILD-TYPE 
              7             118 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6              56 
$`KDM6A MUTATED`
TCGA-2J-AAB9 TCGA-2L-AAQE TCGA-2L-AAQI TCGA-FZ-5926 TCGA-HV-AA8X TCGA-IB-A5SP 
       20.61        22.49         3.39        17.79        17.49        15.85 
TCGA-US-A779 
       16.80 

$`KDM6A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-2L-AAQL 
       15.22         9.11        21.44         4.70        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 
       24.36         2.01         5.10        36.20        20.35        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        10.85         0.23        19.82        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        41.33        15.19        12.00         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G 
        3.12        15.32         9.40         0.30        39.98         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  KDM6A MUTATED KDM6A WILD-TYPE 
           3.39            0.23 
  KDM6A MUTATED KDM6A WILD-TYPE 
          22.49           90.12 
  KDM6A MUTATED KDM6A WILD-TYPE 
          17.49           15.09 
[1] "3.4 - 22.5 (17.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.7"
D403V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KDM6A MUTATED         0        0        0         1         5         1
  KDM6A WILD-TYPE       1        3       12        18        77         3
                 vv
clus              STAGE IV
  KDM6A MUTATED          0
  KDM6A WILD-TYPE        3
D403V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KDM6A MUTATED    0  1     6
  KDM6A WILD-TYPE  5 16    96
D403V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V5, binary
                 cls
clus               0  1
  KDM6A MUTATED    1  6
  KDM6A WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    6
  KDM6A WILD-TYPE   34   83
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D403V6, binary
                 cls
clus               0  1
  KDM6A MUTATED    4  0
  KDM6A WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4    0
  KDM6A WILD-TYPE   53    3
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D403V7, binary
                 cls
clus               0  1
  KDM6A MUTATED    4  3
  KDM6A WILD-TYPE 47 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4    3
  KDM6A WILD-TYPE   47   72
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4              47
  MALE               3              72
[1] 2 2
[1] FALSE
D403V8, binary
                 cls
clus               0  1
  KDM6A MUTATED    5  1
  KDM6A WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      5    1
  KDM6A WILD-TYPE   83   29
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KDM6A MUTATED                                     7
  KDM6A WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KDM6A MUTATED                                       0
  KDM6A WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KDM6A MUTATED                                                  0
  KDM6A WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KDM6A MUTATED                                     0
  KDM6A WILD-TYPE                                   1
D403V9, multiclass
                                                  clus
vv                                                 KDM6A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KDM6A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V10, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
D403V11, continuous
                 vv
clus              R0 R1 R2 RX
  KDM6A MUTATED    4  2  1  0
  KDM6A WILD-TYPE 76 33  3  2
D403V12, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0             4              76
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       1                         0     6
  KDM6A WILD-TYPE     5                         5   108
D403V14, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V15, binary
                 cls
clus               0  1
  KDM6A MUTATED    0  2
  KDM6A WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    2
  KDM6A WILD-TYPE    5   89
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(404) Variable = PRG4 MUTATION ANALYSIS
D404V1, survival
                sevent
clus2             0  1
  PRG4 MUTATED    4  7
  PRG4 WILD-TYPE 59 55
  PRG4 MUTATED PRG4 WILD-TYPE 
            11            114 
  PRG4 MUTATED PRG4 WILD-TYPE 
             7             55 
$`PRG4 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-FB-AAPU TCGA-FB-AAQ2 TCGA-HV-A7OP 
       22.49        10.13        24.43        12.53         5.03        32.15 
TCGA-IB-7651 TCGA-IB-A5SO TCGA-US-A77J TCGA-YB-A89D TCGA-Z5-AAPL 
       19.82        12.00        18.67        11.51        15.35 

$`PRG4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       36.26        34.09        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
        9.40         0.30        39.98        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 

  PRG4 MUTATED PRG4 WILD-TYPE 
          5.03           0.23 
  PRG4 MUTATED PRG4 WILD-TYPE 
         32.15          90.12 
  PRG4 MUTATED PRG4 WILD-TYPE 
        15.350         15.205 
[1] "5.0 - 32.1 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D404V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRG4 MUTATED         0        0        0         2        10         0
  PRG4 WILD-TYPE       1        3       12        17        72         4
                vv
clus             STAGE IV
  PRG4 MUTATED          0
  PRG4 WILD-TYPE        3
D404V3, multiclass
           clus
vv          PRG4 MUTATED PRG4 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB           10             72
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PRG4 MUTATED    0  0    12
  PRG4 WILD-TYPE  5 17    90
D404V4, multiclass
       clus
vv      PRG4 MUTATED PRG4 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4           12             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V5, binary
                cls
clus              0  1
  PRG4 MUTATED    2 10
  PRG4 WILD-TYPE 33 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      2   10
  PRG4 WILD-TYPE   33   79
   clus
vv  PRG4 MUTATED PRG4 WILD-TYPE
  0            2             33
  1           10             79
[1] 2 2
[1] FALSE
D404V6, binary
                cls
clus              0  1
  PRG4 MUTATED    5  0
  PRG4 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      5    0
  PRG4 WILD-TYPE   52    3
   clus
vv  PRG4 MUTATED PRG4 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D404V7, binary
                cls
clus              0  1
  PRG4 MUTATED    5  7
  PRG4 WILD-TYPE 46 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      5    7
  PRG4 WILD-TYPE   46   68
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  FEMALE            5             46
  MALE              7             68
[1] 2 2
[1] FALSE
D404V8, binary
                cls
clus              0  1
  PRG4 MUTATED    8  2
  PRG4 WILD-TYPE 80 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      8    2
  PRG4 WILD-TYPE   80   28
     clus
vv    PRG4 MUTATED PRG4 WILD-TYPE
  NO             8             80
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRG4 MUTATED                                    11
  PRG4 WILD-TYPE                                  94
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRG4 MUTATED                                       1
  PRG4 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRG4 MUTATED                                                  0
  PRG4 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRG4 MUTATED                                     0
  PRG4 WILD-TYPE                                   1
D404V9, multiclass
                                                  clus
vv                                                 PRG4 MUTATED PRG4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        11             94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V10, continuous
D404V11, continuous
[1] "Remove cluster labels:" "PRG4 MUTATED"          
clus
  PRG4 MUTATED PRG4 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PRG4 MUTATED    9  3  0  0
  PRG4 WILD-TYPE 71 32  4  2
D404V12, multiclass
    clus
vv   PRG4 MUTATED PRG4 WILD-TYPE
  R0            9             71
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRG4 MUTATED       2                         0    10
  PRG4 WILD-TYPE     4                         5   104
D404V14, multiclass
                           clus
vv                          PRG4 MUTATED PRG4 WILD-TYPE
  ASIAN                                2              4
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               10            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V15, binary
                cls
clus              0  1
  PRG4 MUTATED    1  8
  PRG4 WILD-TYPE  4 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      1    8
  PRG4 WILD-TYPE    4   83
                        clus
vv                       PRG4 MUTATED PRG4 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(405) Variable = PHF14 MUTATION ANALYSIS
D405V1, survival
                 sevent
clus2              0  1
  PHF14 MUTATED    2  1
  PHF14 WILD-TYPE 61 61
  PHF14 MUTATED PHF14 WILD-TYPE 
              3             122 
  PHF14 MUTATED PHF14 WILD-TYPE 
              1              61 
$`PHF14 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-LB-A8F3 
       19.82        15.19        12.46 

$`PHF14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PHF14 MUTATED PHF14 WILD-TYPE 
          12.46            0.23 
  PHF14 MUTATED PHF14 WILD-TYPE 
          19.82           90.12 
  PHF14 MUTATED PHF14 WILD-TYPE 
          15.19           15.27 
[1] "12.5 - 19.8 (15.2)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.3"
D405V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHF14 MUTATED         0        0        0         1         1         1
  PHF14 WILD-TYPE       1        3       12        18        81         3
                 vv
clus              STAGE IV
  PHF14 MUTATED          0
  PHF14 WILD-TYPE        3
D405V3, multiclass
           clus
vv          PHF14 MUTATED PHF14 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PHF14 MUTATED    0  0     3
  PHF14 WILD-TYPE  5 17    99
D405V4, multiclass
       clus
vv      PHF14 MUTATED PHF14 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V5, binary
                 cls
clus               0  1
  PHF14 MUTATED    1  2
  PHF14 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      1    2
  PHF14 WILD-TYPE   34   87
   clus
vv  PHF14 MUTATED PHF14 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D405V6, binary
                 cls
clus               0  1
  PHF14 MUTATED    2  0
  PHF14 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      2    0
  PHF14 WILD-TYPE   55    3
   clus
vv  PHF14 MUTATED PHF14 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D405V7, binary
                 cls
clus               0  1
  PHF14 MUTATED    3  0
  PHF14 WILD-TYPE 48 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      3    0
  PHF14 WILD-TYPE   48   75
        clus
vv       PHF14 MUTATED PHF14 WILD-TYPE
  FEMALE             3              48
  MALE               0              75
[1] 2 2
[1] FALSE
D405V8, binary
                 cls
clus               0  1
  PHF14 MUTATED    2  1
  PHF14 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      2    1
  PHF14 WILD-TYPE   86   29
     clus
vv    PHF14 MUTATED PHF14 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF14 MUTATED                                     3
  PHF14 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF14 MUTATED                                       0
  PHF14 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF14 MUTATED                                                  0
  PHF14 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHF14 MUTATED                                     0
  PHF14 WILD-TYPE                                   1
D405V9, multiclass
                                                  clus
vv                                                 PHF14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PHF14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V10, continuous
[1] "Remove cluster labels:" "PHF14 MUTATED"         
clus
  PHF14 MUTATED PHF14 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-YY-A8LH 
"PHF14 WILD-TYPE" 
D405V11, continuous
[1] "Remove cluster labels:" "PHF14 MUTATED"         
clus
  PHF14 MUTATED PHF14 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PHF14 WILD-TYPE" "PHF14 WILD-TYPE" "PHF14 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PHF14 MUTATED    2  1  0  0
  PHF14 WILD-TYPE 78 34  4  2
D405V12, multiclass
    clus
vv   PHF14 MUTATED PHF14 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF14 MUTATED       0                         1     2
  PHF14 WILD-TYPE     6                         4   112
D405V14, multiclass
                           clus
vv                          PHF14 MUTATED PHF14 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V15, binary
                 cls
clus               0  1
  PHF14 MUTATED    0  3
  PHF14 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      0    3
  PHF14 WILD-TYPE    5   88
                        clus
vv                       PHF14 MUTATED PHF14 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(406) Variable = RASGRF2 MUTATION ANALYSIS
D406V1, survival
                   sevent
clus2                0  1
  RASGRF2 MUTATED    3  3
  RASGRF2 WILD-TYPE 60 59
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                6               119 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                3                59 
$`RASGRF2 MUTATED`
TCGA-3A-A9IV TCGA-FB-AAPP TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-A7M4 TCGA-RB-A7B8 
       36.26        15.95        19.82        36.69        15.88        15.32 

$`RASGRF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM 
        7.20        20.88        21.90         1.35         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
            15.32              0.23 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
            36.69             90.12 
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
           17.885            15.060 
[1] "15.3 - 36.7 (17.9)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.3"
D406V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RASGRF2 MUTATED         0        0        1         0         5         0
  RASGRF2 WILD-TYPE       1        3       11        19        77         4
                   vv
clus                STAGE IV
  RASGRF2 MUTATED          0
  RASGRF2 WILD-TYPE        3
D406V3, multiclass
           clus
vv          RASGRF2 MUTATED RASGRF2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  RASGRF2 MUTATED    0  1     5
  RASGRF2 WILD-TYPE  5 16    97
D406V4, multiclass
       clus
vv      RASGRF2 MUTATED RASGRF2 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V5, binary
                   cls
clus                 0  1
  RASGRF2 MUTATED    1  5
  RASGRF2 WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      1    5
  RASGRF2 WILD-TYPE   34   84
   clus
vv  RASGRF2 MUTATED RASGRF2 WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D406V6, binary
                   cls
clus                 0  1
  RASGRF2 MUTATED    2  0
  RASGRF2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      2    0
  RASGRF2 WILD-TYPE   55    3
   clus
vv  RASGRF2 MUTATED RASGRF2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D406V7, binary
                   cls
clus                 0  1
  RASGRF2 MUTATED    4  2
  RASGRF2 WILD-TYPE 47 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      4    2
  RASGRF2 WILD-TYPE   47   73
        clus
vv       RASGRF2 MUTATED RASGRF2 WILD-TYPE
  FEMALE               4                47
  MALE                 2                73
[1] 2 2
[1] FALSE
D406V8, binary
                   cls
clus                 0  1
  RASGRF2 MUTATED    5  1
  RASGRF2 WILD-TYPE 83 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      5    1
  RASGRF2 WILD-TYPE   83   29
     clus
vv    RASGRF2 MUTATED RASGRF2 WILD-TYPE
  NO                5                83
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RASGRF2 MUTATED                                     4
  RASGRF2 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RASGRF2 MUTATED                                       2
  RASGRF2 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RASGRF2 MUTATED                                                  0
  RASGRF2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  RASGRF2 MUTATED                                     0
  RASGRF2 WILD-TYPE                                   1
D406V9, multiclass
                                                  clus
vv                                                 RASGRF2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 RASGRF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V10, continuous
[1] "Remove cluster labels:" "RASGRF2 MUTATED"       
clus
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-YY-A8LH 
"RASGRF2 WILD-TYPE" 
D406V11, continuous
[1] "Remove cluster labels:" "RASGRF2 MUTATED"       
clus
  RASGRF2 MUTATED RASGRF2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-AAUQ 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" "RASGRF2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  RASGRF2 MUTATED    5  1  0  0
  RASGRF2 WILD-TYPE 75 34  4  2
D406V12, multiclass
    clus
vv   RASGRF2 MUTATED RASGRF2 WILD-TYPE
  R0               5                75
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASGRF2 MUTATED       1                         0     5
  RASGRF2 WILD-TYPE     5                         5   109
D406V14, multiclass
                           clus
vv                          RASGRF2 MUTATED RASGRF2 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V15, binary
                   cls
clus                 0  1
  RASGRF2 MUTATED    0  6
  RASGRF2 WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRF2 MUTATED      0    6
  RASGRF2 WILD-TYPE    5   85
                        clus
vv                       RASGRF2 MUTATED RASGRF2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(407) Variable = PNMAL1 MUTATION ANALYSIS
D407V1, survival
                  sevent
clus2               0  1
  PNMAL1 MUTATED    3  1
  PNMAL1 WILD-TYPE 60 61
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               4              121 
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               1               61 
$`PNMAL1 MUTATED`
TCGA-3A-A9IH TCGA-3A-A9IS TCGA-IB-7651 TCGA-LB-A8F3 
       33.57        32.81        19.82        12.46 

$`PNMAL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
        7.36        24.26        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28         7.56        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
           12.46             0.23 
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
           33.57            90.12 
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
          26.315           15.190 
[1] "12.5 - 33.6 (26.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.9"
D407V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PNMAL1 MUTATED         0        1        1         1         1         0
  PNMAL1 WILD-TYPE       1        2       11        18        81         4
                  vv
clus               STAGE IV
  PNMAL1 MUTATED          0
  PNMAL1 WILD-TYPE        3
D407V3, multiclass
           clus
vv          PNMAL1 MUTATED PNMAL1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PNMAL1 MUTATED     1   1     2
  PNMAL1 WILD-TYPE   4  16   100
D407V4, multiclass
       clus
vv      PNMAL1 MUTATED PNMAL1 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V5, binary
                  cls
clus                0  1
  PNMAL1 MUTATED    3  1
  PNMAL1 WILD-TYPE 32 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNMAL1 MUTATED      3    1
  PNMAL1 WILD-TYPE   32   88
   clus
vv  PNMAL1 MUTATED PNMAL1 WILD-TYPE
  0              3               32
  1              1               88
[1] 2 2
[1] FALSE
D407V6, binary
                  cls
clus                0  1
  PNMAL1 MUTATED    1  0
  PNMAL1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNMAL1 MUTATED      1    0
  PNMAL1 WILD-TYPE   56    3
   clus
vv  PNMAL1 MUTATED PNMAL1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D407V7, binary
                  cls
clus                0  1
  PNMAL1 MUTATED    3  1
  PNMAL1 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNMAL1 MUTATED      3    1
  PNMAL1 WILD-TYPE   48   74
        clus
vv       PNMAL1 MUTATED PNMAL1 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D407V8, binary
                  cls
clus                0  1
  PNMAL1 MUTATED    3  1
  PNMAL1 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNMAL1 MUTATED      3    1
  PNMAL1 WILD-TYPE   85   29
     clus
vv    PNMAL1 MUTATED PNMAL1 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PNMAL1 MUTATED                                     3
  PNMAL1 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PNMAL1 MUTATED                                       1
  PNMAL1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PNMAL1 MUTATED                                                  0
  PNMAL1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PNMAL1 MUTATED                                     0
  PNMAL1 WILD-TYPE                                   1
D407V9, multiclass
                                                  clus
vv                                                 PNMAL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PNMAL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V10, continuous
[1] "Remove cluster labels:" "PNMAL1 MUTATED"        
clus
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
D407V11, continuous
[1] "Remove cluster labels:" "PNMAL1 MUTATED"        
clus
  PNMAL1 MUTATED PNMAL1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" "PNMAL1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PNMAL1 MUTATED    4  0  0  0
  PNMAL1 WILD-TYPE 76 35  4  2
D407V12, multiclass
    clus
vv   PNMAL1 MUTATED PNMAL1 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PNMAL1 MUTATED       0                         1     3
  PNMAL1 WILD-TYPE     6                         4   111
D407V14, multiclass
                           clus
vv                          PNMAL1 MUTATED PNMAL1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V15, binary
                  cls
clus                0  1
  PNMAL1 MUTATED    0  4
  PNMAL1 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNMAL1 MUTATED      0    4
  PNMAL1 WILD-TYPE    5   87
                        clus
vv                       PNMAL1 MUTATED PNMAL1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(408) Variable = FOXP2 MUTATION ANALYSIS
D408V1, survival
                 sevent
clus2              0  1
  FOXP2 MUTATED    4  6
  FOXP2 WILD-TYPE 59 56
  FOXP2 MUTATED FOXP2 WILD-TYPE 
             10             115 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              6              56 
$`FOXP2 MUTATED`
TCGA-2J-AABP TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-3A-A9IB TCGA-3A-A9IX TCGA-F2-7273 
       15.22         4.70        12.95         7.36        34.09        19.46 
TCGA-FZ-5920 TCGA-HZ-A77P TCGA-IB-7651 TCGA-Q3-AA2A 
        2.01        10.85        19.82         3.12 

$`FOXP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQL 
       14.47         9.11        21.44        22.49         3.39         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       45.47        43.50        20.84        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 
       50.70        32.81        15.06        36.26        10.13        24.43 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       75.12        71.74         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03         1.02        24.36         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FOXP2 MUTATED FOXP2 WILD-TYPE 
           2.01            0.23 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
          34.09           90.12 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
          11.90           15.35 
[1] "2.0 - 34.1 (11.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D408V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FOXP2 MUTATED         0        1        1         0         7         1
  FOXP2 WILD-TYPE       1        2       11        19        75         3
                 vv
clus              STAGE IV
  FOXP2 MUTATED          0
  FOXP2 WILD-TYPE        3
D408V3, multiclass
           clus
vv          FOXP2 MUTATED FOXP2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             7              75
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FOXP2 MUTATED    1  0     9
  FOXP2 WILD-TYPE  4 17    93
D408V4, multiclass
       clus
vv      FOXP2 MUTATED FOXP2 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             9              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V5, binary
                 cls
clus               0  1
  FOXP2 MUTATED    2  8
  FOXP2 WILD-TYPE 33 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      2    8
  FOXP2 WILD-TYPE   33   81
   clus
vv  FOXP2 MUTATED FOXP2 WILD-TYPE
  0             2              33
  1             8              81
[1] 2 2
[1] FALSE
D408V6, binary
                 cls
clus               0  1
  FOXP2 MUTATED    4  0
  FOXP2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      4    0
  FOXP2 WILD-TYPE   53    3
   clus
vv  FOXP2 MUTATED FOXP2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D408V7, binary
                 cls
clus               0  1
  FOXP2 MUTATED    5  5
  FOXP2 WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      5    5
  FOXP2 WILD-TYPE   46   70
        clus
vv       FOXP2 MUTATED FOXP2 WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D408V8, binary
                 cls
clus               0  1
  FOXP2 MUTATED    8  2
  FOXP2 WILD-TYPE 80 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      8    2
  FOXP2 WILD-TYPE   80   28
     clus
vv    FOXP2 MUTATED FOXP2 WILD-TYPE
  NO              8              80
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FOXP2 MUTATED                                     8
  FOXP2 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FOXP2 MUTATED                                       1
  FOXP2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FOXP2 MUTATED                                                  0
  FOXP2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FOXP2 MUTATED                                     1
  FOXP2 WILD-TYPE                                   0
D408V9, multiclass
                                                  clus
vv                                                 FOXP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 FOXP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V10, continuous
D408V11, continuous
                 vv
clus              R0 R1 R2 RX
  FOXP2 MUTATED    6  3  0  1
  FOXP2 WILD-TYPE 74 32  4  1
D408V12, multiclass
    clus
vv   FOXP2 MUTATED FOXP2 WILD-TYPE
  R0             6              74
  R1             3              32
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXP2 MUTATED       0                         2     8
  FOXP2 WILD-TYPE     6                         3   106
D408V14, multiclass
                           clus
vv                          FOXP2 MUTATED FOXP2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V15, binary
                 cls
clus               0  1
  FOXP2 MUTATED    0  7
  FOXP2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      0    7
  FOXP2 WILD-TYPE    5   84
                        clus
vv                       FOXP2 MUTATED FOXP2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(409) Variable = CGREF1 MUTATION ANALYSIS
D409V1, survival
                  sevent
clus2               0  1
  CGREF1 MUTATED    3  3
  CGREF1 WILD-TYPE 60 59
  CGREF1 MUTATED CGREF1 WILD-TYPE 
               6              119 
  CGREF1 MUTATED CGREF1 WILD-TYPE 
               3               59 
$`CGREF1 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABH TCGA-3E-AAAY TCGA-FB-AAQ2 TCGA-IB-AAUU TCGA-OE-A75W 
        2.17        42.31        75.12         5.03         8.05         8.78 

$`CGREF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        7.40        13.28         7.56        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CGREF1 MUTATED CGREF1 WILD-TYPE 
            2.17             0.23 
  CGREF1 MUTATED CGREF1 WILD-TYPE 
           75.12            90.12 
  CGREF1 MUTATED CGREF1 WILD-TYPE 
           8.415           15.320 
[1] "2.2 - 75.1 (8.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D409V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CGREF1 MUTATED         0        0        0         2         4         0
  CGREF1 WILD-TYPE       1        3       12        17        78         4
                  vv
clus               STAGE IV
  CGREF1 MUTATED          0
  CGREF1 WILD-TYPE        3
D409V3, multiclass
           clus
vv          CGREF1 MUTATED CGREF1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CGREF1 MUTATED    0  0     6
  CGREF1 WILD-TYPE  5 17    96
D409V4, multiclass
       clus
vv      CGREF1 MUTATED CGREF1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V5, binary
                  cls
clus                0  1
  CGREF1 MUTATED    2  4
  CGREF1 WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CGREF1 MUTATED      2    4
  CGREF1 WILD-TYPE   33   85
   clus
vv  CGREF1 MUTATED CGREF1 WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D409V6, binary
                  cls
clus                0  1
  CGREF1 MUTATED    4  0
  CGREF1 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CGREF1 MUTATED      4    0
  CGREF1 WILD-TYPE   53    3
   clus
vv  CGREF1 MUTATED CGREF1 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D409V7, binary
                  cls
clus                0  1
  CGREF1 MUTATED    1  5
  CGREF1 WILD-TYPE 50 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CGREF1 MUTATED      1    5
  CGREF1 WILD-TYPE   50   70
        clus
vv       CGREF1 MUTATED CGREF1 WILD-TYPE
  FEMALE              1               50
  MALE                5               70
[1] 2 2
[1] FALSE
D409V8, binary
                  cls
clus                0  1
  CGREF1 MUTATED    5  1
  CGREF1 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CGREF1 MUTATED      5    1
  CGREF1 WILD-TYPE   83   29
     clus
vv    CGREF1 MUTATED CGREF1 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CGREF1 MUTATED                                     4
  CGREF1 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CGREF1 MUTATED                                       2
  CGREF1 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CGREF1 MUTATED                                                  0
  CGREF1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CGREF1 MUTATED                                     0
  CGREF1 WILD-TYPE                                   1
D409V9, multiclass
                                                  clus
vv                                                 CGREF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CGREF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V10, continuous
D409V11, continuous
[1] "Remove cluster labels:" "CGREF1 MUTATED"        
clus
  CGREF1 MUTATED CGREF1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AABE       TCGA-2J-AABF 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" "CGREF1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CGREF1 MUTATED    4  1  0  0
  CGREF1 WILD-TYPE 76 34  4  2
D409V12, multiclass
    clus
vv   CGREF1 MUTATED CGREF1 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CGREF1 MUTATED       0                         0     6
  CGREF1 WILD-TYPE     6                         5   108
D409V14, multiclass
                           clus
vv                          CGREF1 MUTATED CGREF1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V15, binary
                  cls
clus                0  1
  CGREF1 MUTATED    0  4
  CGREF1 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CGREF1 MUTATED      0    4
  CGREF1 WILD-TYPE    5   87
                        clus
vv                       CGREF1 MUTATED CGREF1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(410) Variable = ZNF780A MUTATION ANALYSIS
D410V1, survival
                   sevent
clus2                0  1
  ZNF780A MUTATED    3  4
  ZNF780A WILD-TYPE 60 58
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                7               118 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                4                58 
$`ZNF780A MUTATED`
TCGA-IB-A5SS TCGA-US-A77E TCGA-2L-AAQA TCGA-HZ-A8P1 TCGA-IB-8126 TCGA-Q3-A5QY 
       15.12        14.14         4.70         0.23        15.19        13.68 
TCGA-US-A779 
       16.80 

$`ZNF780A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL 
        8.02        15.78         1.08        12.92        17.26        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26        10.85        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       19.82        36.69        41.33        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G 
        3.12        15.32         9.40         0.30        39.98         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ZNF780A MUTATED ZNF780A WILD-TYPE 
             0.23              0.26 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            16.80             90.12 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            14.14             15.45 
[1] "0.2 - 16.8 (14.1)" "0.3 - 90.1 (15.4)"
[1] "hr=" "2"  
D410V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF780A MUTATED         0        0        1         0         5         1
  ZNF780A WILD-TYPE       1        3       11        19        77         3
                   vv
clus                STAGE IV
  ZNF780A MUTATED          0
  ZNF780A WILD-TYPE        3
D410V3, multiclass
           clus
vv          ZNF780A MUTATED ZNF780A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               5                77
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ZNF780A MUTATED    0  1     6
  ZNF780A WILD-TYPE  5 16    96
D410V4, multiclass
       clus
vv      ZNF780A MUTATED ZNF780A WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V5, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    1  6
  ZNF780A WILD-TYPE 34 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      1    6
  ZNF780A WILD-TYPE   34   83
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               1                34
  1               6                83
[1] 2 2
[1] FALSE
D410V6, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    2  0
  ZNF780A WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      2    0
  ZNF780A WILD-TYPE   55    3
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D410V7, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    3  4
  ZNF780A WILD-TYPE 48 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      3    4
  ZNF780A WILD-TYPE   48   71
        clus
vv       ZNF780A MUTATED ZNF780A WILD-TYPE
  FEMALE               3                48
  MALE                 4                71
[1] 2 2
[1] FALSE
D410V8, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    5  0
  ZNF780A WILD-TYPE 83 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      5    0
  ZNF780A WILD-TYPE   83   30
     clus
vv    ZNF780A MUTATED ZNF780A WILD-TYPE
  NO                5                83
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF780A MUTATED                                     6
  ZNF780A WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF780A MUTATED                                       1
  ZNF780A WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF780A MUTATED                                                  0
  ZNF780A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF780A MUTATED                                     0
  ZNF780A WILD-TYPE                                   1
D410V9, multiclass
                                                  clus
vv                                                 ZNF780A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ZNF780A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V10, continuous
D410V11, continuous
                   vv
clus                R0 R1 R2 RX
  ZNF780A MUTATED    4  3  0  0
  ZNF780A WILD-TYPE 76 32  4  2
D410V12, multiclass
    clus
vv   ZNF780A MUTATED ZNF780A WILD-TYPE
  R0               4                76
  R1               3                32
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780A MUTATED       0                         0     7
  ZNF780A WILD-TYPE     6                         5   107
D410V14, multiclass
                           clus
vv                          ZNF780A MUTATED ZNF780A WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   7               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V15, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    0  6
  ZNF780A WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      0    6
  ZNF780A WILD-TYPE    5   85
                        clus
vv                       ZNF780A MUTATED ZNF780A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(411) Variable = ADC MUTATION ANALYSIS
D411V1, survival
               sevent
clus2            0  1
  ADC MUTATED    1  2
  ADC WILD-TYPE 62 60
  ADC MUTATED ADC WILD-TYPE 
            3           122 
  ADC MUTATED ADC WILD-TYPE 
            2            60 
$`ADC MUTATED`
TCGA-IB-AAUQ TCGA-US-A776 TCGA-US-A77J 
        6.02        39.98        18.67 

$`ADC WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86        14.17        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
       15.32         9.40         0.30        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ADC MUTATED ADC WILD-TYPE 
         6.02          0.23 
  ADC MUTATED ADC WILD-TYPE 
        39.98         90.12 
  ADC MUTATED ADC WILD-TYPE 
       18.670        15.205 
[1] "6.0 - 40.0 (18.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D411V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ADC MUTATED         0        0        0         1         2         0
  ADC WILD-TYPE       1        3       12        18        80         4
               vv
clus            STAGE IV
  ADC MUTATED          0
  ADC WILD-TYPE        3
D411V3, multiclass
           clus
vv          ADC MUTATED ADC WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           1            18
  STAGE IIB           2            80
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  ADC MUTATED    0  0     3
  ADC WILD-TYPE  5 17    99
D411V4, multiclass
       clus
vv      ADC MUTATED ADC WILD-TYPE
  T1              0             5
  T2              0            17
  T3+T4           3            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V5, binary
               cls
clus             0  1
  ADC MUTATED    1  2
  ADC WILD-TYPE 34 87
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      1    2
  ADC WILD-TYPE   34   87
   clus
vv  ADC MUTATED ADC WILD-TYPE
  0           1            34
  1           2            87
[1] 2 2
[1] FALSE
D411V6, binary
               cls
clus             0  1
  ADC MUTATED    1  0
  ADC WILD-TYPE 56  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      1    0
  ADC WILD-TYPE   56    3
   clus
vv  ADC MUTATED ADC WILD-TYPE
  0           1            56
  1           0             3
[1] 2 2
[1] FALSE
D411V7, binary
               cls
clus             0  1
  ADC MUTATED    1  2
  ADC WILD-TYPE 50 73
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      1    2
  ADC WILD-TYPE   50   73
        clus
vv       ADC MUTATED ADC WILD-TYPE
  FEMALE           1            50
  MALE             2            73
[1] 2 2
[1] FALSE
D411V8, binary
               cls
clus             0  1
  ADC MUTATED    2  0
  ADC WILD-TYPE 86 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      2    0
  ADC WILD-TYPE   86   30
     clus
vv    ADC MUTATED ADC WILD-TYPE
  NO            2            86
  YES           0            30
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ADC MUTATED                                     2
  ADC WILD-TYPE                                 103
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ADC MUTATED                                       0
  ADC WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ADC MUTATED                                                  1
  ADC WILD-TYPE                                                0
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  ADC MUTATED                                     0
  ADC WILD-TYPE                                   1
D411V9, multiclass
                                                  clus
vv                                                 ADC MUTATED ADC WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        2           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           1             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V10, continuous
[1] "Remove cluster labels:" "ADC MUTATED"           
clus
  ADC MUTATED ADC WILD-TYPE 
            1            38 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-IB-7651    TCGA-IB-7885    TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-OE-A75W    TCGA-XN-A8T5    TCGA-YY-A8LH 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
D411V11, continuous
[1] "Remove cluster labels:" "ADC MUTATED"           
clus
  ADC MUTATED ADC WILD-TYPE 
            1            32 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7651 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI 
"ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" "ADC WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"ADC WILD-TYPE" "ADC WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  ADC MUTATED    2  1  0  0
  ADC WILD-TYPE 78 34  4  2
D411V12, multiclass
    clus
vv   ADC MUTATED ADC WILD-TYPE
  R0           2            78
  R1           1            34
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADC MUTATED       0                         0     3
  ADC WILD-TYPE     6                         5   111
D411V14, multiclass
                           clus
vv                          ADC MUTATED ADC WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V15, binary
               cls
clus             0  1
  ADC MUTATED    0  3
  ADC WILD-TYPE  5 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADC MUTATED      0    3
  ADC WILD-TYPE    5   88
                        clus
vv                       ADC MUTATED ADC WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3            88
[1] 2 2
[1] FALSE

Clustering(412) Variable = FHDC1 MUTATION ANALYSIS
D412V1, survival
                 sevent
clus2              0  1
  FHDC1 MUTATED    3  3
  FHDC1 WILD-TYPE 60 59
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              6             119 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              3              59 
$`FHDC1 MUTATED`
TCGA-3A-A9IS TCGA-F2-A7TX TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-IB-7651 TCGA-XN-A8T3 
       32.81         3.12        22.06        20.19        19.82        31.27 

$`FHDC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  FHDC1 MUTATED FHDC1 WILD-TYPE 
           3.12            0.23 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
          32.81           90.12 
  FHDC1 MUTATED FHDC1 WILD-TYPE 
         21.125          15.120 
[1] "3.1 - 32.8 (21.1)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.3"
D412V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FHDC1 MUTATED         0        0        2         1         3         0
  FHDC1 WILD-TYPE       1        3       10        18        79         4
                 vv
clus              STAGE IV
  FHDC1 MUTATED          0
  FHDC1 WILD-TYPE        3
D412V3, multiclass
           clus
vv          FHDC1 MUTATED FHDC1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FHDC1 MUTATED    0  2     4
  FHDC1 WILD-TYPE  5 15    98
D412V4, multiclass
       clus
vv      FHDC1 MUTATED FHDC1 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V5, binary
                 cls
clus               0  1
  FHDC1 MUTATED    3  3
  FHDC1 WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      3    3
  FHDC1 WILD-TYPE   32   86
   clus
vv  FHDC1 MUTATED FHDC1 WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D412V6, binary
                 cls
clus               0  1
  FHDC1 MUTATED    3  0
  FHDC1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      3    0
  FHDC1 WILD-TYPE   54    3
   clus
vv  FHDC1 MUTATED FHDC1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D412V7, binary
                 cls
clus               0  1
  FHDC1 MUTATED    1  5
  FHDC1 WILD-TYPE 50 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      1    5
  FHDC1 WILD-TYPE   50   70
        clus
vv       FHDC1 MUTATED FHDC1 WILD-TYPE
  FEMALE             1              50
  MALE               5              70
[1] 2 2
[1] FALSE
D412V8, binary
                 cls
clus               0  1
  FHDC1 MUTATED    5  1
  FHDC1 WILD-TYPE 83 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      5    1
  FHDC1 WILD-TYPE   83   29
     clus
vv    FHDC1 MUTATED FHDC1 WILD-TYPE
  NO              5              83
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FHDC1 MUTATED                                     4
  FHDC1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FHDC1 MUTATED                                       2
  FHDC1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FHDC1 MUTATED                                                  0
  FHDC1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FHDC1 MUTATED                                     0
  FHDC1 WILD-TYPE                                   1
D412V9, multiclass
                                                  clus
vv                                                 FHDC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FHDC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V10, continuous
[1] "Remove cluster labels:" "FHDC1 MUTATED"         
clus
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-YY-A8LH 
"FHDC1 WILD-TYPE" 
D412V11, continuous
[1] "Remove cluster labels:" "FHDC1 MUTATED"         
clus
  FHDC1 MUTATED FHDC1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" "FHDC1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  FHDC1 MUTATED    4  2  0  0
  FHDC1 WILD-TYPE 76 33  4  2
D412V12, multiclass
    clus
vv   FHDC1 MUTATED FHDC1 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FHDC1 MUTATED       0                         0     6
  FHDC1 WILD-TYPE     6                         5   108
D412V14, multiclass
                           clus
vv                          FHDC1 MUTATED FHDC1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V15, binary
                 cls
clus               0  1
  FHDC1 MUTATED    1  4
  FHDC1 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHDC1 MUTATED      1    4
  FHDC1 WILD-TYPE    4   87
                        clus
vv                       FHDC1 MUTATED FHDC1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(413) Variable = ZNF709 MUTATION ANALYSIS
D413V1, survival
                  sevent
clus2               0  1
  ZNF709 MUTATED    6  3
  ZNF709 WILD-TYPE 57 59
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               9              116 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               3               59 
$`ZNF709 MUTATED`
TCGA-3A-A9IL TCGA-2J-AABE TCGA-2L-AAQL TCGA-3A-A9IV TCGA-IB-7651 TCGA-IB-A7M4 
       90.12        22.22         9.60        36.26        19.82        15.88 
TCGA-IB-AAUM TCGA-IB-AAUQ TCGA-Q3-A5QY 
        0.26         6.02        13.68 

$`ZNF709 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUN TCGA-IB-AAUO 
       20.88        21.90         1.35         8.22         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
       14.17        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
            0.26             0.23 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           90.12            75.12 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
          15.880           15.205 
[1] "0.3 - 90.1 (15.9)" "0.2 - 75.1 (15.2)"
[1] "hr=" "1.7"
D413V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF709 MUTATED         1        0        1         1         6         0
  ZNF709 WILD-TYPE       0        3       11        18        76         4
                  vv
clus               STAGE IV
  ZNF709 MUTATED          0
  ZNF709 WILD-TYPE        3
D413V3, multiclass
           clus
vv          ZNF709 MUTATED ZNF709 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF709 MUTATED    1  2     6
  ZNF709 WILD-TYPE  4 15    96
D413V4, multiclass
       clus
vv      ZNF709 MUTATED ZNF709 WILD-TYPE
  T1                 1                4
  T2                 2               15
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V5, binary
                  cls
clus                0  1
  ZNF709 MUTATED    2  6
  ZNF709 WILD-TYPE 33 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      2    6
  ZNF709 WILD-TYPE   33   83
   clus
vv  ZNF709 MUTATED ZNF709 WILD-TYPE
  0              2               33
  1              6               83
[1] 2 2
[1] FALSE
D413V6, binary
                  cls
clus                0  1
  ZNF709 MUTATED    4  0
  ZNF709 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      4    0
  ZNF709 WILD-TYPE   53    3
   clus
vv  ZNF709 MUTATED ZNF709 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D413V7, binary
                  cls
clus                0  1
  ZNF709 MUTATED    3  6
  ZNF709 WILD-TYPE 48 69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      3    6
  ZNF709 WILD-TYPE   48   69
        clus
vv       ZNF709 MUTATED ZNF709 WILD-TYPE
  FEMALE              3               48
  MALE                6               69
[1] 2 2
[1] FALSE
D413V8, binary
                  cls
clus                0  1
  ZNF709 MUTATED    8  1
  ZNF709 WILD-TYPE 80 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      8    1
  ZNF709 WILD-TYPE   80   29
     clus
vv    ZNF709 MUTATED ZNF709 WILD-TYPE
  NO               8               80
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF709 MUTATED                                     7
  ZNF709 WILD-TYPE                                  98
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF709 MUTATED                                       2
  ZNF709 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF709 MUTATED                                                  0
  ZNF709 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF709 MUTATED                                     0
  ZNF709 WILD-TYPE                                   1
D413V9, multiclass
                                                  clus
vv                                                 ZNF709 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF709 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V10, continuous
D413V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF709 MUTATED    7  1  0  1
  ZNF709 WILD-TYPE 73 34  4  1
D413V12, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  R0              7               73
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF709 MUTATED       0                         0     9
  ZNF709 WILD-TYPE     6                         5   105
D413V14, multiclass
                           clus
vv                          ZNF709 MUTATED ZNF709 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V15, binary
                  cls
clus                0  1
  ZNF709 MUTATED    0  7
  ZNF709 WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    7
  ZNF709 WILD-TYPE    5   84
                        clus
vv                       ZNF709 MUTATED ZNF709 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(414) Variable = OR2J2 MUTATION ANALYSIS
D414V1, survival
                 sevent
clus2              0  1
  OR2J2 MUTATED    3  1
  OR2J2 WILD-TYPE 60 61
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              4             121 
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              1              61 
$`OR2J2 MUTATED`
TCGA-3A-A9IO TCGA-3A-A9J0 TCGA-HZ-A77P TCGA-IB-7651 
       63.85        24.43        10.85        19.82 

$`OR2J2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OR2J2 MUTATED OR2J2 WILD-TYPE 
          10.85            0.23 
  OR2J2 MUTATED OR2J2 WILD-TYPE 
          63.85           90.12 
  OR2J2 MUTATED OR2J2 WILD-TYPE 
         22.125          15.190 
[1] "10.8 - 63.9 (22.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3"  
D414V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR2J2 MUTATED         0        0        0         0         3         0
  OR2J2 WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  OR2J2 MUTATED          0
  OR2J2 WILD-TYPE        3
D414V3, multiclass
           clus
vv          OR2J2 MUTATED OR2J2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  OR2J2 MUTATED    0  0     3
  OR2J2 WILD-TYPE  5 17    99
D414V4, multiclass
       clus
vv      OR2J2 MUTATED OR2J2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V5, binary
                 cls
clus               0  1
  OR2J2 MUTATED    0  3
  OR2J2 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J2 MUTATED      0    3
  OR2J2 WILD-TYPE   35   86
   clus
vv  OR2J2 MUTATED OR2J2 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D414V6, binary
                 cls
clus               0  1
  OR2J2 MUTATED    1  0
  OR2J2 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J2 MUTATED      1    0
  OR2J2 WILD-TYPE   56    3
   clus
vv  OR2J2 MUTATED OR2J2 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D414V7, binary
                 cls
clus               0  1
  OR2J2 MUTATED    1  3
  OR2J2 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J2 MUTATED      1    3
  OR2J2 WILD-TYPE   50   72
        clus
vv       OR2J2 MUTATED OR2J2 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D414V8, binary
                 cls
clus               0  1
  OR2J2 MUTATED    4  0
  OR2J2 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J2 MUTATED      4    0
  OR2J2 WILD-TYPE   84   30
     clus
vv    OR2J2 MUTATED OR2J2 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR2J2 MUTATED                                     2
  OR2J2 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR2J2 MUTATED                                       2
  OR2J2 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR2J2 MUTATED                                                  0
  OR2J2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR2J2 MUTATED                                     0
  OR2J2 WILD-TYPE                                   1
D414V9, multiclass
                                                  clus
vv                                                 OR2J2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 OR2J2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V10, continuous
[1] "Remove cluster labels:" "OR2J2 MUTATED"         
clus
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
D414V11, continuous
[1] "Remove cluster labels:" "OR2J2 MUTATED"         
clus
  OR2J2 MUTATED OR2J2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" "OR2J2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR2J2 MUTATED    4  0  0  0
  OR2J2 WILD-TYPE 76 35  4  2
D414V12, multiclass
    clus
vv   OR2J2 MUTATED OR2J2 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2J2 MUTATED       0                         0     4
  OR2J2 WILD-TYPE     6                         5   110
D414V14, multiclass
                           clus
vv                          OR2J2 MUTATED OR2J2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V15, binary
                 cls
clus               0  1
  OR2J2 MUTATED    0  4
  OR2J2 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2J2 MUTATED      0    4
  OR2J2 WILD-TYPE    5   87
                        clus
vv                       OR2J2 MUTATED OR2J2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(415) Variable = PLD2 MUTATION ANALYSIS
D415V1, survival
                sevent
clus2             0  1
  PLD2 MUTATED    1  2
  PLD2 WILD-TYPE 62 60
  PLD2 MUTATED PLD2 WILD-TYPE 
             3            122 
  PLD2 MUTATED PLD2 WILD-TYPE 
             2             60 
$`PLD2 MUTATED`
TCGA-FB-AAQ6 TCGA-S4-A8RO TCGA-IB-7651 
        8.02        17.26        19.82 

$`PLD2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PLD2 MUTATED PLD2 WILD-TYPE 
          8.02           0.23 
  PLD2 MUTATED PLD2 WILD-TYPE 
         19.82          90.12 
  PLD2 MUTATED PLD2 WILD-TYPE 
        17.260         15.205 
[1] "8.0 - 19.8 (17.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D415V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PLD2 MUTATED         0        1        0         0         2         0
  PLD2 WILD-TYPE       1        2       12        19        80         4
                vv
clus             STAGE IV
  PLD2 MUTATED          0
  PLD2 WILD-TYPE        3
D415V3, multiclass
           clus
vv          PLD2 MUTATED PLD2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  PLD2 MUTATED     1   0     2
  PLD2 WILD-TYPE   4  17   100
D415V4, multiclass
       clus
vv      PLD2 MUTATED PLD2 WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V5, binary
                cls
clus              0  1
  PLD2 MUTATED    1  2
  PLD2 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD2 MUTATED      1    2
  PLD2 WILD-TYPE   34   87
   clus
vv  PLD2 MUTATED PLD2 WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D415V6, binary
                cls
clus              0  1
  PLD2 MUTATED    1  0
  PLD2 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD2 MUTATED      1    0
  PLD2 WILD-TYPE   56    3
   clus
vv  PLD2 MUTATED PLD2 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D415V7, binary
                cls
clus              0  1
  PLD2 MUTATED    2  1
  PLD2 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD2 MUTATED      2    1
  PLD2 WILD-TYPE   49   74
        clus
vv       PLD2 MUTATED PLD2 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D415V8, binary
                cls
clus              0  1
  PLD2 MUTATED    2  1
  PLD2 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD2 MUTATED      2    1
  PLD2 WILD-TYPE   86   29
     clus
vv    PLD2 MUTATED PLD2 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLD2 MUTATED                                     3
  PLD2 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLD2 MUTATED                                       0
  PLD2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLD2 MUTATED                                                  0
  PLD2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PLD2 MUTATED                                     0
  PLD2 WILD-TYPE                                   1
D415V9, multiclass
                                                  clus
vv                                                 PLD2 MUTATED PLD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V10, continuous
[1] "Remove cluster labels:" "PLD2 MUTATED"          
clus
  PLD2 MUTATED PLD2 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
D415V11, continuous
[1] "Remove cluster labels:" "PLD2 MUTATED"          
clus
  PLD2 MUTATED PLD2 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" "PLD2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PLD2 MUTATED    2  1  0  0
  PLD2 WILD-TYPE 78 34  4  2
D415V12, multiclass
    clus
vv   PLD2 MUTATED PLD2 WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLD2 MUTATED       0                         0     3
  PLD2 WILD-TYPE     6                         5   111
D415V14, multiclass
                           clus
vv                          PLD2 MUTATED PLD2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V15, binary
                cls
clus              0  1
  PLD2 MUTATED    0  3
  PLD2 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD2 MUTATED      0    3
  PLD2 WILD-TYPE    5   88
                        clus
vv                       PLD2 MUTATED PLD2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(416) Variable = SYCP1 MUTATION ANALYSIS
D416V1, survival
                 sevent
clus2              0  1
  SYCP1 MUTATED    3  2
  SYCP1 WILD-TYPE 60 60
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              5             120 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              2              60 
$`SYCP1 MUTATED`
TCGA-3A-A9IJ TCGA-2J-AABO TCGA-2L-AAQI TCGA-FB-AAQ3 TCGA-YB-A89D 
       60.95        14.47         3.39         1.02        11.51 

$`SYCP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 
       12.53        23.54        15.55         4.04         5.03        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  SYCP1 MUTATED SYCP1 WILD-TYPE 
           1.02            0.23 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
          60.95           90.12 
  SYCP1 MUTATED SYCP1 WILD-TYPE 
         11.510          15.335 
[1] "1.0 - 61.0 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D416V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYCP1 MUTATED         0        0        1         0         4         0
  SYCP1 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  SYCP1 MUTATED          0
  SYCP1 WILD-TYPE        3
D416V3, multiclass
           clus
vv          SYCP1 MUTATED SYCP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SYCP1 MUTATED    0  1     4
  SYCP1 WILD-TYPE  5 16    98
D416V4, multiclass
       clus
vv      SYCP1 MUTATED SYCP1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V5, binary
                 cls
clus               0  1
  SYCP1 MUTATED    1  4
  SYCP1 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      1    4
  SYCP1 WILD-TYPE   34   85
   clus
vv  SYCP1 MUTATED SYCP1 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D416V6, binary
                 cls
clus               0  1
  SYCP1 MUTATED    1  0
  SYCP1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      1    0
  SYCP1 WILD-TYPE   56    3
   clus
vv  SYCP1 MUTATED SYCP1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D416V7, binary
                 cls
clus               0  1
  SYCP1 MUTATED    1  4
  SYCP1 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      1    4
  SYCP1 WILD-TYPE   50   71
        clus
vv       SYCP1 MUTATED SYCP1 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D416V8, binary
                 cls
clus               0  1
  SYCP1 MUTATED    3  2
  SYCP1 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      3    2
  SYCP1 WILD-TYPE   85   28
     clus
vv    SYCP1 MUTATED SYCP1 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYCP1 MUTATED                                     4
  SYCP1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYCP1 MUTATED                                       1
  SYCP1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYCP1 MUTATED                                                  0
  SYCP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYCP1 MUTATED                                     0
  SYCP1 WILD-TYPE                                   1
D416V9, multiclass
                                                  clus
vv                                                 SYCP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SYCP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V10, continuous
[1] "Remove cluster labels:" "SYCP1 MUTATED"         
clus
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              2              37 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-YY-A8LH 
"SYCP1 WILD-TYPE" 
D416V11, continuous
[1] "Remove cluster labels:" "SYCP1 MUTATED"         
clus
  SYCP1 MUTATED SYCP1 WILD-TYPE 
              2              31 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX      TCGA-FB-A5VM 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" "SYCP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SYCP1 MUTATED    4  1  0  0
  SYCP1 WILD-TYPE 76 34  4  2
D416V12, multiclass
    clus
vv   SYCP1 MUTATED SYCP1 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYCP1 MUTATED       0                         0     5
  SYCP1 WILD-TYPE     6                         5   109
D416V14, multiclass
                           clus
vv                          SYCP1 MUTATED SYCP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V15, binary
                 cls
clus               0  1
  SYCP1 MUTATED    0  3
  SYCP1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP1 MUTATED      0    3
  SYCP1 WILD-TYPE    5   88
                        clus
vv                       SYCP1 MUTATED SYCP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(417) Variable = RUNX2 MUTATION ANALYSIS
D417V1, survival
                 sevent
clus2              0  1
  RUNX2 MUTATED    4  3
  RUNX2 WILD-TYPE 59 59
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              7             118 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              3              59 
$`RUNX2 MUTATED`
TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5ST TCGA-LB-A9Q5 TCGA-US-A77G 
       17.00        19.82        15.19        20.88        10.29         0.39 
TCGA-YH-A8SY 
       12.76 

$`RUNX2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        66.28        15.35 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
           0.39            0.23 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          20.88           90.12 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          15.19           15.27 
[1] "0.4 - 20.9 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D417V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RUNX2 MUTATED         0        0        0         1         4         2
  RUNX2 WILD-TYPE       1        3       12        18        78         2
                 vv
clus              STAGE IV
  RUNX2 MUTATED          0
  RUNX2 WILD-TYPE        3
D417V3, multiclass
           clus
vv          RUNX2 MUTATED RUNX2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             2               2
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RUNX2 MUTATED    0  0     7
  RUNX2 WILD-TYPE  5 17    95
D417V4, multiclass
       clus
vv      RUNX2 MUTATED RUNX2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             7              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V5, binary
                 cls
clus               0  1
  RUNX2 MUTATED    1  6
  RUNX2 WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      1    6
  RUNX2 WILD-TYPE   34   83
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D417V6, binary
                 cls
clus               0  1
  RUNX2 MUTATED    4  0
  RUNX2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      4    0
  RUNX2 WILD-TYPE   53    3
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D417V7, binary
                 cls
clus               0  1
  RUNX2 MUTATED    5  2
  RUNX2 WILD-TYPE 46 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      5    2
  RUNX2 WILD-TYPE   46   73
        clus
vv       RUNX2 MUTATED RUNX2 WILD-TYPE
  FEMALE             5              46
  MALE               2              73
[1] 2 2
[1] FALSE
D417V8, binary
                 cls
clus               0  1
  RUNX2 MUTATED    5  2
  RUNX2 WILD-TYPE 83 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      5    2
  RUNX2 WILD-TYPE   83   28
     clus
vv    RUNX2 MUTATED RUNX2 WILD-TYPE
  NO              5              83
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RUNX2 MUTATED                                     6
  RUNX2 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RUNX2 MUTATED                                       0
  RUNX2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RUNX2 MUTATED                                                  0
  RUNX2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RUNX2 MUTATED                                     0
  RUNX2 WILD-TYPE                                   1
D417V9, multiclass
                                                  clus
vv                                                 RUNX2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RUNX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V10, continuous
D417V11, continuous
                 vv
clus              R0 R1 R2 RX
  RUNX2 MUTATED    4  2  0  0
  RUNX2 WILD-TYPE 76 33  4  2
D417V12, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX2 MUTATED       0                         0     7
  RUNX2 WILD-TYPE     6                         5   107
D417V14, multiclass
                           clus
vv                          RUNX2 MUTATED RUNX2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V15, binary
                 cls
clus               0  1
  RUNX2 MUTATED    0  7
  RUNX2 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      0    7
  RUNX2 WILD-TYPE    5   84
                        clus
vv                       RUNX2 MUTATED RUNX2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(418) Variable = KRTAP5-3 MUTATION ANALYSIS
D418V1, survival
                    sevent
clus2                 0  1
  KRTAP5-3 MUTATED    4  3
  KRTAP5-3 WILD-TYPE 59 59
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 7                118 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 3                 59 
$`KRTAP5-3 MUTATED`
TCGA-2J-AAB6 TCGA-HV-AA8X TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-LB-A8F3 TCGA-US-A779 
        9.63        17.49        10.85        19.82        12.46        16.80 
TCGA-XD-AAUH 
       12.99 

$`KRTAP5-3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        13.81        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
              9.63               0.23 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             19.82              90.12 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             12.99              15.27 
[1] "9.6 - 19.8 (13.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D418V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KRTAP5-3 MUTATED         0        0        0         2         4         0
  KRTAP5-3 WILD-TYPE       1        3       12        17        78         4
                    vv
clus                 STAGE IV
  KRTAP5-3 MUTATED          1
  KRTAP5-3 WILD-TYPE        2
D418V3, multiclass
           clus
vv          KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                2                 17
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 1                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KRTAP5-3 MUTATED    0  1     6
  KRTAP5-3 WILD-TYPE  5 16    96
D418V4, multiclass
       clus
vv      KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V5, binary
                    cls
clus                  0  1
  KRTAP5-3 MUTATED    3  4
  KRTAP5-3 WILD-TYPE 32 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      3    4
  KRTAP5-3 WILD-TYPE   32   85
   clus
vv  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  0                3                 32
  1                4                 85
[1] 2 2
[1] FALSE
D418V6, binary
                    cls
clus                  0  1
  KRTAP5-3 MUTATED    2  1
  KRTAP5-3 WILD-TYPE 55  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      2    1
  KRTAP5-3 WILD-TYPE   55    2
   clus
vv  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  0                2                 55
  1                1                  2
[1] 2 2
[1] FALSE
D418V7, binary
                    cls
clus                  0  1
  KRTAP5-3 MUTATED    4  3
  KRTAP5-3 WILD-TYPE 47 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    3
  KRTAP5-3 WILD-TYPE   47   72
        clus
vv       KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  FEMALE                4                 47
  MALE                  3                 72
[1] 2 2
[1] FALSE
D418V8, binary
                    cls
clus                  0  1
  KRTAP5-3 MUTATED    4  2
  KRTAP5-3 WILD-TYPE 84 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    2
  KRTAP5-3 WILD-TYPE   84   28
     clus
vv    KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  NO                 4                 84
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRTAP5-3 MUTATED                                     5
  KRTAP5-3 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRTAP5-3 MUTATED                                       2
  KRTAP5-3 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRTAP5-3 MUTATED                                                  0
  KRTAP5-3 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KRTAP5-3 MUTATED                                     0
  KRTAP5-3 WILD-TYPE                                   1
D418V9, multiclass
                                                  clus
vv                                                 KRTAP5-3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KRTAP5-3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V10, continuous
D418V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KRTAP5-3 MUTATED    5  0  2  0
  KRTAP5-3 WILD-TYPE 75 35  2  2
D418V12, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  R0                5                 75
  R1                0                 35
  R2                2                  2
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-3 MUTATED       1                         1     5
  KRTAP5-3 WILD-TYPE     5                         4   109
D418V14, multiclass
                           clus
vv                          KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V15, binary
                    cls
clus                  0  1
  KRTAP5-3 MUTATED    0  5
  KRTAP5-3 WILD-TYPE  5 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      0    5
  KRTAP5-3 WILD-TYPE    5   86
                        clus
vv                       KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                 86
[1] 2 2
[1] FALSE

Clustering(419) Variable = SSBP3 MUTATION ANALYSIS
D419V1, survival
                 sevent
clus2              0  1
  SSBP3 MUTATED    0  3
  SSBP3 WILD-TYPE 63 59
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             122 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3              59 
$`SSBP3 MUTATED`
TCGA-FB-AAQ2 TCGA-IB-A5SO TCGA-OE-A75W 
        5.03        12.00         8.78 

$`SSBP3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SSBP3 MUTATED SSBP3 WILD-TYPE 
           5.03            0.23 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          12.00           90.12 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          8.780          15.335 
[1] "5.0 - 12.0 (8.8)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "5.7"
D419V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SSBP3 MUTATED         0        0        0         1         2         0
  SSBP3 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  SSBP3 MUTATED          0
  SSBP3 WILD-TYPE        3
D419V3, multiclass
           clus
vv          SSBP3 MUTATED SSBP3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SSBP3 MUTATED    0  0     3
  SSBP3 WILD-TYPE  5 17    99
D419V4, multiclass
       clus
vv      SSBP3 MUTATED SSBP3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V5, binary
                 cls
clus               0  1
  SSBP3 MUTATED    1  2
  SSBP3 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   34   87
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D419V6, binary
                 cls
clus               0  1
  SSBP3 MUTATED    2  0
  SSBP3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    0
  SSBP3 WILD-TYPE   55    3
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D419V7, binary
                 cls
clus               0  1
  SSBP3 MUTATED    1  2
  SSBP3 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   50   73
        clus
vv       SSBP3 MUTATED SSBP3 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D419V8, binary
                 cls
clus               0  1
  SSBP3 MUTATED    2  1
  SSBP3 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    1
  SSBP3 WILD-TYPE   86   29
     clus
vv    SSBP3 MUTATED SSBP3 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SSBP3 MUTATED                                     3
  SSBP3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SSBP3 MUTATED                                       0
  SSBP3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SSBP3 MUTATED                                                  0
  SSBP3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SSBP3 MUTATED                                     0
  SSBP3 WILD-TYPE                                   1
D419V9, multiclass
                                                  clus
vv                                                 SSBP3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SSBP3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V10, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
D419V11, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SSBP3 MUTATED    2  1  0  0
  SSBP3 WILD-TYPE 78 34  4  2
D419V12, multiclass
    clus
vv   SSBP3 MUTATED SSBP3 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSBP3 MUTATED       0                         0     3
  SSBP3 WILD-TYPE     6                         5   111
D419V14, multiclass
                           clus
vv                          SSBP3 MUTATED SSBP3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V15, binary
                 cls
clus               0  1
  SSBP3 MUTATED    0  2
  SSBP3 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      0    2
  SSBP3 WILD-TYPE    5   89
                        clus
vv                       SSBP3 MUTATED SSBP3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(420) Variable = ZNF347 MUTATION ANALYSIS
D420V1, survival
                  sevent
clus2               0  1
  ZNF347 MUTATED    3  2
  ZNF347 WILD-TYPE 60 60
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               5              120 
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               2               60 
$`ZNF347 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABH TCGA-FB-AAQ1 TCGA-IB-7651 TCGA-XN-A8T3 
       23.97        42.31         4.04        19.82        31.27 

$`ZNF347 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        22.72        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        23.67        11.51        12.76        66.28        15.35 

  ZNF347 MUTATED ZNF347 WILD-TYPE 
            4.04             0.23 
  ZNF347 MUTATED ZNF347 WILD-TYPE 
           42.31            90.12 
  ZNF347 MUTATED ZNF347 WILD-TYPE 
          23.970           15.155 
[1] "4.0 - 42.3 (24.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D420V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF347 MUTATED         0        0        1         1         3         0
  ZNF347 WILD-TYPE       1        3       11        18        79         4
                  vv
clus               STAGE IV
  ZNF347 MUTATED          0
  ZNF347 WILD-TYPE        3
D420V3, multiclass
           clus
vv          ZNF347 MUTATED ZNF347 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF347 MUTATED    0  2     3
  ZNF347 WILD-TYPE  5 15    99
D420V4, multiclass
       clus
vv      ZNF347 MUTATED ZNF347 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V5, binary
                  cls
clus                0  1
  ZNF347 MUTATED    2  3
  ZNF347 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF347 MUTATED      2    3
  ZNF347 WILD-TYPE   33   86
   clus
vv  ZNF347 MUTATED ZNF347 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D420V6, binary
                  cls
clus                0  1
  ZNF347 MUTATED    4  0
  ZNF347 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF347 MUTATED      4    0
  ZNF347 WILD-TYPE   53    3
   clus
vv  ZNF347 MUTATED ZNF347 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D420V7, binary
                  cls
clus                0  1
  ZNF347 MUTATED    1  4
  ZNF347 WILD-TYPE 50 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF347 MUTATED      1    4
  ZNF347 WILD-TYPE   50   71
        clus
vv       ZNF347 MUTATED ZNF347 WILD-TYPE
  FEMALE              1               50
  MALE                4               71
[1] 2 2
[1] FALSE
D420V8, binary
                  cls
clus                0  1
  ZNF347 MUTATED    4  1
  ZNF347 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF347 MUTATED      4    1
  ZNF347 WILD-TYPE   84   29
     clus
vv    ZNF347 MUTATED ZNF347 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF347 MUTATED                                     3
  ZNF347 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF347 MUTATED                                       2
  ZNF347 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF347 MUTATED                                                  0
  ZNF347 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF347 MUTATED                                     0
  ZNF347 WILD-TYPE                                   1
D420V9, multiclass
                                                  clus
vv                                                 ZNF347 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF347 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V10, continuous
[1] "Remove cluster labels:" "ZNF347 MUTATED"        
clus
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
D420V11, continuous
[1] "Remove cluster labels:" "ZNF347 MUTATED"        
clus
  ZNF347 MUTATED ZNF347 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" "ZNF347 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF347 MUTATED    3  2  0  0
  ZNF347 WILD-TYPE 77 33  4  2
D420V12, multiclass
    clus
vv   ZNF347 MUTATED ZNF347 WILD-TYPE
  R0              3               77
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF347 MUTATED       0                         0     5
  ZNF347 WILD-TYPE     6                         5   109
D420V14, multiclass
                           clus
vv                          ZNF347 MUTATED ZNF347 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V15, binary
                  cls
clus                0  1
  ZNF347 MUTATED    1  2
  ZNF347 WILD-TYPE  4 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF347 MUTATED      1    2
  ZNF347 WILD-TYPE    4   89
                        clus
vv                       ZNF347 MUTATED ZNF347 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(421) Variable = IPO13 MUTATION ANALYSIS
D421V1, survival
                 sevent
clus2              0  1
  IPO13 MUTATED    1  3
  IPO13 WILD-TYPE 62 59
  IPO13 MUTATED IPO13 WILD-TYPE 
              4             121 
  IPO13 MUTATED IPO13 WILD-TYPE 
              3              59 
$`IPO13 MUTATED`
TCGA-US-A77E TCGA-FB-A5VM TCGA-IB-7651 TCGA-US-A776 
       14.14        16.37        19.82        39.98 

$`IPO13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  IPO13 MUTATED IPO13 WILD-TYPE 
          14.14            0.23 
  IPO13 MUTATED IPO13 WILD-TYPE 
          39.98           90.12 
  IPO13 MUTATED IPO13 WILD-TYPE 
         18.095          15.190 
[1] "14.1 - 40.0 (18.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D421V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  IPO13 MUTATED         0        0        1         1         2         0
  IPO13 WILD-TYPE       1        3       11        18        80         4
                 vv
clus              STAGE IV
  IPO13 MUTATED          0
  IPO13 WILD-TYPE        3
D421V3, multiclass
           clus
vv          IPO13 MUTATED IPO13 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  IPO13 MUTATED    0  1     3
  IPO13 WILD-TYPE  5 16    99
D421V4, multiclass
       clus
vv      IPO13 MUTATED IPO13 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V5, binary
                 cls
clus               0  1
  IPO13 MUTATED    2  2
  IPO13 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO13 MUTATED      2    2
  IPO13 WILD-TYPE   33   87
   clus
vv  IPO13 MUTATED IPO13 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D421V6, binary
                 cls
clus               0  1
  IPO13 MUTATED    2  0
  IPO13 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO13 MUTATED      2    0
  IPO13 WILD-TYPE   55    3
   clus
vv  IPO13 MUTATED IPO13 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D421V7, binary
                 cls
clus               0  1
  IPO13 MUTATED    1  3
  IPO13 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO13 MUTATED      1    3
  IPO13 WILD-TYPE   50   72
        clus
vv       IPO13 MUTATED IPO13 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D421V8, binary
                 cls
clus               0  1
  IPO13 MUTATED    4  0
  IPO13 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO13 MUTATED      4    0
  IPO13 WILD-TYPE   84   30
     clus
vv    IPO13 MUTATED IPO13 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IPO13 MUTATED                                     2
  IPO13 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IPO13 MUTATED                                       1
  IPO13 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IPO13 MUTATED                                                  1
  IPO13 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  IPO13 MUTATED                                     0
  IPO13 WILD-TYPE                                   1
D421V9, multiclass
                                                  clus
vv                                                 IPO13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 IPO13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V10, continuous
[1] "Remove cluster labels:" "IPO13 MUTATED"         
clus
  IPO13 MUTATED IPO13 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-YY-A8LH 
"IPO13 WILD-TYPE" 
D421V11, continuous
[1] "Remove cluster labels:" "IPO13 MUTATED"         
clus
  IPO13 MUTATED IPO13 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"IPO13 WILD-TYPE" "IPO13 WILD-TYPE" "IPO13 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  IPO13 MUTATED    3  1  0  0
  IPO13 WILD-TYPE 77 34  4  2
D421V12, multiclass
    clus
vv   IPO13 MUTATED IPO13 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPO13 MUTATED       0                         0     4
  IPO13 WILD-TYPE     6                         5   110
D421V14, multiclass
                           clus
vv                          IPO13 MUTATED IPO13 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V15, binary
                 cls
clus               0  1
  IPO13 MUTATED    0  4
  IPO13 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO13 MUTATED      0    4
  IPO13 WILD-TYPE    5   87
                        clus
vv                       IPO13 MUTATED IPO13 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(422) Variable = ACSM4 MUTATION ANALYSIS
D422V1, survival
                 sevent
clus2              0  1
  ACSM4 MUTATED    1  3
  ACSM4 WILD-TYPE 62 59
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              4             121 
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              3              59 
$`ACSM4 MUTATED`
TCGA-2J-AABA TCGA-2L-AAQM TCGA-HZ-A77O TCGA-IB-7651 
       19.96        45.47         5.26        19.82 

$`ACSM4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ACSM4 MUTATED ACSM4 WILD-TYPE 
           5.26            0.23 
  ACSM4 MUTATED ACSM4 WILD-TYPE 
          45.47           90.12 
  ACSM4 MUTATED ACSM4 WILD-TYPE 
          19.89           15.19 
[1] "5.3 - 45.5 (19.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D422V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ACSM4 MUTATED         0        0        0         0         4         0
  ACSM4 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  ACSM4 MUTATED          0
  ACSM4 WILD-TYPE        3
D422V3, multiclass
           clus
vv          ACSM4 MUTATED ACSM4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ACSM4 MUTATED    0  1     3
  ACSM4 WILD-TYPE  5 16    99
D422V4, multiclass
       clus
vv      ACSM4 MUTATED ACSM4 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V5, binary
                 cls
clus               0  1
  ACSM4 MUTATED    0  4
  ACSM4 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSM4 MUTATED      0    4
  ACSM4 WILD-TYPE   35   85
   clus
vv  ACSM4 MUTATED ACSM4 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D422V6, binary
                 cls
clus               0  1
  ACSM4 MUTATED    2  0
  ACSM4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSM4 MUTATED      2    0
  ACSM4 WILD-TYPE   55    3
   clus
vv  ACSM4 MUTATED ACSM4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D422V7, binary
                 cls
clus               0  1
  ACSM4 MUTATED    2  2
  ACSM4 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSM4 MUTATED      2    2
  ACSM4 WILD-TYPE   49   73
        clus
vv       ACSM4 MUTATED ACSM4 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D422V8, binary
                 cls
clus               0  1
  ACSM4 MUTATED    4  0
  ACSM4 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSM4 MUTATED      4    0
  ACSM4 WILD-TYPE   84   30
     clus
vv    ACSM4 MUTATED ACSM4 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACSM4 MUTATED                                     3
  ACSM4 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACSM4 MUTATED                                       1
  ACSM4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACSM4 MUTATED                                                  0
  ACSM4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ACSM4 MUTATED                                     0
  ACSM4 WILD-TYPE                                   1
D422V9, multiclass
                                                  clus
vv                                                 ACSM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ACSM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V10, continuous
[1] "Remove cluster labels:" "ACSM4 MUTATED"         
clus
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-YY-A8LH 
"ACSM4 WILD-TYPE" 
D422V11, continuous
[1] "Remove cluster labels:" "ACSM4 MUTATED"         
clus
  ACSM4 MUTATED ACSM4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" "ACSM4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ACSM4 MUTATED    2  2  0  0
  ACSM4 WILD-TYPE 78 33  4  2
D422V12, multiclass
    clus
vv   ACSM4 MUTATED ACSM4 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACSM4 MUTATED       0                         0     4
  ACSM4 WILD-TYPE     6                         5   110
D422V14, multiclass
                           clus
vv                          ACSM4 MUTATED ACSM4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V15, binary
                 cls
clus               0  1
  ACSM4 MUTATED    0  2
  ACSM4 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSM4 MUTATED      0    2
  ACSM4 WILD-TYPE    5   89
                        clus
vv                       ACSM4 MUTATED ACSM4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(423) Variable = SPAG17 MUTATION ANALYSIS
D423V1, survival
                  sevent
clus2               0  1
  SPAG17 MUTATED    4  4
  SPAG17 WILD-TYPE 59 58
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               8              117 
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               4               58 
$`SPAG17 MUTATED`
TCGA-3A-A9IL TCGA-S4-A8RO TCGA-2J-AAB1 TCGA-FZ-5926 TCGA-HZ-8637 TCGA-IB-7651 
       90.12        17.26         2.17        17.79        17.00        19.82 
TCGA-Q3-AA2A TCGA-YB-A89D 
        3.12        11.51 

$`SPAG17 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        14.14        16.37 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE 
       23.97         9.63         2.63        20.61        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 
       24.36         2.01         5.10        36.20        20.35        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SPAG17 MUTATED SPAG17 WILD-TYPE 
            2.17             0.23 
  SPAG17 MUTATED SPAG17 WILD-TYPE 
           90.12            75.12 
  SPAG17 MUTATED SPAG17 WILD-TYPE 
           17.13            15.19 
[1] "2.2 - 90.1 (17.1)" "0.2 - 75.1 (15.2)"
[1] "hr=" "1"  
D423V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SPAG17 MUTATED         1        0        1         0         5         1
  SPAG17 WILD-TYPE       0        3       11        19        77         3
                  vv
clus               STAGE IV
  SPAG17 MUTATED          0
  SPAG17 WILD-TYPE        3
D423V3, multiclass
           clus
vv          SPAG17 MUTATED SPAG17 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SPAG17 MUTATED    1  0     7
  SPAG17 WILD-TYPE  4 17    95
D423V4, multiclass
       clus
vv      SPAG17 MUTATED SPAG17 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V5, binary
                  cls
clus                0  1
  SPAG17 MUTATED    0  7
  SPAG17 WILD-TYPE 35 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPAG17 MUTATED      0    7
  SPAG17 WILD-TYPE   35   82
   clus
vv  SPAG17 MUTATED SPAG17 WILD-TYPE
  0              0               35
  1              7               82
[1] 2 2
[1] FALSE
D423V6, binary
                  cls
clus                0  1
  SPAG17 MUTATED    3  0
  SPAG17 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPAG17 MUTATED      3    0
  SPAG17 WILD-TYPE   54    3
   clus
vv  SPAG17 MUTATED SPAG17 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D423V7, binary
                  cls
clus                0  1
  SPAG17 MUTATED    6  2
  SPAG17 WILD-TYPE 45 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPAG17 MUTATED      6    2
  SPAG17 WILD-TYPE   45   73
        clus
vv       SPAG17 MUTATED SPAG17 WILD-TYPE
  FEMALE              6               45
  MALE                2               73
[1] 2 2
[1] FALSE
D423V8, binary
                  cls
clus                0  1
  SPAG17 MUTATED    5  3
  SPAG17 WILD-TYPE 83 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPAG17 MUTATED      5    3
  SPAG17 WILD-TYPE   83   27
     clus
vv    SPAG17 MUTATED SPAG17 WILD-TYPE
  NO               5               83
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPAG17 MUTATED                                     6
  SPAG17 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPAG17 MUTATED                                       2
  SPAG17 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPAG17 MUTATED                                                  0
  SPAG17 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SPAG17 MUTATED                                     0
  SPAG17 WILD-TYPE                                   1
D423V9, multiclass
                                                  clus
vv                                                 SPAG17 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SPAG17 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V10, continuous
[1] "Remove cluster labels:" "SPAG17 MUTATED"        
clus
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AABA       TCGA-2J-AABE 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-YY-A8LH 
"SPAG17 WILD-TYPE" 
D423V11, continuous
[1] "Remove cluster labels:" "SPAG17 MUTATED"        
clus
  SPAG17 MUTATED SPAG17 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AABE       TCGA-2J-AABF 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" "SPAG17 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SPAG17 MUTATED    6  1  0  1
  SPAG17 WILD-TYPE 74 34  4  1
D423V12, multiclass
    clus
vv   SPAG17 MUTATED SPAG17 WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPAG17 MUTATED       0                         0     8
  SPAG17 WILD-TYPE     6                         5   106
D423V14, multiclass
                           clus
vv                          SPAG17 MUTATED SPAG17 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V15, binary
                  cls
clus                0  1
  SPAG17 MUTATED    1  6
  SPAG17 WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPAG17 MUTATED      1    6
  SPAG17 WILD-TYPE    4   85
                        clus
vv                       SPAG17 MUTATED SPAG17 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(424) Variable = OGFOD1 MUTATION ANALYSIS
D424V1, survival
                  sevent
clus2               0  1
  OGFOD1 MUTATED    2  1
  OGFOD1 WILD-TYPE 61 61
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               3              122 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               1               61 
$`OGFOD1 MUTATED`
TCGA-3A-A9IS TCGA-FB-A78T TCGA-IB-A5SP 
       32.81        12.33        15.85 

$`OGFOD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
           12.33             0.23 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
           32.81            90.12 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
          15.850           15.205 
[1] "12.3 - 32.8 (15.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.7"
D424V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OGFOD1 MUTATED         0        0        1         1         1         0
  OGFOD1 WILD-TYPE       1        3       11        18        81         4
                  vv
clus               STAGE IV
  OGFOD1 MUTATED          0
  OGFOD1 WILD-TYPE        3
D424V3, multiclass
           clus
vv          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  OGFOD1 MUTATED     0   1     2
  OGFOD1 WILD-TYPE   5  16   100
D424V4, multiclass
       clus
vv      OGFOD1 MUTATED OGFOD1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V5, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    2  1
  OGFOD1 WILD-TYPE 33 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      2    1
  OGFOD1 WILD-TYPE   33   88
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              2               33
  1              1               88
[1] 2 2
[1] FALSE
D424V6, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    2  0
  OGFOD1 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      2    0
  OGFOD1 WILD-TYPE   55    3
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D424V7, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    1  2
  OGFOD1 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      1    2
  OGFOD1 WILD-TYPE   50   73
        clus
vv       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D424V8, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    3  0
  OGFOD1 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      3    0
  OGFOD1 WILD-TYPE   85   30
     clus
vv    OGFOD1 MUTATED OGFOD1 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OGFOD1 MUTATED                                     2
  OGFOD1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OGFOD1 MUTATED                                       1
  OGFOD1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OGFOD1 MUTATED                                                  0
  OGFOD1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OGFOD1 MUTATED                                     0
  OGFOD1 WILD-TYPE                                   1
D424V9, multiclass
                                                  clus
vv                                                 OGFOD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 OGFOD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V10, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-AAPQ 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
D424V11, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OGFOD1 MUTATED    2  1  0  0
  OGFOD1 WILD-TYPE 78 34  4  2
D424V12, multiclass
    clus
vv   OGFOD1 MUTATED OGFOD1 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGFOD1 MUTATED       0                         0     3
  OGFOD1 WILD-TYPE     6                         5   111
D424V14, multiclass
                           clus
vv                          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V15, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    0  2
  OGFOD1 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      0    2
  OGFOD1 WILD-TYPE    5   89
                        clus
vv                       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(425) Variable = ZADH2 MUTATION ANALYSIS
D425V1, survival
                 sevent
clus2              0  1
  ZADH2 MUTATED    2  1
  ZADH2 WILD-TYPE 61 61
  ZADH2 MUTATED ZADH2 WILD-TYPE 
              3             122 
  ZADH2 MUTATED ZADH2 WILD-TYPE 
              1              61 
$`ZADH2 MUTATED`
TCGA-3A-A9IH TCGA-Q3-A5QY TCGA-US-A77J 
       33.57        13.68        18.67 

$`ZADH2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29         8.78         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
        9.40         0.30        39.98        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZADH2 MUTATED ZADH2 WILD-TYPE 
          13.68            0.23 
  ZADH2 MUTATED ZADH2 WILD-TYPE 
          33.57           90.12 
  ZADH2 MUTATED ZADH2 WILD-TYPE 
         18.670          15.205 
[1] "13.7 - 33.6 (18.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.9"
D425V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZADH2 MUTATED         0        1        0         0         2         0
  ZADH2 WILD-TYPE       1        2       12        19        80         4
                 vv
clus              STAGE IV
  ZADH2 MUTATED          0
  ZADH2 WILD-TYPE        3
D425V3, multiclass
           clus
vv          ZADH2 MUTATED ZADH2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ZADH2 MUTATED     1   0     2
  ZADH2 WILD-TYPE   4  17   100
D425V4, multiclass
       clus
vv      ZADH2 MUTATED ZADH2 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V5, binary
                 cls
clus               0  1
  ZADH2 MUTATED    1  2
  ZADH2 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZADH2 MUTATED      1    2
  ZADH2 WILD-TYPE   34   87
   clus
vv  ZADH2 MUTATED ZADH2 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D425V6, binary
                 cls
clus               0  1
  ZADH2 MUTATED    0  0
  ZADH2 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZADH2 MUTATED      0    0
  ZADH2 WILD-TYPE   57    3
D425V7, binary
                 cls
clus               0  1
  ZADH2 MUTATED    2  1
  ZADH2 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZADH2 MUTATED      2    1
  ZADH2 WILD-TYPE   49   74
        clus
vv       ZADH2 MUTATED ZADH2 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D425V8, binary
                 cls
clus               0  1
  ZADH2 MUTATED    2  0
  ZADH2 WILD-TYPE 86 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZADH2 MUTATED      2    0
  ZADH2 WILD-TYPE   86   30
     clus
vv    ZADH2 MUTATED ZADH2 WILD-TYPE
  NO              2              86
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZADH2 MUTATED                                     3
  ZADH2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZADH2 MUTATED                                       0
  ZADH2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZADH2 MUTATED                                                  0
  ZADH2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZADH2 MUTATED                                     0
  ZADH2 WILD-TYPE                                   1
D425V9, multiclass
                                                  clus
vv                                                 ZADH2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ZADH2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V10, continuous
D425V11, continuous
                 vv
clus              R0 R1 R2 RX
  ZADH2 MUTATED    3  0  0  0
  ZADH2 WILD-TYPE 77 35  4  2
D425V12, multiclass
    clus
vv   ZADH2 MUTATED ZADH2 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZADH2 MUTATED       0                         0     3
  ZADH2 WILD-TYPE     6                         5   111
D425V14, multiclass
                           clus
vv                          ZADH2 MUTATED ZADH2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V15, binary
                 cls
clus               0  1
  ZADH2 MUTATED    0  3
  ZADH2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZADH2 MUTATED      0    3
  ZADH2 WILD-TYPE    5   88
                        clus
vv                       ZADH2 MUTATED ZADH2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(426) Variable = G2E3 MUTATION ANALYSIS
D426V1, survival
                sevent
clus2             0  1
  G2E3 MUTATED    1  3
  G2E3 WILD-TYPE 62 59
  G2E3 MUTATED G2E3 WILD-TYPE 
             4            121 
  G2E3 MUTATED G2E3 WILD-TYPE 
             3             59 
$`G2E3 MUTATED`
TCGA-2J-AABK TCGA-FB-A5VM TCGA-IB-7651 TCGA-US-A77J 
       15.91        16.37        19.82        18.67 

$`G2E3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  G2E3 MUTATED G2E3 WILD-TYPE 
         15.91           0.23 
  G2E3 MUTATED G2E3 WILD-TYPE 
         19.82          90.12 
  G2E3 MUTATED G2E3 WILD-TYPE 
         17.52          15.12 
[1] "15.9 - 19.8 (17.5)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.4"
D426V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  G2E3 MUTATED         0        0        1         0         3         0
  G2E3 WILD-TYPE       1        3       11        19        79         4
                vv
clus             STAGE IV
  G2E3 MUTATED          0
  G2E3 WILD-TYPE        3
D426V3, multiclass
           clus
vv          G2E3 MUTATED G2E3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  G2E3 MUTATED    0  1     3
  G2E3 WILD-TYPE  5 16    99
D426V4, multiclass
       clus
vv      G2E3 MUTATED G2E3 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V5, binary
                cls
clus              0  1
  G2E3 MUTATED    1  3
  G2E3 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      1    3
  G2E3 WILD-TYPE   34   86
   clus
vv  G2E3 MUTATED G2E3 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D426V6, binary
                cls
clus              0  1
  G2E3 MUTATED    3  0
  G2E3 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      3    0
  G2E3 WILD-TYPE   54    3
   clus
vv  G2E3 MUTATED G2E3 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D426V7, binary
                cls
clus              0  1
  G2E3 MUTATED    2  2
  G2E3 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      2    2
  G2E3 WILD-TYPE   49   73
        clus
vv       G2E3 MUTATED G2E3 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D426V8, binary
                cls
clus              0  1
  G2E3 MUTATED    2  1
  G2E3 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      2    1
  G2E3 WILD-TYPE   86   29
     clus
vv    G2E3 MUTATED G2E3 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  G2E3 MUTATED                                     4
  G2E3 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  G2E3 MUTATED                                       0
  G2E3 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  G2E3 MUTATED                                                  0
  G2E3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  G2E3 MUTATED                                     0
  G2E3 WILD-TYPE                                   1
D426V9, multiclass
                                                  clus
vv                                                 G2E3 MUTATED G2E3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V10, continuous
[1] "Remove cluster labels:" "G2E3 MUTATED"          
clus
  G2E3 MUTATED G2E3 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A78T     TCGA-FB-AAPQ 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-YY-A8LH 
"G2E3 WILD-TYPE" 
D426V11, continuous
[1] "Remove cluster labels:" "G2E3 MUTATED"          
clus
  G2E3 MUTATED G2E3 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"G2E3 WILD-TYPE" "G2E3 WILD-TYPE" "G2E3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  G2E3 MUTATED    3  1  0  0
  G2E3 WILD-TYPE 77 34  4  2
D426V12, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  G2E3 MUTATED       0                         0     4
  G2E3 WILD-TYPE     6                         5   110
D426V14, multiclass
                           clus
vv                          G2E3 MUTATED G2E3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V15, binary
                cls
clus              0  1
  G2E3 MUTATED    0  3
  G2E3 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      0    3
  G2E3 WILD-TYPE    5   88
                        clus
vv                       G2E3 MUTATED G2E3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(427) Variable = TPTE2 MUTATION ANALYSIS
D427V1, survival
                 sevent
clus2              0  1
  TPTE2 MUTATED    4  3
  TPTE2 WILD-TYPE 59 59
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              7             118 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              3              59 
$`TPTE2 MUTATED`
TCGA-2J-AABT TCGA-2J-AABO TCGA-2L-AAQA TCGA-3A-A9J0 TCGA-IB-7651 TCGA-IB-AAUN 
       10.49        14.47         4.70        24.43        19.82         4.73 
TCGA-YB-A89D 
       11.51 

$`TPTE2 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           4.70            0.23 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          24.43           90.12 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
         11.510          15.335 
[1] "4.7 - 24.4 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D427V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TPTE2 MUTATED         0        0        1         0         6         0
  TPTE2 WILD-TYPE       1        3       11        19        76         4
                 vv
clus              STAGE IV
  TPTE2 MUTATED          0
  TPTE2 WILD-TYPE        3
D427V3, multiclass
           clus
vv          TPTE2 MUTATED TPTE2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TPTE2 MUTATED    0  1     6
  TPTE2 WILD-TYPE  5 16    96
D427V4, multiclass
       clus
vv      TPTE2 MUTATED TPTE2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V5, binary
                 cls
clus               0  1
  TPTE2 MUTATED    1  6
  TPTE2 WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      1    6
  TPTE2 WILD-TYPE   34   83
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D427V6, binary
                 cls
clus               0  1
  TPTE2 MUTATED    4  0
  TPTE2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      4    0
  TPTE2 WILD-TYPE   53    3
   clus
vv  TPTE2 MUTATED TPTE2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D427V7, binary
                 cls
clus               0  1
  TPTE2 MUTATED    3  4
  TPTE2 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      3    4
  TPTE2 WILD-TYPE   48   71
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D427V8, binary
                 cls
clus               0  1
  TPTE2 MUTATED    4  2
  TPTE2 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      4    2
  TPTE2 WILD-TYPE   84   28
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TPTE2 MUTATED                                     7
  TPTE2 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TPTE2 MUTATED                                       0
  TPTE2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TPTE2 MUTATED                                                  0
  TPTE2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TPTE2 MUTATED                                     0
  TPTE2 WILD-TYPE                                   1
D427V9, multiclass
                                                  clus
vv                                                 TPTE2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TPTE2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V10, continuous
D427V11, continuous
[1] "Remove cluster labels:" "TPTE2 MUTATED"         
clus
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TPTE2 MUTATED    5  2  0  0
  TPTE2 WILD-TYPE 75 33  4  2
D427V12, multiclass
    clus
vv   TPTE2 MUTATED TPTE2 WILD-TYPE
  R0             5              75
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED       0                         0     7
  TPTE2 WILD-TYPE     6                         5   107
D427V14, multiclass
                           clus
vv                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V15, binary
                 cls
clus               0  1
  TPTE2 MUTATED    0  4
  TPTE2 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      0    4
  TPTE2 WILD-TYPE    5   87
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(428) Variable = SCLT1 MUTATION ANALYSIS
D428V1, survival
                 sevent
clus2              0  1
  SCLT1 MUTATED    3  2
  SCLT1 WILD-TYPE 60 60
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              5             120 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              2              60 
$`SCLT1 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABP TCGA-2J-AABU TCGA-FZ-5926 TCGA-YH-A8SY 
        1.08        15.22         9.11        17.79        12.76 

$`SCLT1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 
       24.36         2.01         5.10        36.20        20.35        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
           1.08            0.23 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          17.79           90.12 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         12.760          15.335 
[1] "1.1 - 17.8 (12.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D428V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SCLT1 MUTATED         0        0        0         0         3         2
  SCLT1 WILD-TYPE       1        3       12        19        79         2
                 vv
clus              STAGE IV
  SCLT1 MUTATED          0
  SCLT1 WILD-TYPE        3
D428V3, multiclass
           clus
vv          SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             2               2
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SCLT1 MUTATED    0  0     5
  SCLT1 WILD-TYPE  5 17    97
D428V4, multiclass
       clus
vv      SCLT1 MUTATED SCLT1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V5, binary
                 cls
clus               0  1
  SCLT1 MUTATED    0  5
  SCLT1 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      0    5
  SCLT1 WILD-TYPE   35   84
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D428V6, binary
                 cls
clus               0  1
  SCLT1 MUTATED    3  0
  SCLT1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      3    0
  SCLT1 WILD-TYPE   54    3
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D428V7, binary
                 cls
clus               0  1
  SCLT1 MUTATED    4  1
  SCLT1 WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      4    1
  SCLT1 WILD-TYPE   47   74
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D428V8, binary
                 cls
clus               0  1
  SCLT1 MUTATED    3  1
  SCLT1 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      3    1
  SCLT1 WILD-TYPE   85   29
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SCLT1 MUTATED                                     2
  SCLT1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SCLT1 MUTATED                                       1
  SCLT1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SCLT1 MUTATED                                                  0
  SCLT1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SCLT1 MUTATED                                     1
  SCLT1 WILD-TYPE                                   0
D428V9, multiclass
                                                  clus
vv                                                 SCLT1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 SCLT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V10, continuous
[1] "Remove cluster labels:" "SCLT1 MUTATED"         
clus
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
D428V11, continuous
[1] "Remove cluster labels:" "SCLT1 MUTATED"         
clus
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" "SCLT1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SCLT1 MUTATED    4  0  0  0
  SCLT1 WILD-TYPE 76 35  4  2
D428V12, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCLT1 MUTATED       0                         0     5
  SCLT1 WILD-TYPE     6                         5   109
D428V14, multiclass
                           clus
vv                          SCLT1 MUTATED SCLT1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V15, binary
                 cls
clus               0  1
  SCLT1 MUTATED    0  3
  SCLT1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      0    3
  SCLT1 WILD-TYPE    5   88
                        clus
vv                       SCLT1 MUTATED SCLT1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(429) Variable = EAF2 MUTATION ANALYSIS
D429V1, survival
                sevent
clus2             0  1
  EAF2 MUTATED    2  1
  EAF2 WILD-TYPE 61 61
  EAF2 MUTATED EAF2 WILD-TYPE 
             3            122 
  EAF2 MUTATED EAF2 WILD-TYPE 
             1             61 
$`EAF2 MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9I9 TCGA-YB-A89D 
       60.95        20.84        11.51 

$`EAF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  EAF2 MUTATED EAF2 WILD-TYPE 
         11.51           0.23 
  EAF2 MUTATED EAF2 WILD-TYPE 
         60.95          90.12 
  EAF2 MUTATED EAF2 WILD-TYPE 
        20.840         15.205 
[1] "11.5 - 61.0 (20.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.1"
D429V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EAF2 MUTATED         0        0        1         1         1         0
  EAF2 WILD-TYPE       1        3       11        18        81         4
                vv
clus             STAGE IV
  EAF2 MUTATED          0
  EAF2 WILD-TYPE        3
D429V3, multiclass
           clus
vv          EAF2 MUTATED EAF2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            1             81
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  EAF2 MUTATED     0   1     2
  EAF2 WILD-TYPE   5  16   100
D429V4, multiclass
       clus
vv      EAF2 MUTATED EAF2 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V5, binary
                cls
clus              0  1
  EAF2 MUTATED    2  1
  EAF2 WILD-TYPE 33 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      2    1
  EAF2 WILD-TYPE   33   88
   clus
vv  EAF2 MUTATED EAF2 WILD-TYPE
  0            2             33
  1            1             88
[1] 2 2
[1] FALSE
D429V6, binary
                cls
clus              0  1
  EAF2 MUTATED    0  0
  EAF2 WILD-TYPE 57  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    0
  EAF2 WILD-TYPE   57    3
D429V7, binary
                cls
clus              0  1
  EAF2 MUTATED    0  3
  EAF2 WILD-TYPE 51 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    3
  EAF2 WILD-TYPE   51   72
        clus
vv       EAF2 MUTATED EAF2 WILD-TYPE
  FEMALE            0             51
  MALE              3             72
[1] 2 2
[1] FALSE
D429V8, binary
                cls
clus              0  1
  EAF2 MUTATED    1  2
  EAF2 WILD-TYPE 87 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      1    2
  EAF2 WILD-TYPE   87   28
     clus
vv    EAF2 MUTATED EAF2 WILD-TYPE
  NO             1             87
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EAF2 MUTATED                                     2
  EAF2 WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EAF2 MUTATED                                       1
  EAF2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EAF2 MUTATED                                                  0
  EAF2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EAF2 MUTATED                                     0
  EAF2 WILD-TYPE                                   1
D429V9, multiclass
                                                  clus
vv                                                 EAF2 MUTATED EAF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V10, continuous
[1] "Remove cluster labels:" "EAF2 MUTATED"          
clus
  EAF2 MUTATED EAF2 WILD-TYPE 
             2             37 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-YY-A8LH 
"EAF2 WILD-TYPE" 
D429V11, continuous
[1] "Remove cluster labels:" "EAF2 MUTATED"          
clus
  EAF2 MUTATED EAF2 WILD-TYPE 
             1             32 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" "EAF2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  EAF2 MUTATED    3  0  0  0
  EAF2 WILD-TYPE 77 35  4  2
D429V12, multiclass
    clus
vv   EAF2 MUTATED EAF2 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EAF2 MUTATED       0                         0     3
  EAF2 WILD-TYPE     6                         5   111
D429V14, multiclass
                           clus
vv                          EAF2 MUTATED EAF2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V15, binary
                cls
clus              0  1
  EAF2 MUTATED    0  3
  EAF2 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAF2 MUTATED      0    3
  EAF2 WILD-TYPE    5   88
                        clus
vv                       EAF2 MUTATED EAF2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(430) Variable = REPS1 MUTATION ANALYSIS
D430V1, survival
                 sevent
clus2              0  1
  REPS1 MUTATED    0  4
  REPS1 WILD-TYPE 63 58
  REPS1 MUTATED REPS1 WILD-TYPE 
              4             121 
  REPS1 MUTATED REPS1 WILD-TYPE 
              4              58 
$`REPS1 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-FB-A78T TCGA-IB-7651 
        4.70        22.49        12.33        19.82 

$`REPS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQI TCGA-2L-AAQJ 
       14.47        15.22         9.11        21.44         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  REPS1 MUTATED REPS1 WILD-TYPE 
           4.70            0.23 
  REPS1 MUTATED REPS1 WILD-TYPE 
          22.49           90.12 
  REPS1 MUTATED REPS1 WILD-TYPE 
         16.075          15.220 
[1] "4.7 - 22.5 (16.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.3"
D430V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  REPS1 MUTATED         0        0        0         0         4         0
  REPS1 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  REPS1 MUTATED          0
  REPS1 WILD-TYPE        3
D430V3, multiclass
           clus
vv          REPS1 MUTATED REPS1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  REPS1 MUTATED    0  0     4
  REPS1 WILD-TYPE  5 17    98
D430V4, multiclass
       clus
vv      REPS1 MUTATED REPS1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V5, binary
                 cls
clus               0  1
  REPS1 MUTATED    0  4
  REPS1 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REPS1 MUTATED      0    4
  REPS1 WILD-TYPE   35   85
   clus
vv  REPS1 MUTATED REPS1 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D430V6, binary
                 cls
clus               0  1
  REPS1 MUTATED    3  0
  REPS1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REPS1 MUTATED      3    0
  REPS1 WILD-TYPE   54    3
   clus
vv  REPS1 MUTATED REPS1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D430V7, binary
                 cls
clus               0  1
  REPS1 MUTATED    2  2
  REPS1 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REPS1 MUTATED      2    2
  REPS1 WILD-TYPE   49   73
        clus
vv       REPS1 MUTATED REPS1 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D430V8, binary
                 cls
clus               0  1
  REPS1 MUTATED    4  0
  REPS1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REPS1 MUTATED      4    0
  REPS1 WILD-TYPE   84   30
     clus
vv    REPS1 MUTATED REPS1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  REPS1 MUTATED                                     4
  REPS1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  REPS1 MUTATED                                       0
  REPS1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  REPS1 MUTATED                                                  0
  REPS1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  REPS1 MUTATED                                     0
  REPS1 WILD-TYPE                                   1
D430V9, multiclass
                                                  clus
vv                                                 REPS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 REPS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V10, continuous
D430V11, continuous
[1] "Remove cluster labels:" "REPS1 MUTATED"         
clus
  REPS1 MUTATED REPS1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"REPS1 WILD-TYPE" "REPS1 WILD-TYPE" "REPS1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  REPS1 MUTATED    3  1  0  0
  REPS1 WILD-TYPE 77 34  4  2
D430V12, multiclass
    clus
vv   REPS1 MUTATED REPS1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  REPS1 MUTATED       0                         0     4
  REPS1 WILD-TYPE     6                         5   110
D430V14, multiclass
                           clus
vv                          REPS1 MUTATED REPS1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V15, binary
                 cls
clus               0  1
  REPS1 MUTATED    0  2
  REPS1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REPS1 MUTATED      0    2
  REPS1 WILD-TYPE    5   89
                        clus
vv                       REPS1 MUTATED REPS1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(431) Variable = ZNF43 MUTATION ANALYSIS
D431V1, survival
                 sevent
clus2              0  1
  ZNF43 MUTATED    3  4
  ZNF43 WILD-TYPE 60 58
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              7             118 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              4              58 
$`ZNF43 MUTATED`
TCGA-2J-AABA TCGA-2J-AABH TCGA-2J-AABP TCGA-FB-AAQ0 TCGA-HV-AA8X TCGA-IB-7651 
       19.96        42.31        15.22        15.55        17.49        19.82 
TCGA-IB-AAUU 
        8.05 

$`ZNF43 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABU 
       20.61        22.22        22.72        15.91        14.47         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ZNF43 MUTATED ZNF43 WILD-TYPE 
           8.05            0.23 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          42.31           90.12 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          17.49           15.09 
[1] "8.1 - 42.3 (17.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D431V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF43 MUTATED         0        0        0         2         5         0
  ZNF43 WILD-TYPE       1        3       12        17        77         4
                 vv
clus              STAGE IV
  ZNF43 MUTATED          0
  ZNF43 WILD-TYPE        3
D431V3, multiclass
           clus
vv          ZNF43 MUTATED ZNF43 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZNF43 MUTATED    0  1     6
  ZNF43 WILD-TYPE  5 16    96
D431V4, multiclass
       clus
vv      ZNF43 MUTATED ZNF43 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V5, binary
                 cls
clus               0  1
  ZNF43 MUTATED    2  5
  ZNF43 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      2    5
  ZNF43 WILD-TYPE   33   84
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D431V6, binary
                 cls
clus               0  1
  ZNF43 MUTATED    5  0
  ZNF43 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      5    0
  ZNF43 WILD-TYPE   52    3
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D431V7, binary
                 cls
clus               0  1
  ZNF43 MUTATED    3  4
  ZNF43 WILD-TYPE 48 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      3    4
  ZNF43 WILD-TYPE   48   71
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  FEMALE             3              48
  MALE               4              71
[1] 2 2
[1] FALSE
D431V8, binary
                 cls
clus               0  1
  ZNF43 MUTATED    7  0
  ZNF43 WILD-TYPE 81 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      7    0
  ZNF43 WILD-TYPE   81   30
     clus
vv    ZNF43 MUTATED ZNF43 WILD-TYPE
  NO              7              81
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF43 MUTATED                                     5
  ZNF43 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF43 MUTATED                                       1
  ZNF43 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF43 MUTATED                                                  0
  ZNF43 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF43 MUTATED                                     1
  ZNF43 WILD-TYPE                                   0
D431V9, multiclass
                                                  clus
vv                                                 ZNF43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 ZNF43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V10, continuous
D431V11, continuous
[1] "Remove cluster labels:" "ZNF43 MUTATED"         
clus
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" "ZNF43 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZNF43 MUTATED    5  1  1  0
  ZNF43 WILD-TYPE 75 34  3  2
D431V12, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF43 MUTATED       1                         0     6
  ZNF43 WILD-TYPE     5                         5   108
D431V14, multiclass
                           clus
vv                          ZNF43 MUTATED ZNF43 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V15, binary
                 cls
clus               0  1
  ZNF43 MUTATED    0  3
  ZNF43 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED      0    3
  ZNF43 WILD-TYPE    5   88
                        clus
vv                       ZNF43 MUTATED ZNF43 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(432) Variable = PRPF4 MUTATION ANALYSIS
D432V1, survival
                 sevent
clus2              0  1
  PRPF4 MUTATED    2  1
  PRPF4 WILD-TYPE 61 61
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              3             122 
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              1              61 
$`PRPF4 MUTATED`
TCGA-3A-A9IR TCGA-IB-A5SP TCGA-IB-A6UG 
       50.70        15.85         1.35 

$`PRPF4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       15.19        12.00         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PRPF4 MUTATED PRPF4 WILD-TYPE 
           1.35            0.23 
  PRPF4 MUTATED PRPF4 WILD-TYPE 
          50.70           90.12 
  PRPF4 MUTATED PRPF4 WILD-TYPE 
         15.850          15.205 
[1] "1.4 - 50.7 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D432V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRPF4 MUTATED         0        0        1         1         1         0
  PRPF4 WILD-TYPE       1        3       11        18        81         4
                 vv
clus              STAGE IV
  PRPF4 MUTATED          0
  PRPF4 WILD-TYPE        3
D432V3, multiclass
           clus
vv          PRPF4 MUTATED PRPF4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  PRPF4 MUTATED     0   1     2
  PRPF4 WILD-TYPE   5  16   100
D432V4, multiclass
       clus
vv      PRPF4 MUTATED PRPF4 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V5, binary
                 cls
clus               0  1
  PRPF4 MUTATED    2  1
  PRPF4 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPF4 MUTATED      2    1
  PRPF4 WILD-TYPE   33   88
   clus
vv  PRPF4 MUTATED PRPF4 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D432V6, binary
                 cls
clus               0  1
  PRPF4 MUTATED    2  0
  PRPF4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPF4 MUTATED      2    0
  PRPF4 WILD-TYPE   55    3
   clus
vv  PRPF4 MUTATED PRPF4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D432V7, binary
                 cls
clus               0  1
  PRPF4 MUTATED    1  2
  PRPF4 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPF4 MUTATED      1    2
  PRPF4 WILD-TYPE   50   73
        clus
vv       PRPF4 MUTATED PRPF4 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D432V8, binary
                 cls
clus               0  1
  PRPF4 MUTATED    3  0
  PRPF4 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPF4 MUTATED      3    0
  PRPF4 WILD-TYPE   85   30
     clus
vv    PRPF4 MUTATED PRPF4 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRPF4 MUTATED                                     2
  PRPF4 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRPF4 MUTATED                                       1
  PRPF4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRPF4 MUTATED                                                  0
  PRPF4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRPF4 MUTATED                                     0
  PRPF4 WILD-TYPE                                   1
D432V9, multiclass
                                                  clus
vv                                                 PRPF4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRPF4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V10, continuous
[1] "Remove cluster labels:" "PRPF4 MUTATED"         
clus
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
D432V11, continuous
[1] "Remove cluster labels:" "PRPF4 MUTATED"         
clus
  PRPF4 MUTATED PRPF4 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IX 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" "PRPF4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRPF4 MUTATED    1  2  0  0
  PRPF4 WILD-TYPE 79 33  4  2
D432V12, multiclass
    clus
vv   PRPF4 MUTATED PRPF4 WILD-TYPE
  R0             1              79
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRPF4 MUTATED       0                         0     3
  PRPF4 WILD-TYPE     6                         5   111
D432V14, multiclass
                           clus
vv                          PRPF4 MUTATED PRPF4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V15, binary
                 cls
clus               0  1
  PRPF4 MUTATED    0  2
  PRPF4 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPF4 MUTATED      0    2
  PRPF4 WILD-TYPE    5   89
                        clus
vv                       PRPF4 MUTATED PRPF4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(433) Variable = CMTM1 MUTATION ANALYSIS
D433V1, survival
                 sevent
clus2              0  1
  CMTM1 MUTATED    2  1
  CMTM1 WILD-TYPE 61 61
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              3             122 
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              1              61 
$`CMTM1 MUTATED`
TCGA-3A-A9IO TCGA-IB-A7LX TCGA-Z5-AAPL 
       63.85         8.22        15.35 

$`CMTM1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH 
       12.76        66.28 

  CMTM1 MUTATED CMTM1 WILD-TYPE 
           8.22            0.23 
  CMTM1 MUTATED CMTM1 WILD-TYPE 
          63.85           90.12 
  CMTM1 MUTATED CMTM1 WILD-TYPE 
         15.350          15.205 
[1] "8.2 - 63.9 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D433V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CMTM1 MUTATED         0        0        0         1         1         0
  CMTM1 WILD-TYPE       1        3       12        18        81         4
                 vv
clus              STAGE IV
  CMTM1 MUTATED          0
  CMTM1 WILD-TYPE        3
D433V3, multiclass
[1] "Remove cluster labels:" "CMTM1 MUTATED"         
clus
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9IJ      TCGA-3A-A9IL 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924      TCGA-HZ-A77Q 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX      TCGA-S4-A8RO 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AAB4 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9      TCGA-2J-AABA 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH      TCGA-2J-AABK 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU      TCGA-2J-AABV 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IR 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV      TCGA-3A-A9IX 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-3E-AAAZ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5919      TCGA-FZ-5920 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923      TCGA-FZ-5926 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP      TCGA-HV-AA8V 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-YH-A8SY      TCGA-YY-A8LH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
                 vv
clus               T1  T2 T3+T4
  CMTM1 MUTATED     0   0     2
  CMTM1 WILD-TYPE   5  17   100
D433V4, multiclass
[1] "Remove cluster labels:" "CMTM1 MUTATED"         
clus
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9IJ      TCGA-3A-A9IL 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924      TCGA-HZ-A77Q 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX      TCGA-S4-A8RO 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AAB4 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9      TCGA-2J-AABA 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH      TCGA-2J-AABK 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU      TCGA-2J-AABV 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IR 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV      TCGA-3A-A9IX 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-3E-AAAZ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5919      TCGA-FZ-5920 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923      TCGA-FZ-5926 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP      TCGA-HV-AA8V 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-YH-A8SY      TCGA-YY-A8LH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
D433V5, binary
                 cls
clus               0  1
  CMTM1 MUTATED    1  1
  CMTM1 WILD-TYPE 34 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM1 MUTATED      1    1
  CMTM1 WILD-TYPE   34   88
   clus
vv  CMTM1 MUTATED CMTM1 WILD-TYPE
  0             1              34
  1             1              88
[1] 2 2
[1] FALSE
D433V6, binary
                 cls
clus               0  1
  CMTM1 MUTATED    1  0
  CMTM1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM1 MUTATED      1    0
  CMTM1 WILD-TYPE   56    3
   clus
vv  CMTM1 MUTATED CMTM1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D433V7, binary
                 cls
clus               0  1
  CMTM1 MUTATED    1  2
  CMTM1 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM1 MUTATED      1    2
  CMTM1 WILD-TYPE   50   73
        clus
vv       CMTM1 MUTATED CMTM1 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D433V8, binary
                 cls
clus               0  1
  CMTM1 MUTATED    3  0
  CMTM1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM1 MUTATED      3    0
  CMTM1 WILD-TYPE   85   30
     clus
vv    CMTM1 MUTATED CMTM1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CMTM1 MUTATED                                     2
  CMTM1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CMTM1 MUTATED                                       1
  CMTM1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CMTM1 MUTATED                                                  0
  CMTM1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CMTM1 MUTATED                                     0
  CMTM1 WILD-TYPE                                   1
D433V9, multiclass
                                                  clus
vv                                                 CMTM1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CMTM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V10, continuous
D433V11, continuous
                 vv
clus              R0 R1 R2 RX
  CMTM1 MUTATED    3  0  0  0
  CMTM1 WILD-TYPE 77 35  4  2
D433V12, multiclass
    clus
vv   CMTM1 MUTATED CMTM1 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V13, continuous
[1] "Remove cluster labels:" "CMTM1 MUTATED"         
clus
  CMTM1 MUTATED CMTM1 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5919 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FZ-5920      TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OP      TCGA-HV-AA8V 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
     TCGA-YH-A8SY      TCGA-YY-A8LH 
"CMTM1 WILD-TYPE" "CMTM1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CMTM1 MUTATED       0                         0     3
  CMTM1 WILD-TYPE     6                         5   111
D433V14, multiclass
                           clus
vv                          CMTM1 MUTATED CMTM1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V15, binary
                 cls
clus               0  1
  CMTM1 MUTATED    0  3
  CMTM1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMTM1 MUTATED      0    3
  CMTM1 WILD-TYPE    5   88
                        clus
vv                       CMTM1 MUTATED CMTM1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(434) Variable = L1CAM MUTATION ANALYSIS
D434V1, survival
                 sevent
clus2              0  1
  L1CAM MUTATED    1  5
  L1CAM WILD-TYPE 62 57
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             119 
  L1CAM MUTATED L1CAM WILD-TYPE 
              5              57 
$`L1CAM MUTATED`
TCGA-US-A77E TCGA-2J-AAB9 TCGA-HZ-7925 TCGA-HZ-A9TJ TCGA-IB-AAUO TCGA-US-A77J 
       14.14        20.61        20.19        19.82         7.86        18.67 

$`L1CAM WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63         2.63        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        17.00        10.13         5.26        10.85         0.23 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  L1CAM MUTATED L1CAM WILD-TYPE 
           7.86            0.23 
  L1CAM MUTATED L1CAM WILD-TYPE 
          20.61           90.12 
  L1CAM MUTATED L1CAM WILD-TYPE 
         19.245          15.190 
[1] "7.9 - 20.6 (19.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D434V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  L1CAM MUTATED         0        0        0         0         5         0
  L1CAM WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  L1CAM MUTATED          1
  L1CAM WILD-TYPE        2
D434V3, multiclass
           clus
vv          L1CAM MUTATED L1CAM WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  L1CAM MUTATED    0  0     6
  L1CAM WILD-TYPE  5 17    96
D434V4, multiclass
       clus
vv      L1CAM MUTATED L1CAM WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V5, binary
                 cls
clus               0  1
  L1CAM MUTATED    1  5
  L1CAM WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      1    5
  L1CAM WILD-TYPE   34   84
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D434V6, binary
                 cls
clus               0  1
  L1CAM MUTATED    2  1
  L1CAM WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      2    1
  L1CAM WILD-TYPE   55    2
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D434V7, binary
                 cls
clus               0  1
  L1CAM MUTATED    3  3
  L1CAM WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      3    3
  L1CAM WILD-TYPE   48   72
        clus
vv       L1CAM MUTATED L1CAM WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D434V8, binary
                 cls
clus               0  1
  L1CAM MUTATED    4  1
  L1CAM WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      4    1
  L1CAM WILD-TYPE   84   29
     clus
vv    L1CAM MUTATED L1CAM WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  L1CAM MUTATED                                     4
  L1CAM WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  L1CAM MUTATED                                       2
  L1CAM WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  L1CAM MUTATED                                                  0
  L1CAM WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  L1CAM MUTATED                                     0
  L1CAM WILD-TYPE                                   1
D434V9, multiclass
                                                  clus
vv                                                 L1CAM MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 L1CAM WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V10, continuous
D434V11, continuous
                 vv
clus              R0 R1 R2 RX
  L1CAM MUTATED    4  2  0  0
  L1CAM WILD-TYPE 76 33  4  2
D434V12, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  L1CAM MUTATED       0                         0     6
  L1CAM WILD-TYPE     6                         5   108
D434V14, multiclass
                           clus
vv                          L1CAM MUTATED L1CAM WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V15, binary
                 cls
clus               0  1
  L1CAM MUTATED    0  5
  L1CAM WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      0    5
  L1CAM WILD-TYPE    5   86
                        clus
vv                       L1CAM MUTATED L1CAM WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(435) Variable = MMP14 MUTATION ANALYSIS
D435V1, survival
                 sevent
clus2              0  1
  MMP14 MUTATED    1  3
  MMP14 WILD-TYPE 62 59
  MMP14 MUTATED MMP14 WILD-TYPE 
              4             121 
  MMP14 MUTATED MMP14 WILD-TYPE 
              3              59 
$`MMP14 MUTATED`
TCGA-FB-A78T TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-A5SP 
       12.33        17.00        19.82        15.85 

$`MMP14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        20.19        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MMP14 MUTATED MMP14 WILD-TYPE 
          12.33            0.23 
  MMP14 MUTATED MMP14 WILD-TYPE 
          19.82           90.12 
  MMP14 MUTATED MMP14 WILD-TYPE 
         16.425          15.190 
[1] "12.3 - 19.8 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.6"
D435V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MMP14 MUTATED         0        0        0         1         3         0
  MMP14 WILD-TYPE       1        3       12        18        79         4
                 vv
clus              STAGE IV
  MMP14 MUTATED          0
  MMP14 WILD-TYPE        3
D435V3, multiclass
           clus
vv          MMP14 MUTATED MMP14 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MMP14 MUTATED    0  0     4
  MMP14 WILD-TYPE  5 17    98
D435V4, multiclass
       clus
vv      MMP14 MUTATED MMP14 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V5, binary
                 cls
clus               0  1
  MMP14 MUTATED    1  3
  MMP14 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      1    3
  MMP14 WILD-TYPE   34   86
   clus
vv  MMP14 MUTATED MMP14 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D435V6, binary
                 cls
clus               0  1
  MMP14 MUTATED    3  0
  MMP14 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      3    0
  MMP14 WILD-TYPE   54    3
   clus
vv  MMP14 MUTATED MMP14 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D435V7, binary
                 cls
clus               0  1
  MMP14 MUTATED    3  1
  MMP14 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      3    1
  MMP14 WILD-TYPE   48   74
        clus
vv       MMP14 MUTATED MMP14 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D435V8, binary
                 cls
clus               0  1
  MMP14 MUTATED    3  1
  MMP14 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      3    1
  MMP14 WILD-TYPE   85   29
     clus
vv    MMP14 MUTATED MMP14 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP14 MUTATED                                     4
  MMP14 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP14 MUTATED                                       0
  MMP14 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP14 MUTATED                                                  0
  MMP14 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MMP14 MUTATED                                     0
  MMP14 WILD-TYPE                                   1
D435V9, multiclass
                                                  clus
vv                                                 MMP14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MMP14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V10, continuous
[1] "Remove cluster labels:" "MMP14 MUTATED"         
clus
  MMP14 MUTATED MMP14 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-AAPQ 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-YY-A8LH 
"MMP14 WILD-TYPE" 
D435V11, continuous
[1] "Remove cluster labels:" "MMP14 MUTATED"         
clus
  MMP14 MUTATED MMP14 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MMP14 MUTATED    3  1  0  0
  MMP14 WILD-TYPE 77 34  4  2
D435V12, multiclass
    clus
vv   MMP14 MUTATED MMP14 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP14 MUTATED       0                         0     4
  MMP14 WILD-TYPE     6                         5   110
D435V14, multiclass
                           clus
vv                          MMP14 MUTATED MMP14 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V15, binary
                 cls
clus               0  1
  MMP14 MUTATED    1  2
  MMP14 WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      1    2
  MMP14 WILD-TYPE    4   89
                        clus
vv                       MMP14 MUTATED MMP14 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(436) Variable = CENPF MUTATION ANALYSIS
D436V1, survival
                 sevent
clus2              0  1
  CENPF MUTATED    4  1
  CENPF WILD-TYPE 59 61
  CENPF MUTATED CENPF WILD-TYPE 
              5             120 
  CENPF MUTATED CENPF WILD-TYPE 
              1              61 
$`CENPF MUTATED`
TCGA-2J-AABE TCGA-2J-AABP TCGA-HV-A7OP TCGA-IB-7651 TCGA-LB-A8F3 
       22.22        15.22        32.15        19.82        12.46 

$`CENPF WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A9Q5 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CENPF MUTATED CENPF WILD-TYPE 
          12.46            0.23 
  CENPF MUTATED CENPF WILD-TYPE 
          32.15           90.12 
  CENPF MUTATED CENPF WILD-TYPE 
         19.820          15.155 
[1] "12.5 - 32.1 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "3.1"
D436V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CENPF MUTATED         0        0        0         2         3         0
  CENPF WILD-TYPE       1        3       12        17        79         4
                 vv
clus              STAGE IV
  CENPF MUTATED          0
  CENPF WILD-TYPE        3
D436V3, multiclass
           clus
vv          CENPF MUTATED CENPF WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  CENPF MUTATED    0  0     5
  CENPF WILD-TYPE  5 17    97
D436V4, multiclass
       clus
vv      CENPF MUTATED CENPF WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V5, binary
                 cls
clus               0  1
  CENPF MUTATED    2  3
  CENPF WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED      2    3
  CENPF WILD-TYPE   33   86
   clus
vv  CENPF MUTATED CENPF WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D436V6, binary
                 cls
clus               0  1
  CENPF MUTATED    4  0
  CENPF WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED      4    0
  CENPF WILD-TYPE   53    3
   clus
vv  CENPF MUTATED CENPF WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D436V7, binary
                 cls
clus               0  1
  CENPF MUTATED    3  2
  CENPF WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED      3    2
  CENPF WILD-TYPE   48   73
        clus
vv       CENPF MUTATED CENPF WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D436V8, binary
                 cls
clus               0  1
  CENPF MUTATED    2  3
  CENPF WILD-TYPE 86 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED      2    3
  CENPF WILD-TYPE   86   27
     clus
vv    CENPF MUTATED CENPF WILD-TYPE
  NO              2              86
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CENPF MUTATED                                     3
  CENPF WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CENPF MUTATED                                       1
  CENPF WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CENPF MUTATED                                                  0
  CENPF WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CENPF MUTATED                                     1
  CENPF WILD-TYPE                                   0
D436V9, multiclass
                                                  clus
vv                                                 CENPF MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 CENPF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V10, continuous
[1] "Remove cluster labels:" "CENPF MUTATED"         
clus
  CENPF MUTATED CENPF WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-YY-A8LH 
"CENPF WILD-TYPE" 
D436V11, continuous
[1] "Remove cluster labels:" "CENPF MUTATED"         
clus
  CENPF MUTATED CENPF WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABF 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CENPF WILD-TYPE" "CENPF WILD-TYPE" "CENPF WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CENPF MUTATED    5  0  0  0
  CENPF WILD-TYPE 75 35  4  2
D436V12, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CENPF MUTATED       1                         1     3
  CENPF WILD-TYPE     5                         4   111
D436V14, multiclass
                           clus
vv                          CENPF MUTATED CENPF WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V15, binary
                 cls
clus               0  1
  CENPF MUTATED    0  2
  CENPF WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED      0    2
  CENPF WILD-TYPE    5   89
                        clus
vv                       CENPF MUTATED CENPF WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(437) Variable = AMAC1L2 MUTATION ANALYSIS
D437V1, survival
                   sevent
clus2                0  1
  AMAC1L2 MUTATED    3  3
  AMAC1L2 WILD-TYPE 60 59
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                6               119 
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                3                59 
$`AMAC1L2 MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABP TCGA-HZ-8637 TCGA-IB-A5SO TCGA-US-A77J TCGA-YY-A8LH 
        2.63        15.22        17.00        12.00        18.67        66.28 

$`AMAC1L2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
       19.82        19.82        36.69        41.33        15.19        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
             2.63              0.23 
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
            66.28             90.12 
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
            16.11             15.19 
[1] "2.6 - 66.3 (16.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D437V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMAC1L2 MUTATED         0        0        0         0         6         0
  AMAC1L2 WILD-TYPE       1        3       12        19        76         4
                   vv
clus                STAGE IV
  AMAC1L2 MUTATED          0
  AMAC1L2 WILD-TYPE        3
D437V3, multiclass
           clus
vv          AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               6                76
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  AMAC1L2 MUTATED    0  0     6
  AMAC1L2 WILD-TYPE  5 17    96
D437V4, multiclass
       clus
vv      AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V5, binary
                   cls
clus                 0  1
  AMAC1L2 MUTATED    0  6
  AMAC1L2 WILD-TYPE 35 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L2 MUTATED      0    6
  AMAC1L2 WILD-TYPE   35   83
   clus
vv  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  0               0                35
  1               6                83
[1] 2 2
[1] FALSE
D437V6, binary
                   cls
clus                 0  1
  AMAC1L2 MUTATED    3  0
  AMAC1L2 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L2 MUTATED      3    0
  AMAC1L2 WILD-TYPE   54    3
   clus
vv  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D437V7, binary
                   cls
clus                 0  1
  AMAC1L2 MUTATED    4  2
  AMAC1L2 WILD-TYPE 47 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L2 MUTATED      4    2
  AMAC1L2 WILD-TYPE   47   73
        clus
vv       AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  FEMALE               4                47
  MALE                 2                73
[1] 2 2
[1] FALSE
D437V8, binary
                   cls
clus                 0  1
  AMAC1L2 MUTATED    2  2
  AMAC1L2 WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L2 MUTATED      2    2
  AMAC1L2 WILD-TYPE   86   28
     clus
vv    AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMAC1L2 MUTATED                                     5
  AMAC1L2 WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMAC1L2 MUTATED                                       0
  AMAC1L2 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMAC1L2 MUTATED                                                  0
  AMAC1L2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  AMAC1L2 MUTATED                                     1
  AMAC1L2 WILD-TYPE                                   0
D437V9, multiclass
                                                  clus
vv                                                 AMAC1L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 AMAC1L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V10, continuous
[1] "Remove cluster labels:" "AMAC1L2 MUTATED"       
clus
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XN-A8T5 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
D437V11, continuous
[1] "Remove cluster labels:" "AMAC1L2 MUTATED"       
clus
  AMAC1L2 MUTATED AMAC1L2 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5 
"AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" "AMAC1L2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  AMAC1L2 MUTATED    5  1  0  0
  AMAC1L2 WILD-TYPE 75 34  4  2
D437V12, multiclass
    clus
vv   AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  R0               5                75
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMAC1L2 MUTATED       0                         0     6
  AMAC1L2 WILD-TYPE     6                         5   108
D437V14, multiclass
                           clus
vv                          AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V15, binary
                   cls
clus                 0  1
  AMAC1L2 MUTATED    1  2
  AMAC1L2 WILD-TYPE  4 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L2 MUTATED      1    2
  AMAC1L2 WILD-TYPE    4   89
                        clus
vv                       AMAC1L2 MUTATED AMAC1L2 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(438) Variable = PPARGC1B MUTATION ANALYSIS
D438V1, survival
                    sevent
clus2                 0  1
  PPARGC1B MUTATED    2  3
  PPARGC1B WILD-TYPE 61 59
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 5                120 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                 59 
$`PPARGC1B MUTATED`
TCGA-3A-A9IJ TCGA-3A-A9I9 TCGA-HZ-7918 TCGA-HZ-8637 TCGA-IB-7651 
       60.95        20.84        31.86        17.00        19.82 

$`PPARGC1B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             17.00               0.23 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             60.95              90.12 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             20.84              15.09 
[1] "17.0 - 61.0 (20.8)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.3"
D438V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPARGC1B MUTATED         0        0        1         1         3         0
  PPARGC1B WILD-TYPE       1        3       11        18        79         4
                    vv
clus                 STAGE IV
  PPARGC1B MUTATED          0
  PPARGC1B WILD-TYPE        3
D438V3, multiclass
           clus
vv          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  PPARGC1B MUTATED    0  1     4
  PPARGC1B WILD-TYPE  5 16    98
D438V4, multiclass
       clus
vv      PPARGC1B MUTATED PPARGC1B WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V5, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    2  3
  PPARGC1B WILD-TYPE 33 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      2    3
  PPARGC1B WILD-TYPE   33   86
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0                2                 33
  1                3                 86
[1] 2 2
[1] FALSE
D438V6, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    2  0
  PPARGC1B WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      2    0
  PPARGC1B WILD-TYPE   55    3
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D438V7, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    2  3
  PPARGC1B WILD-TYPE 49 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      2    3
  PPARGC1B WILD-TYPE   49   72
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                2                 49
  MALE                  3                 72
[1] 2 2
[1] FALSE
D438V8, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    2  3
  PPARGC1B WILD-TYPE 86 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      2    3
  PPARGC1B WILD-TYPE   86   27
     clus
vv    PPARGC1B MUTATED PPARGC1B WILD-TYPE
  NO                 2                 86
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPARGC1B MUTATED                                     4
  PPARGC1B WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPARGC1B MUTATED                                       1
  PPARGC1B WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPARGC1B MUTATED                                                  0
  PPARGC1B WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPARGC1B MUTATED                                     0
  PPARGC1B WILD-TYPE                                   1
D438V9, multiclass
                                                  clus
vv                                                 PPARGC1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 PPARGC1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V10, continuous
D438V11, continuous
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 31 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-IB-A5SS 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-XD-AAUL         TCGA-2J-AAB1 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-YY-A8LH 
"PPARGC1B WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  PPARGC1B MUTATED    5  0  0  0
  PPARGC1B WILD-TYPE 75 35  4  2
D438V12, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  R0                5                 75
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPARGC1B MUTATED       0                         0     5
  PPARGC1B WILD-TYPE     6                         5   109
D438V14, multiclass
                           clus
vv                          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V15, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    1  4
  PPARGC1B WILD-TYPE  4 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      1    4
  PPARGC1B WILD-TYPE    4   87
                        clus
vv                       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(439) Variable = ERBB2IP MUTATION ANALYSIS
D439V1, survival
                   sevent
clus2                0  1
  ERBB2IP MUTATED    3  2
  ERBB2IP WILD-TYPE 60 60
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                5               120 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                2                60 
$`ERBB2IP MUTATED`
TCGA-3A-A9IV TCGA-HV-A7OL TCGA-HV-AA8X TCGA-IB-7651 TCGA-RB-AA9M 
       36.26         8.28        17.49        19.82         9.40 

$`ERBB2IP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 
       20.35        17.79        22.06        32.15        30.25        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
             8.28              0.23 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
            36.26             90.12 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           17.490            15.205 
[1] "8.3 - 36.3 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D439V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ERBB2IP MUTATED         0        0        1         1         3         0
  ERBB2IP WILD-TYPE       1        3       11        18        79         4
                   vv
clus                STAGE IV
  ERBB2IP MUTATED          0
  ERBB2IP WILD-TYPE        3
D439V3, multiclass
           clus
vv          ERBB2IP MUTATED ERBB2IP WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  ERBB2IP MUTATED     1   2     2
  ERBB2IP WILD-TYPE   4  15   100
D439V4, multiclass
       clus
vv      ERBB2IP MUTATED ERBB2IP WILD-TYPE
  T1                  1                 4
  T2                  2                15
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V5, binary
                   cls
clus                 0  1
  ERBB2IP MUTATED    2  3
  ERBB2IP WILD-TYPE 33 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      2    3
  ERBB2IP WILD-TYPE   33   86
   clus
vv  ERBB2IP MUTATED ERBB2IP WILD-TYPE
  0               2                33
  1               3                86
[1] 2 2
[1] FALSE
D439V6, binary
                   cls
clus                 0  1
  ERBB2IP MUTATED    1  0
  ERBB2IP WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      1    0
  ERBB2IP WILD-TYPE   56    3
   clus
vv  ERBB2IP MUTATED ERBB2IP WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D439V7, binary
                   cls
clus                 0  1
  ERBB2IP MUTATED    3  2
  ERBB2IP WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      3    2
  ERBB2IP WILD-TYPE   48   73
        clus
vv       ERBB2IP MUTATED ERBB2IP WILD-TYPE
  FEMALE               3                48
  MALE                 2                73
[1] 2 2
[1] FALSE
D439V8, binary
                   cls
clus                 0  1
  ERBB2IP MUTATED    4  1
  ERBB2IP WILD-TYPE 84 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      4    1
  ERBB2IP WILD-TYPE   84   29
     clus
vv    ERBB2IP MUTATED ERBB2IP WILD-TYPE
  NO                4                84
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ERBB2IP MUTATED                                     4
  ERBB2IP WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ERBB2IP MUTATED                                       1
  ERBB2IP WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ERBB2IP MUTATED                                                  0
  ERBB2IP WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ERBB2IP MUTATED                                     0
  ERBB2IP WILD-TYPE                                   1
D439V9, multiclass
                                                  clus
vv                                                 ERBB2IP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ERBB2IP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V10, continuous
[1] "Remove cluster labels:" "ERBB2IP MUTATED"       
clus
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
D439V11, continuous
[1] "Remove cluster labels:" "ERBB2IP MUTATED"       
clus
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" "ERBB2IP WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ERBB2IP MUTATED    3  0  2  0
  ERBB2IP WILD-TYPE 77 35  2  2
D439V12, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  R0               3                77
  R1               0                35
  R2               2                 2
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB2IP MUTATED       2                         0     3
  ERBB2IP WILD-TYPE     4                         5   111
D439V14, multiclass
                           clus
vv                          ERBB2IP MUTATED ERBB2IP WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V15, binary
                   cls
clus                 0  1
  ERBB2IP MUTATED    0  3
  ERBB2IP WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      0    3
  ERBB2IP WILD-TYPE    5   88
                        clus
vv                       ERBB2IP MUTATED ERBB2IP WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(440) Variable = PRF1 MUTATION ANALYSIS
D440V1, survival
                sevent
clus2             0  1
  PRF1 MUTATED    2  4
  PRF1 WILD-TYPE 61 58
  PRF1 MUTATED PRF1 WILD-TYPE 
             6            119 
  PRF1 MUTATED PRF1 WILD-TYPE 
             4             58 
$`PRF1 MUTATED`
TCGA-FZ-5920 TCGA-FZ-5922 TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO 
        2.01        36.20         8.28        19.82        41.33        12.00 

$`PRF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5923 
        4.04         5.03         1.02        24.36         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       19.82        36.69        15.19        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PRF1 MUTATED PRF1 WILD-TYPE 
          2.01           0.23 
  PRF1 MUTATED PRF1 WILD-TYPE 
         41.33          90.12 
  PRF1 MUTATED PRF1 WILD-TYPE 
         15.91          15.22 
[1] "2.0 - 41.3 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D440V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRF1 MUTATED         0        0        0         2         4         0
  PRF1 WILD-TYPE       1        3       12        17        78         4
                vv
clus             STAGE IV
  PRF1 MUTATED          0
  PRF1 WILD-TYPE        3
D440V3, multiclass
           clus
vv          PRF1 MUTATED PRF1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PRF1 MUTATED    0  0     6
  PRF1 WILD-TYPE  5 17    96
D440V4, multiclass
       clus
vv      PRF1 MUTATED PRF1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V5, binary
                cls
clus              0  1
  PRF1 MUTATED    2  4
  PRF1 WILD-TYPE 33 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRF1 MUTATED      2    4
  PRF1 WILD-TYPE   33   85
   clus
vv  PRF1 MUTATED PRF1 WILD-TYPE
  0            2             33
  1            4             85
[1] 2 2
[1] FALSE
D440V6, binary
                cls
clus              0  1
  PRF1 MUTATED    5  0
  PRF1 WILD-TYPE 52  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRF1 MUTATED      5    0
  PRF1 WILD-TYPE   52    3
   clus
vv  PRF1 MUTATED PRF1 WILD-TYPE
  0            5             52
  1            0              3
[1] 2 2
[1] FALSE
D440V7, binary
                cls
clus              0  1
  PRF1 MUTATED    2  4
  PRF1 WILD-TYPE 49 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRF1 MUTATED      2    4
  PRF1 WILD-TYPE   49   71
        clus
vv       PRF1 MUTATED PRF1 WILD-TYPE
  FEMALE            2             49
  MALE              4             71
[1] 2 2
[1] FALSE
D440V8, binary
                cls
clus              0  1
  PRF1 MUTATED    6  0
  PRF1 WILD-TYPE 82 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRF1 MUTATED      6    0
  PRF1 WILD-TYPE   82   30
     clus
vv    PRF1 MUTATED PRF1 WILD-TYPE
  NO             6             82
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRF1 MUTATED                                     6
  PRF1 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRF1 MUTATED                                       0
  PRF1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRF1 MUTATED                                                  0
  PRF1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRF1 MUTATED                                     0
  PRF1 WILD-TYPE                                   1
D440V9, multiclass
                                                  clus
vv                                                 PRF1 MUTATED PRF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V10, continuous
[1] "Remove cluster labels:" "PRF1 MUTATED"          
clus
  PRF1 MUTATED PRF1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-YY-A8LH 
"PRF1 WILD-TYPE" 
D440V11, continuous
[1] "Remove cluster labels:" "PRF1 MUTATED"          
clus
  PRF1 MUTATED PRF1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-8126 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"PRF1 WILD-TYPE" "PRF1 WILD-TYPE" "PRF1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  PRF1 MUTATED    5  0  1  0
  PRF1 WILD-TYPE 75 35  3  2
D440V12, multiclass
    clus
vv   PRF1 MUTATED PRF1 WILD-TYPE
  R0            5             75
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRF1 MUTATED       1                         1     4
  PRF1 WILD-TYPE     5                         4   110
D440V14, multiclass
                           clus
vv                          PRF1 MUTATED PRF1 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V15, binary
                cls
clus              0  1
  PRF1 MUTATED    0  4
  PRF1 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRF1 MUTATED      0    4
  PRF1 WILD-TYPE    5   87
                        clus
vv                       PRF1 MUTATED PRF1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(441) Variable = WNT2 MUTATION ANALYSIS
D441V1, survival
                sevent
clus2             0  1
  WNT2 MUTATED    3  3
  WNT2 WILD-TYPE 60 59
  WNT2 MUTATED WNT2 WILD-TYPE 
             6            119 
  WNT2 MUTATED WNT2 WILD-TYPE 
             3             59 
$`WNT2 MUTATED`
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IZ TCGA-F2-A8YN TCGA-FB-AAQ2 TCGA-IB-7651 
       45.47        43.50        10.13        17.00         5.03        19.82 

$`WNT2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39        12.95         9.60        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       23.54        15.55         4.04         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  WNT2 MUTATED WNT2 WILD-TYPE 
          5.03           0.23 
  WNT2 MUTATED WNT2 WILD-TYPE 
         45.47          90.12 
  WNT2 MUTATED WNT2 WILD-TYPE 
         18.41          15.19 
[1] "5.0 - 45.5 (18.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D441V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WNT2 MUTATED         0        0        0         1         5         0
  WNT2 WILD-TYPE       1        3       12        18        77         4
                vv
clus             STAGE IV
  WNT2 MUTATED          0
  WNT2 WILD-TYPE        3
D441V3, multiclass
           clus
vv          WNT2 MUTATED WNT2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  WNT2 MUTATED    0  0     6
  WNT2 WILD-TYPE  5 17    96
D441V4, multiclass
       clus
vv      WNT2 MUTATED WNT2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V5, binary
                cls
clus              0  1
  WNT2 MUTATED    1  5
  WNT2 WILD-TYPE 34 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT2 MUTATED      1    5
  WNT2 WILD-TYPE   34   84
   clus
vv  WNT2 MUTATED WNT2 WILD-TYPE
  0            1             34
  1            5             84
[1] 2 2
[1] FALSE
D441V6, binary
                cls
clus              0  1
  WNT2 MUTATED    2  0
  WNT2 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT2 MUTATED      2    0
  WNT2 WILD-TYPE   55    3
   clus
vv  WNT2 MUTATED WNT2 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D441V7, binary
                cls
clus              0  1
  WNT2 MUTATED    2  4
  WNT2 WILD-TYPE 49 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT2 MUTATED      2    4
  WNT2 WILD-TYPE   49   71
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  FEMALE            2             49
  MALE              4             71
[1] 2 2
[1] FALSE
D441V8, binary
                cls
clus              0  1
  WNT2 MUTATED    5  1
  WNT2 WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT2 MUTATED      5    1
  WNT2 WILD-TYPE   83   29
     clus
vv    WNT2 MUTATED WNT2 WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WNT2 MUTATED                                     5
  WNT2 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WNT2 MUTATED                                       1
  WNT2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WNT2 MUTATED                                                  0
  WNT2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  WNT2 MUTATED                                     0
  WNT2 WILD-TYPE                                   1
D441V9, multiclass
                                                  clus
vv                                                 WNT2 MUTATED WNT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V10, continuous
[1] "Remove cluster labels:" "WNT2 MUTATED"          
clus
  WNT2 MUTATED WNT2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-YY-A8LH 
"WNT2 WILD-TYPE" 
D441V11, continuous
[1] "Remove cluster labels:" "WNT2 MUTATED"          
clus
  WNT2 MUTATED WNT2 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  WNT2 MUTATED    2  4  0  0
  WNT2 WILD-TYPE 78 31  4  2
D441V12, multiclass
    clus
vv   WNT2 MUTATED WNT2 WILD-TYPE
  R0            2             78
  R1            4             31
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WNT2 MUTATED       0                         1     5
  WNT2 WILD-TYPE     6                         4   109
D441V14, multiclass
                           clus
vv                          WNT2 MUTATED WNT2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V15, binary
                cls
clus              0  1
  WNT2 MUTATED    1  4
  WNT2 WILD-TYPE  4 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT2 MUTATED      1    4
  WNT2 WILD-TYPE    4   87
                        clus
vv                       WNT2 MUTATED WNT2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(442) Variable = R3HDM1 MUTATION ANALYSIS
D442V1, survival
                  sevent
clus2               0  1
  R3HDM1 MUTATED    3  2
  R3HDM1 WILD-TYPE 60 60
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               5              120 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               2               60 
$`R3HDM1 MUTATED`
TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A7M4 TCGA-RB-A7B8 TCGA-YH-A8SY 
       32.15        19.82        15.88        15.32        12.76 

$`R3HDM1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
           12.76             0.23 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
           32.15            90.12 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
          15.880           15.155 
[1] "12.8 - 32.1 (15.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D442V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  R3HDM1 MUTATED         0        0        0         0         4         1
  R3HDM1 WILD-TYPE       1        3       12        19        78         3
                  vv
clus               STAGE IV
  R3HDM1 MUTATED          0
  R3HDM1 WILD-TYPE        3
D442V3, multiclass
           clus
vv          R3HDM1 MUTATED R3HDM1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  R3HDM1 MUTATED    0  0     5
  R3HDM1 WILD-TYPE  5 17    97
D442V4, multiclass
       clus
vv      R3HDM1 MUTATED R3HDM1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V5, binary
                  cls
clus                0  1
  R3HDM1 MUTATED    0  5
  R3HDM1 WILD-TYPE 35 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      0    5
  R3HDM1 WILD-TYPE   35   84
   clus
vv  R3HDM1 MUTATED R3HDM1 WILD-TYPE
  0              0               35
  1              5               84
[1] 2 2
[1] FALSE
D442V6, binary
                  cls
clus                0  1
  R3HDM1 MUTATED    2  0
  R3HDM1 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      2    0
  R3HDM1 WILD-TYPE   55    3
   clus
vv  R3HDM1 MUTATED R3HDM1 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D442V7, binary
                  cls
clus                0  1
  R3HDM1 MUTATED    3  2
  R3HDM1 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      3    2
  R3HDM1 WILD-TYPE   48   73
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D442V8, binary
                  cls
clus                0  1
  R3HDM1 MUTATED    3  2
  R3HDM1 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      3    2
  R3HDM1 WILD-TYPE   85   28
     clus
vv    R3HDM1 MUTATED R3HDM1 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  R3HDM1 MUTATED                                     2
  R3HDM1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  R3HDM1 MUTATED                                       2
  R3HDM1 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  R3HDM1 MUTATED                                                  0
  R3HDM1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  R3HDM1 MUTATED                                     0
  R3HDM1 WILD-TYPE                                   1
D442V9, multiclass
                                                  clus
vv                                                 R3HDM1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 R3HDM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V10, continuous
[1] "Remove cluster labels:" "R3HDM1 MUTATED"        
clus
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-YY-A8LH 
"R3HDM1 WILD-TYPE" 
D442V11, continuous
[1] "Remove cluster labels:" "R3HDM1 MUTATED"        
clus
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-AAUQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  R3HDM1 MUTATED    4  0  0  0
  R3HDM1 WILD-TYPE 76 35  4  2
D442V12, multiclass
    clus
vv   R3HDM1 MUTATED R3HDM1 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  R3HDM1 MUTATED       1                         0     4
  R3HDM1 WILD-TYPE     5                         5   110
D442V14, multiclass
                           clus
vv                          R3HDM1 MUTATED R3HDM1 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V15, binary
                  cls
clus                0  1
  R3HDM1 MUTATED    0  4
  R3HDM1 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      0    4
  R3HDM1 WILD-TYPE    5   87
                        clus
vv                       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(443) Variable = THRA MUTATION ANALYSIS
D443V1, survival
                sevent
clus2             0  1
  THRA MUTATED    1  3
  THRA WILD-TYPE 62 59
  THRA MUTATED THRA WILD-TYPE 
             4            121 
  THRA MUTATED THRA WILD-TYPE 
             3             59 
$`THRA MUTATED`
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-IB-A6UG TCGA-OE-A75W 
        7.36        33.57         1.35         8.78 

$`THRA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  THRA MUTATED THRA WILD-TYPE 
          1.35           0.23 
  THRA MUTATED THRA WILD-TYPE 
         33.57          90.12 
  THRA MUTATED THRA WILD-TYPE 
          8.07          15.32 
[1] "1.4 - 33.6 (8.1)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2.4"
D443V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  THRA MUTATED         0        1        0         1         2         0
  THRA WILD-TYPE       1        2       12        18        80         4
                vv
clus             STAGE IV
  THRA MUTATED          0
  THRA WILD-TYPE        3
D443V3, multiclass
           clus
vv          THRA MUTATED THRA WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  THRA MUTATED    1  0     3
  THRA WILD-TYPE  4 17    99
D443V4, multiclass
       clus
vv      THRA MUTATED THRA WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V5, binary
                cls
clus              0  1
  THRA MUTATED    2  2
  THRA WILD-TYPE 33 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  THRA MUTATED      2    2
  THRA WILD-TYPE   33   87
   clus
vv  THRA MUTATED THRA WILD-TYPE
  0            2             33
  1            2             87
[1] 2 2
[1] FALSE
D443V6, binary
                cls
clus              0  1
  THRA MUTATED    2  0
  THRA WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  THRA MUTATED      2    0
  THRA WILD-TYPE   55    3
   clus
vv  THRA MUTATED THRA WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D443V7, binary
                cls
clus              0  1
  THRA MUTATED    2  2
  THRA WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  THRA MUTATED      2    2
  THRA WILD-TYPE   49   73
        clus
vv       THRA MUTATED THRA WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D443V8, binary
                cls
clus              0  1
  THRA MUTATED    3  1
  THRA WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  THRA MUTATED      3    1
  THRA WILD-TYPE   85   29
     clus
vv    THRA MUTATED THRA WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  THRA MUTATED                                     4
  THRA WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  THRA MUTATED                                       0
  THRA WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  THRA MUTATED                                                  0
  THRA WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  THRA MUTATED                                     0
  THRA WILD-TYPE                                   1
D443V9, multiclass
                                                  clus
vv                                                 THRA MUTATED THRA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V10, continuous
D443V11, continuous
                vv
clus             R0 R1 R2 RX
  THRA MUTATED    3  1  0  0
  THRA WILD-TYPE 77 34  4  2
D443V12, multiclass
    clus
vv   THRA MUTATED THRA WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THRA MUTATED       0                         0     4
  THRA WILD-TYPE     6                         5   110
D443V14, multiclass
                           clus
vv                          THRA MUTATED THRA WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V15, binary
                cls
clus              0  1
  THRA MUTATED    0  4
  THRA WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  THRA MUTATED      0    4
  THRA WILD-TYPE    5   87
                        clus
vv                       THRA MUTATED THRA WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(444) Variable = MGAT2 MUTATION ANALYSIS
D444V1, survival
                 sevent
clus2              0  1
  MGAT2 MUTATED    1  3
  MGAT2 WILD-TYPE 62 59
  MGAT2 MUTATED MGAT2 WILD-TYPE 
              4             121 
  MGAT2 MUTATED MGAT2 WILD-TYPE 
              3              59 
$`MGAT2 MUTATED`
TCGA-3A-A9IV TCGA-F2-A7TX TCGA-FB-AAQ1 TCGA-HV-AA8X 
       36.26         3.12         4.04        17.49 

$`MGAT2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MGAT2 MUTATED MGAT2 WILD-TYPE 
           3.12            0.23 
  MGAT2 MUTATED MGAT2 WILD-TYPE 
          36.26           90.12 
  MGAT2 MUTATED MGAT2 WILD-TYPE 
         10.765          15.220 
[1] "3.1 - 36.3 (10.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D444V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MGAT2 MUTATED         0        0        1         0         3         0
  MGAT2 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  MGAT2 MUTATED          0
  MGAT2 WILD-TYPE        3
D444V3, multiclass
           clus
vv          MGAT2 MUTATED MGAT2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  MGAT2 MUTATED     0   2     2
  MGAT2 WILD-TYPE   5  15   100
D444V4, multiclass
       clus
vv      MGAT2 MUTATED MGAT2 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V5, binary
                 cls
clus               0  1
  MGAT2 MUTATED    1  3
  MGAT2 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT2 MUTATED      1    3
  MGAT2 WILD-TYPE   34   86
   clus
vv  MGAT2 MUTATED MGAT2 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D444V6, binary
                 cls
clus               0  1
  MGAT2 MUTATED    1  0
  MGAT2 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT2 MUTATED      1    0
  MGAT2 WILD-TYPE   56    3
   clus
vv  MGAT2 MUTATED MGAT2 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D444V7, binary
                 cls
clus               0  1
  MGAT2 MUTATED    2  2
  MGAT2 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT2 MUTATED      2    2
  MGAT2 WILD-TYPE   49   73
        clus
vv       MGAT2 MUTATED MGAT2 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D444V8, binary
                 cls
clus               0  1
  MGAT2 MUTATED    4  0
  MGAT2 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT2 MUTATED      4    0
  MGAT2 WILD-TYPE   84   30
     clus
vv    MGAT2 MUTATED MGAT2 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MGAT2 MUTATED                                     3
  MGAT2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MGAT2 MUTATED                                       1
  MGAT2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MGAT2 MUTATED                                                  0
  MGAT2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MGAT2 MUTATED                                     0
  MGAT2 WILD-TYPE                                   1
D444V9, multiclass
                                                  clus
vv                                                 MGAT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 MGAT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V10, continuous
D444V11, continuous
                 vv
clus              R0 R1 R2 RX
  MGAT2 MUTATED    1  2  1  0
  MGAT2 WILD-TYPE 79 33  3  2
D444V12, multiclass
    clus
vv   MGAT2 MUTATED MGAT2 WILD-TYPE
  R0             1              79
  R1             2              33
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MGAT2 MUTATED       1                         0     3
  MGAT2 WILD-TYPE     5                         5   111
D444V14, multiclass
                           clus
vv                          MGAT2 MUTATED MGAT2 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V15, binary
                 cls
clus               0  1
  MGAT2 MUTATED    0  2
  MGAT2 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT2 MUTATED      0    2
  MGAT2 WILD-TYPE    5   89
                        clus
vv                       MGAT2 MUTATED MGAT2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(445) Variable = HMX2 MUTATION ANALYSIS
D445V1, survival
                sevent
clus2             0  1
  HMX2 MUTATED    2  2
  HMX2 WILD-TYPE 61 60
  HMX2 MUTATED HMX2 WILD-TYPE 
             4            121 
  HMX2 MUTATED HMX2 WILD-TYPE 
             2             60 
$`HMX2 MUTATED`
TCGA-2J-AAB8 TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-8126 
        2.63        17.00        19.82        15.19 

$`HMX2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        20.19        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HMX2 MUTATED HMX2 WILD-TYPE 
          2.63           0.23 
  HMX2 MUTATED HMX2 WILD-TYPE 
         19.82          90.12 
  HMX2 MUTATED HMX2 WILD-TYPE 
        16.095         15.220 
[1] "2.6 - 19.8 (16.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D445V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HMX2 MUTATED         0        0        0         0         3         1
  HMX2 WILD-TYPE       1        3       12        19        79         3
                vv
clus             STAGE IV
  HMX2 MUTATED          0
  HMX2 WILD-TYPE        3
D445V3, multiclass
           clus
vv          HMX2 MUTATED HMX2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  HMX2 MUTATED    0  0     4
  HMX2 WILD-TYPE  5 17    98
D445V4, multiclass
       clus
vv      HMX2 MUTATED HMX2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V5, binary
                cls
clus              0  1
  HMX2 MUTATED    0  4
  HMX2 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      0    4
  HMX2 WILD-TYPE   35   85
   clus
vv  HMX2 MUTATED HMX2 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D445V6, binary
                cls
clus              0  1
  HMX2 MUTATED    3  0
  HMX2 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      3    0
  HMX2 WILD-TYPE   54    3
   clus
vv  HMX2 MUTATED HMX2 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D445V7, binary
                cls
clus              0  1
  HMX2 MUTATED    3  1
  HMX2 WILD-TYPE 48 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      3    1
  HMX2 WILD-TYPE   48   74
        clus
vv       HMX2 MUTATED HMX2 WILD-TYPE
  FEMALE            3             48
  MALE              1             74
[1] 2 2
[1] FALSE
D445V8, binary
                cls
clus              0  1
  HMX2 MUTATED    2  1
  HMX2 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      2    1
  HMX2 WILD-TYPE   86   29
     clus
vv    HMX2 MUTATED HMX2 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HMX2 MUTATED                                     4
  HMX2 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HMX2 MUTATED                                       0
  HMX2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HMX2 MUTATED                                                  0
  HMX2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  HMX2 MUTATED                                     0
  HMX2 WILD-TYPE                                   1
D445V9, multiclass
                                                  clus
vv                                                 HMX2 MUTATED HMX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V10, continuous
[1] "Remove cluster labels:" "HMX2 MUTATED"          
clus
  HMX2 MUTATED HMX2 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-A6UF     TCGA-IB-A6UG 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-YY-A8LH 
"HMX2 WILD-TYPE" 
D445V11, continuous
[1] "Remove cluster labels:" "HMX2 MUTATED"          
clus
  HMX2 MUTATED HMX2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  HMX2 MUTATED    2  2  0  0
  HMX2 WILD-TYPE 78 33  4  2
D445V12, multiclass
    clus
vv   HMX2 MUTATED HMX2 WILD-TYPE
  R0            2             78
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMX2 MUTATED       0                         0     4
  HMX2 WILD-TYPE     6                         5   110
D445V14, multiclass
                           clus
vv                          HMX2 MUTATED HMX2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V15, binary
                cls
clus              0  1
  HMX2 MUTATED    1  2
  HMX2 WILD-TYPE  4 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      1    2
  HMX2 WILD-TYPE    4   89
                        clus
vv                       HMX2 MUTATED HMX2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(446) Variable = KRTAP4-8 MUTATION ANALYSIS
D446V1, survival
                    sevent
clus2                 0  1
  KRTAP4-8 MUTATED    3  2
  KRTAP4-8 WILD-TYPE 60 60
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 5                120 
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 2                 60 
$`KRTAP4-8 MUTATED`
TCGA-S4-A8RO TCGA-3A-A9J0 TCGA-IB-7651 TCGA-US-A779 TCGA-YB-A89D 
       17.26        24.43        19.82        16.80        11.51 

$`KRTAP4-8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
             11.51               0.23 
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
             24.43              90.12 
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
            17.260             15.155 
[1] "11.5 - 24.4 (17.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D446V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KRTAP4-8 MUTATED         0        0        0         0         5         0
  KRTAP4-8 WILD-TYPE       1        3       12        19        77         4
                    vv
clus                 STAGE IV
  KRTAP4-8 MUTATED          0
  KRTAP4-8 WILD-TYPE        3
D446V3, multiclass
           clus
vv          KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KRTAP4-8 MUTATED    0  0     5
  KRTAP4-8 WILD-TYPE  5 17    97
D446V4, multiclass
       clus
vv      KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V5, binary
                    cls
clus                  0  1
  KRTAP4-8 MUTATED    0  5
  KRTAP4-8 WILD-TYPE 35 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-8 MUTATED      0    5
  KRTAP4-8 WILD-TYPE   35   84
   clus
vv  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  0                0                 35
  1                5                 84
[1] 2 2
[1] FALSE
D446V6, binary
                    cls
clus                  0  1
  KRTAP4-8 MUTATED    1  0
  KRTAP4-8 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-8 MUTATED      1    0
  KRTAP4-8 WILD-TYPE   56    3
   clus
vv  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D446V7, binary
                    cls
clus                  0  1
  KRTAP4-8 MUTATED    3  2
  KRTAP4-8 WILD-TYPE 48 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-8 MUTATED      3    2
  KRTAP4-8 WILD-TYPE   48   73
        clus
vv       KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  FEMALE                3                 48
  MALE                  2                 73
[1] 2 2
[1] FALSE
D446V8, binary
                    cls
clus                  0  1
  KRTAP4-8 MUTATED    2  2
  KRTAP4-8 WILD-TYPE 86 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-8 MUTATED      2    2
  KRTAP4-8 WILD-TYPE   86   28
     clus
vv    KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  NO                 2                 86
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRTAP4-8 MUTATED                                     5
  KRTAP4-8 WILD-TYPE                                 100
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRTAP4-8 MUTATED                                       0
  KRTAP4-8 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRTAP4-8 MUTATED                                                  0
  KRTAP4-8 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KRTAP4-8 MUTATED                                     0
  KRTAP4-8 WILD-TYPE                                   1
D446V9, multiclass
                                                  clus
vv                                                 KRTAP4-8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KRTAP4-8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V10, continuous
[1] "Remove cluster labels:" "KRTAP4-8 MUTATED"      
clus
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
D446V11, continuous
[1] "Remove cluster labels:" "KRTAP4-8 MUTATED"      
clus
  KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"KRTAP4-8 WILD-TYPE" "KRTAP4-8 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  KRTAP4-8 MUTATED    4  1  0  0
  KRTAP4-8 WILD-TYPE 76 34  4  2
D446V12, multiclass
    clus
vv   KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  R0                4                 76
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP4-8 MUTATED       0                         0     5
  KRTAP4-8 WILD-TYPE     6                         5   109
D446V14, multiclass
                           clus
vv                          KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V15, binary
                    cls
clus                  0  1
  KRTAP4-8 MUTATED    0  5
  KRTAP4-8 WILD-TYPE  5 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-8 MUTATED      0    5
  KRTAP4-8 WILD-TYPE    5   86
                        clus
vv                       KRTAP4-8 MUTATED KRTAP4-8 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                 86
[1] 2 2
[1] FALSE

Clustering(447) Variable = TBC1D1 MUTATION ANALYSIS
D447V1, survival
                  sevent
clus2               0  1
  TBC1D1 MUTATED    2  2
  TBC1D1 WILD-TYPE 61 60
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               4              121 
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               2               60 
$`TBC1D1 MUTATED`
TCGA-3A-A9IL TCGA-IB-A5SS TCGA-IB-A5SQ TCGA-IB-AAUU 
       90.12        15.12         7.20         8.05 

$`TBC1D1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
            7.20             0.23 
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
           90.12            75.12 
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
          11.585           15.320 
[1] "7.2 - 90.1 (11.6)" "0.2 - 75.1 (15.3)"
[1] "hr=" "1"  
D447V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TBC1D1 MUTATED         1        0        1         0         2         0
  TBC1D1 WILD-TYPE       0        3       11        19        80         4
                  vv
clus               STAGE IV
  TBC1D1 MUTATED          0
  TBC1D1 WILD-TYPE        3
D447V3, multiclass
           clus
vv          TBC1D1 MUTATED TBC1D1 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TBC1D1 MUTATED     1   1     2
  TBC1D1 WILD-TYPE   4  16   100
D447V4, multiclass
       clus
vv      TBC1D1 MUTATED TBC1D1 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V5, binary
                  cls
clus                0  1
  TBC1D1 MUTATED    1  2
  TBC1D1 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D1 MUTATED      1    2
  TBC1D1 WILD-TYPE   34   87
   clus
vv  TBC1D1 MUTATED TBC1D1 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D447V6, binary
                  cls
clus                0  1
  TBC1D1 MUTATED    3  0
  TBC1D1 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D1 MUTATED      3    0
  TBC1D1 WILD-TYPE   54    3
   clus
vv  TBC1D1 MUTATED TBC1D1 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D447V7, binary
                  cls
clus                0  1
  TBC1D1 MUTATED    3  1
  TBC1D1 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D1 MUTATED      3    1
  TBC1D1 WILD-TYPE   48   74
        clus
vv       TBC1D1 MUTATED TBC1D1 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D447V8, binary
                  cls
clus                0  1
  TBC1D1 MUTATED    4  0
  TBC1D1 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D1 MUTATED      4    0
  TBC1D1 WILD-TYPE   84   30
     clus
vv    TBC1D1 MUTATED TBC1D1 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TBC1D1 MUTATED                                     3
  TBC1D1 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TBC1D1 MUTATED                                       1
  TBC1D1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TBC1D1 MUTATED                                                  0
  TBC1D1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TBC1D1 MUTATED                                     0
  TBC1D1 WILD-TYPE                                   1
D447V9, multiclass
                                                  clus
vv                                                 TBC1D1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TBC1D1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V10, continuous
[1] "Remove cluster labels:" "TBC1D1 MUTATED"        
clus
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-LB-A7SX 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-YY-A8LH 
"TBC1D1 WILD-TYPE" 
D447V11, continuous
[1] "Remove cluster labels:" "TBC1D1 MUTATED"        
clus
  TBC1D1 MUTATED TBC1D1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-LB-A7SX 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" "TBC1D1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TBC1D1 MUTATED    4  0  0  0
  TBC1D1 WILD-TYPE 76 35  4  2
D447V12, multiclass
    clus
vv   TBC1D1 MUTATED TBC1D1 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TBC1D1 MUTATED       0                         0     4
  TBC1D1 WILD-TYPE     6                         5   110
D447V14, multiclass
                           clus
vv                          TBC1D1 MUTATED TBC1D1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V15, binary
                  cls
clus                0  1
  TBC1D1 MUTATED    0  4
  TBC1D1 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TBC1D1 MUTATED      0    4
  TBC1D1 WILD-TYPE    5   87
                        clus
vv                       TBC1D1 MUTATED TBC1D1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(448) Variable = MTR MUTATION ANALYSIS
D448V1, survival
               sevent
clus2            0  1
  MTR MUTATED    5  2
  MTR WILD-TYPE 58 60
  MTR MUTATED MTR WILD-TYPE 
            7           118 
  MTR MUTATED MTR WILD-TYPE 
            2            60 
$`MTR MUTATED`
TCGA-2J-AABK TCGA-3A-A9IZ TCGA-IB-7651 TCGA-IB-A6UF TCGA-IB-AAUS TCGA-YB-A89D 
       15.91        10.13        19.82        21.90         7.40        11.51 
TCGA-Z5-AAPL 
       15.35 

$`MTR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        12.76        66.28 

  MTR MUTATED MTR WILD-TYPE 
         7.40          0.23 
  MTR MUTATED MTR WILD-TYPE 
        21.90         90.12 
  MTR MUTATED MTR WILD-TYPE 
       15.350        15.205 
[1] "7.4 - 21.9 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D448V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MTR MUTATED         0        0        0         1         6         0
  MTR WILD-TYPE       1        3       12        18        76         4
               vv
clus            STAGE IV
  MTR MUTATED          0
  MTR WILD-TYPE        3
D448V3, multiclass
           clus
vv          MTR MUTATED MTR WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           1            18
  STAGE IIB           6            76
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  MTR MUTATED    0  0     7
  MTR WILD-TYPE  5 17    95
D448V4, multiclass
       clus
vv      MTR MUTATED MTR WILD-TYPE
  T1              0             5
  T2              0            17
  T3+T4           7            95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V5, binary
               cls
clus             0  1
  MTR MUTATED    1  6
  MTR WILD-TYPE 34 83
[1] "tbl2"
               cls
clus            [,1] [,2]
  MTR MUTATED      1    6
  MTR WILD-TYPE   34   83
   clus
vv  MTR MUTATED MTR WILD-TYPE
  0           1            34
  1           6            83
[1] 2 2
[1] FALSE
D448V6, binary
               cls
clus             0  1
  MTR MUTATED    5  0
  MTR WILD-TYPE 52  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  MTR MUTATED      5    0
  MTR WILD-TYPE   52    3
   clus
vv  MTR MUTATED MTR WILD-TYPE
  0           5            52
  1           0             3
[1] 2 2
[1] FALSE
D448V7, binary
               cls
clus             0  1
  MTR MUTATED    3  4
  MTR WILD-TYPE 48 71
[1] "tbl2"
               cls
clus            [,1] [,2]
  MTR MUTATED      3    4
  MTR WILD-TYPE   48   71
        clus
vv       MTR MUTATED MTR WILD-TYPE
  FEMALE           3            48
  MALE             4            71
[1] 2 2
[1] FALSE
D448V8, binary
               cls
clus             0  1
  MTR MUTATED    5  2
  MTR WILD-TYPE 83 28
[1] "tbl2"
               cls
clus            [,1] [,2]
  MTR MUTATED      5    2
  MTR WILD-TYPE   83   28
     clus
vv    MTR MUTATED MTR WILD-TYPE
  NO            5            83
  YES           2            28
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MTR MUTATED                                     7
  MTR WILD-TYPE                                  98
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MTR MUTATED                                       0
  MTR WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MTR MUTATED                                                  0
  MTR WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  MTR MUTATED                                     0
  MTR WILD-TYPE                                   1
D448V9, multiclass
                                                  clus
vv                                                 MTR MUTATED MTR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        7            98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V10, continuous
D448V11, continuous
               vv
clus            R0 R1 R2 RX
  MTR MUTATED    3  4  0  0
  MTR WILD-TYPE 77 31  4  2
D448V12, multiclass
    clus
vv   MTR MUTATED MTR WILD-TYPE
  R0           3            77
  R1           4            31
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTR MUTATED       0                         0     7
  MTR WILD-TYPE     6                         5   107
D448V14, multiclass
                           clus
vv                          MTR MUTATED MTR WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               7           107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V15, binary
               cls
clus             0  1
  MTR MUTATED    1  5
  MTR WILD-TYPE  4 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  MTR MUTATED      1    5
  MTR WILD-TYPE    4   86
                        clus
vv                       MTR MUTATED MTR WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO           5            86
[1] 2 2
[1] FALSE

Clustering(449) Variable = CCDC103 MUTATION ANALYSIS
D449V1, survival
                   sevent
clus2                0  1
  CCDC103 MUTATED    2  1
  CCDC103 WILD-TYPE 61 61
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                3               122 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                1                61 
$`CCDC103 MUTATED`
TCGA-2J-AABE TCGA-FB-AAQ1 TCGA-IB-8126 
       22.22         4.04        15.19 

$`CCDC103 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
        0.23        19.82        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CCDC103 MUTATED CCDC103 WILD-TYPE 
             4.04              0.23 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
            22.22             90.12 
  CCDC103 MUTATED CCDC103 WILD-TYPE 
            15.19             15.27 
[1] "4.0 - 22.2 (15.2)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D449V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC103 MUTATED         0        0        0         1         1         1
  CCDC103 WILD-TYPE       1        3       12        18        81         3
                   vv
clus                STAGE IV
  CCDC103 MUTATED          0
  CCDC103 WILD-TYPE        3
D449V3, multiclass
           clus
vv          CCDC103 MUTATED CCDC103 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               1                81
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC103 MUTATED    0  0     3
  CCDC103 WILD-TYPE  5 17    99
D449V4, multiclass
       clus
vv      CCDC103 MUTATED CCDC103 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V5, binary
                   cls
clus                 0  1
  CCDC103 MUTATED    1  2
  CCDC103 WILD-TYPE 34 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      1    2
  CCDC103 WILD-TYPE   34   87
   clus
vv  CCDC103 MUTATED CCDC103 WILD-TYPE
  0               1                34
  1               2                87
[1] 2 2
[1] FALSE
D449V6, binary
                   cls
clus                 0  1
  CCDC103 MUTATED    2  0
  CCDC103 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      2    0
  CCDC103 WILD-TYPE   55    3
   clus
vv  CCDC103 MUTATED CCDC103 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D449V7, binary
                   cls
clus                 0  1
  CCDC103 MUTATED    1  2
  CCDC103 WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      1    2
  CCDC103 WILD-TYPE   50   73
        clus
vv       CCDC103 MUTATED CCDC103 WILD-TYPE
  FEMALE               1                50
  MALE                 2                73
[1] 2 2
[1] FALSE
D449V8, binary
                   cls
clus                 0  1
  CCDC103 MUTATED    2  1
  CCDC103 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      2    1
  CCDC103 WILD-TYPE   86   29
     clus
vv    CCDC103 MUTATED CCDC103 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC103 MUTATED                                     3
  CCDC103 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC103 MUTATED                                       0
  CCDC103 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC103 MUTATED                                                  0
  CCDC103 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC103 MUTATED                                     0
  CCDC103 WILD-TYPE                                   1
D449V9, multiclass
                                                  clus
vv                                                 CCDC103 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC103 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V10, continuous
[1] "Remove cluster labels:" "CCDC103 MUTATED"       
clus
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-A6UF        TCGA-IB-A6UG 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-YY-A8LH 
"CCDC103 WILD-TYPE" 
D449V11, continuous
[1] "Remove cluster labels:" "CCDC103 MUTATED"       
clus
  CCDC103 MUTATED CCDC103 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABF 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" "CCDC103 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC103 MUTATED    1  2  0  0
  CCDC103 WILD-TYPE 79 33  4  2
D449V12, multiclass
    clus
vv   CCDC103 MUTATED CCDC103 WILD-TYPE
  R0               1                79
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC103 MUTATED       0                         0     3
  CCDC103 WILD-TYPE     6                         5   111
D449V14, multiclass
                           clus
vv                          CCDC103 MUTATED CCDC103 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V15, binary
                   cls
clus                 0  1
  CCDC103 MUTATED    0  2
  CCDC103 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC103 MUTATED      0    2
  CCDC103 WILD-TYPE    5   89
                        clus
vv                       CCDC103 MUTATED CCDC103 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(450) Variable = RBBP8 MUTATION ANALYSIS
D450V1, survival
                 sevent
clus2              0  1
  RBBP8 MUTATED    1  4
  RBBP8 WILD-TYPE 62 58
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              5             120 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              4              58 
$`RBBP8 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-FB-A5VM TCGA-FZ-5923 TCGA-IB-7651 
       23.97         9.63        16.37        20.35        19.82 

$`RBBP8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14        16.37         2.17         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H8-A6C1 
       24.36         2.01         5.10        36.20        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RBBP8 MUTATED RBBP8 WILD-TYPE 
           9.63            0.23 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
          23.97           90.12 
  RBBP8 MUTATED RBBP8 WILD-TYPE 
         19.820          15.155 
[1] "9.6 - 24.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D450V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBBP8 MUTATED         0        0        1         1         2         0
  RBBP8 WILD-TYPE       1        3       11        18        80         4
                 vv
clus              STAGE IV
  RBBP8 MUTATED          1
  RBBP8 WILD-TYPE        2
D450V3, multiclass
           clus
vv          RBBP8 MUTATED RBBP8 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBBP8 MUTATED    0  2     3
  RBBP8 WILD-TYPE  5 15    99
D450V4, multiclass
       clus
vv      RBBP8 MUTATED RBBP8 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V5, binary
                 cls
clus               0  1
  RBBP8 MUTATED    2  3
  RBBP8 WILD-TYPE 33 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      2    3
  RBBP8 WILD-TYPE   33   86
   clus
vv  RBBP8 MUTATED RBBP8 WILD-TYPE
  0             2              33
  1             3              86
[1] 2 2
[1] FALSE
D450V6, binary
                 cls
clus               0  1
  RBBP8 MUTATED    4  1
  RBBP8 WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      4    1
  RBBP8 WILD-TYPE   53    2
   clus
vv  RBBP8 MUTATED RBBP8 WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D450V7, binary
                 cls
clus               0  1
  RBBP8 MUTATED    1  4
  RBBP8 WILD-TYPE 50 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      1    4
  RBBP8 WILD-TYPE   50   71
        clus
vv       RBBP8 MUTATED RBBP8 WILD-TYPE
  FEMALE             1              50
  MALE               4              71
[1] 2 2
[1] FALSE
D450V8, binary
                 cls
clus               0  1
  RBBP8 MUTATED    5  0
  RBBP8 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      5    0
  RBBP8 WILD-TYPE   83   30
     clus
vv    RBBP8 MUTATED RBBP8 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBBP8 MUTATED                                     4
  RBBP8 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBBP8 MUTATED                                       1
  RBBP8 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBBP8 MUTATED                                                  0
  RBBP8 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBBP8 MUTATED                                     0
  RBBP8 WILD-TYPE                                   1
D450V9, multiclass
                                                  clus
vv                                                 RBBP8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RBBP8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V10, continuous
[1] "Remove cluster labels:" "RBBP8 MUTATED"         
clus
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-YY-A8LH 
"RBBP8 WILD-TYPE" 
D450V11, continuous
[1] "Remove cluster labels:" "RBBP8 MUTATED"         
clus
  RBBP8 MUTATED RBBP8 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" "RBBP8 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RBBP8 MUTATED    5  0  0  0
  RBBP8 WILD-TYPE 75 35  4  2
D450V12, multiclass
    clus
vv   RBBP8 MUTATED RBBP8 WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBBP8 MUTATED       0                         0     5
  RBBP8 WILD-TYPE     6                         5   109
D450V14, multiclass
                           clus
vv                          RBBP8 MUTATED RBBP8 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V15, binary
                 cls
clus               0  1
  RBBP8 MUTATED    0  3
  RBBP8 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP8 MUTATED      0    3
  RBBP8 WILD-TYPE    5   88
                        clus
vv                       RBBP8 MUTATED RBBP8 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(451) Variable = FAM102A MUTATION ANALYSIS
D451V1, survival
                   sevent
clus2                0  1
  FAM102A MUTATED    0  4
  FAM102A WILD-TYPE 63 58
  FAM102A MUTATED FAM102A WILD-TYPE 
                4               121 
  FAM102A MUTATED FAM102A WILD-TYPE 
                4                58 
$`FAM102A MUTATED`
TCGA-US-A77E TCGA-IB-7651 TCGA-LB-A9Q5 TCGA-US-A779 
       14.14        19.82        10.29        16.80 

$`FAM102A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FAM102A MUTATED FAM102A WILD-TYPE 
            10.29              0.23 
  FAM102A MUTATED FAM102A WILD-TYPE 
            19.82             90.12 
  FAM102A MUTATED FAM102A WILD-TYPE 
            15.47             15.22 
[1] "10.3 - 19.8 (15.5)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.4"
D451V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM102A MUTATED         0        0        0         0         4         0
  FAM102A WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  FAM102A MUTATED          0
  FAM102A WILD-TYPE        3
D451V3, multiclass
           clus
vv          FAM102A MUTATED FAM102A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  FAM102A MUTATED    0  0     4
  FAM102A WILD-TYPE  5 17    98
D451V4, multiclass
       clus
vv      FAM102A MUTATED FAM102A WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V5, binary
                   cls
clus                 0  1
  FAM102A MUTATED    0  4
  FAM102A WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM102A MUTATED      0    4
  FAM102A WILD-TYPE   35   85
   clus
vv  FAM102A MUTATED FAM102A WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D451V6, binary
                   cls
clus                 0  1
  FAM102A MUTATED    1  0
  FAM102A WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM102A MUTATED      1    0
  FAM102A WILD-TYPE   56    3
   clus
vv  FAM102A MUTATED FAM102A WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D451V7, binary
                   cls
clus                 0  1
  FAM102A MUTATED    3  1
  FAM102A WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM102A MUTATED      3    1
  FAM102A WILD-TYPE   48   74
        clus
vv       FAM102A MUTATED FAM102A WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D451V8, binary
                   cls
clus                 0  1
  FAM102A MUTATED    2  1
  FAM102A WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM102A MUTATED      2    1
  FAM102A WILD-TYPE   86   29
     clus
vv    FAM102A MUTATED FAM102A WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM102A MUTATED                                     3
  FAM102A WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM102A MUTATED                                       1
  FAM102A WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM102A MUTATED                                                  0
  FAM102A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM102A MUTATED                                     0
  FAM102A WILD-TYPE                                   1
D451V9, multiclass
                                                  clus
vv                                                 FAM102A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 FAM102A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V10, continuous
[1] "Remove cluster labels:" "FAM102A MUTATED"       
clus
  FAM102A MUTATED FAM102A WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-OE-A75W        TCGA-XN-A8T5 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-YY-A8LH 
"FAM102A WILD-TYPE" 
D451V11, continuous
[1] "Remove cluster labels:" "FAM102A MUTATED"       
clus
  FAM102A MUTATED FAM102A WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-OE-A75W 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"FAM102A WILD-TYPE" "FAM102A WILD-TYPE" "FAM102A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  FAM102A MUTATED    3  1  0  0
  FAM102A WILD-TYPE 77 34  4  2
D451V12, multiclass
    clus
vv   FAM102A MUTATED FAM102A WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM102A MUTATED       0                         0     4
  FAM102A WILD-TYPE     6                         5   110
D451V14, multiclass
                           clus
vv                          FAM102A MUTATED FAM102A WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V15, binary
                   cls
clus                 0  1
  FAM102A MUTATED    0  4
  FAM102A WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM102A MUTATED      0    4
  FAM102A WILD-TYPE    5   87
                        clus
vv                       FAM102A MUTATED FAM102A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(452) Variable = FAM18A MUTATION ANALYSIS
D452V1, survival
                  sevent
clus2               0  1
  FAM18A MUTATED    3  0
  FAM18A WILD-TYPE 60 62
  FAM18A MUTATED FAM18A WILD-TYPE 
               3              122 
  FAM18A MUTATED FAM18A WILD-TYPE 
               0               62 
$`FAM18A MUTATED`
TCGA-F2-A8YN TCGA-HV-A7OL TCGA-Q3-A5QY 
       17.00         8.28        13.68 

$`FAM18A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FAM18A MUTATED FAM18A WILD-TYPE 
            8.28             0.23 
  FAM18A MUTATED FAM18A WILD-TYPE 
           17.00            90.12 
  FAM18A MUTATED FAM18A WILD-TYPE 
           13.68            15.27 
[1] "8.3 - 17.0 (13.7)" "0.2 - 90.1 (15.3)"
[1] "hr="     "9200000"
D452V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM18A MUTATED         0        0        0         2         1         0
  FAM18A WILD-TYPE       1        3       12        17        81         4
                  vv
clus               STAGE IV
  FAM18A MUTATED          0
  FAM18A WILD-TYPE        3
D452V3, multiclass
           clus
vv          FAM18A MUTATED FAM18A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  FAM18A MUTATED    0  0     3
  FAM18A WILD-TYPE  5 17    99
D452V4, multiclass
       clus
vv      FAM18A MUTATED FAM18A WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V5, binary
                  cls
clus                0  1
  FAM18A MUTATED    2  1
  FAM18A WILD-TYPE 33 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      2    1
  FAM18A WILD-TYPE   33   88
   clus
vv  FAM18A MUTATED FAM18A WILD-TYPE
  0              2               33
  1              1               88
[1] 2 2
[1] FALSE
D452V6, binary
                  cls
clus                0  1
  FAM18A MUTATED    1  0
  FAM18A WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      1    0
  FAM18A WILD-TYPE   56    3
   clus
vv  FAM18A MUTATED FAM18A WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D452V7, binary
                  cls
clus                0  1
  FAM18A MUTATED    0  3
  FAM18A WILD-TYPE 51 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      0    3
  FAM18A WILD-TYPE   51   72
        clus
vv       FAM18A MUTATED FAM18A WILD-TYPE
  FEMALE              0               51
  MALE                3               72
[1] 2 2
[1] FALSE
D452V8, binary
                  cls
clus                0  1
  FAM18A MUTATED    3  0
  FAM18A WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      3    0
  FAM18A WILD-TYPE   85   30
     clus
vv    FAM18A MUTATED FAM18A WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM18A MUTATED                                     3
  FAM18A WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM18A MUTATED                                       0
  FAM18A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM18A MUTATED                                                  0
  FAM18A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM18A MUTATED                                     0
  FAM18A WILD-TYPE                                   1
D452V9, multiclass
                                                  clus
vv                                                 FAM18A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 FAM18A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V10, continuous
[1] "Remove cluster labels:" "FAM18A MUTATED"        
clus
  FAM18A MUTATED FAM18A WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
D452V11, continuous
                  vv
clus               R0 R1 R2 RX
  FAM18A MUTATED    1  1  1  0
  FAM18A WILD-TYPE 79 34  3  2
D452V12, multiclass
    clus
vv   FAM18A MUTATED FAM18A WILD-TYPE
  R0              1               79
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V13, continuous
[1] "Remove cluster labels:" "FAM18A MUTATED"        
clus
  FAM18A MUTATED FAM18A WILD-TYPE 
               2              122 
      TCGA-2J-AABR       TCGA-2J-AABT       TCGA-3A-A9I5       TCGA-3A-A9IJ 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3A-A9IL       TCGA-F2-A44G       TCGA-FB-AAQ6       TCGA-FZ-5924 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-S4-A8RO       TCGA-US-A77E       TCGA-XD-AAUL       TCGA-2J-AAB1 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2J-AAB4       TCGA-2J-AAB6       TCGA-2J-AAB8       TCGA-2J-AAB9 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABH 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2J-AABK       TCGA-2J-AABO       TCGA-2J-AABP       TCGA-2J-AABU 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-2L-AAQI 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-2L-AAQJ       TCGA-2L-AAQL       TCGA-2L-AAQM       TCGA-3A-A9I7 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IC       TCGA-3A-A9IH 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3A-A9IR       TCGA-3A-A9IS       TCGA-3A-A9IU       TCGA-3A-A9IV 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-3A-A9IZ       TCGA-3A-A9J0       TCGA-3E-AAAY 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-3E-AAAZ       TCGA-F2-7273       TCGA-F2-A7TX       TCGA-FB-A5VM 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPP       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-FB-AAPU       TCGA-FB-AAPZ       TCGA-FB-AAQ0       TCGA-FB-AAQ1 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-FB-AAQ2       TCGA-FB-AAQ3       TCGA-FZ-5919       TCGA-FZ-5920 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-FZ-5921       TCGA-FZ-5922       TCGA-FZ-5923       TCGA-FZ-5926 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HV-A7OP       TCGA-HV-AA8V       TCGA-HV-AA8X 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-HZ-7918       TCGA-HZ-7925       TCGA-HZ-8637       TCGA-HZ-A49I 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-HZ-A77O       TCGA-HZ-A77P       TCGA-HZ-A8P1       TCGA-HZ-A9TJ 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7652       TCGA-IB-7885       TCGA-IB-8126 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-A5SO       TCGA-IB-A5SP       TCGA-IB-A5SQ       TCGA-IB-A5ST 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7LX       TCGA-IB-A7M4 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-AAUM       TCGA-IB-AAUN       TCGA-IB-AAUO       TCGA-IB-AAUP 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUR       TCGA-IB-AAUS       TCGA-IB-AAUU 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-IB-AAUW       TCGA-LB-A8F3       TCGA-LB-A9Q5 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-OE-A75W       TCGA-Q3-AA2A       TCGA-RB-A7B8       TCGA-RB-AA9M 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-RL-AAAS       TCGA-US-A776       TCGA-US-A779       TCGA-US-A77G 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-US-A77J       TCGA-XD-AAUG       TCGA-XD-AAUH       TCGA-XD-AAUI 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-XN-A8T3       TCGA-XN-A8T5       TCGA-YB-A89D       TCGA-YH-A8SY 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
      TCGA-YY-A8LH       TCGA-Z5-AAPL 
"FAM18A WILD-TYPE" "FAM18A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM18A MUTATED       1                         0     2
  FAM18A WILD-TYPE     5                         5   112
D452V14, multiclass
                           clus
vv                          FAM18A MUTATED FAM18A WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V15, binary
                  cls
clus                0  1
  FAM18A MUTATED    0  2
  FAM18A WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM18A MUTATED      0    2
  FAM18A WILD-TYPE    5   89
                        clus
vv                       FAM18A MUTATED FAM18A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(453) Variable = AMAC1 MUTATION ANALYSIS
D453V1, survival
                 sevent
clus2              0  1
  AMAC1 MUTATED    2  5
  AMAC1 WILD-TYPE 61 57
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              7             118 
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              5              57 
$`AMAC1 MUTATED`
TCGA-2J-AAB6 TCGA-FB-A5VM TCGA-HZ-8637 TCGA-IB-7651 TCGA-RB-A7B8 TCGA-RL-AAAS 
        9.63        16.37        17.00        19.82        15.32         0.30 
TCGA-XD-AAUG 
       13.81 

$`AMAC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 
        8.78        13.68         3.12         9.40        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        18.67        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  AMAC1 MUTATED AMAC1 WILD-TYPE 
           0.30            0.23 
  AMAC1 MUTATED AMAC1 WILD-TYPE 
          19.82           90.12 
  AMAC1 MUTATED AMAC1 WILD-TYPE 
         15.320          15.205 
[1] "0.3 - 19.8 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D453V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMAC1 MUTATED         0        0        2         1         3         0
  AMAC1 WILD-TYPE       1        3       10        18        79         4
                 vv
clus              STAGE IV
  AMAC1 MUTATED          1
  AMAC1 WILD-TYPE        2
D453V3, multiclass
           clus
vv          AMAC1 MUTATED AMAC1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AMAC1 MUTATED    0  2     5
  AMAC1 WILD-TYPE  5 15    97
D453V4, multiclass
       clus
vv      AMAC1 MUTATED AMAC1 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V5, binary
                 cls
clus               0  1
  AMAC1 MUTATED    3  4
  AMAC1 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMAC1 MUTATED      3    4
  AMAC1 WILD-TYPE   32   85
   clus
vv  AMAC1 MUTATED AMAC1 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D453V6, binary
                 cls
clus               0  1
  AMAC1 MUTATED    4  1
  AMAC1 WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMAC1 MUTATED      4    1
  AMAC1 WILD-TYPE   53    2
   clus
vv  AMAC1 MUTATED AMAC1 WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D453V7, binary
                 cls
clus               0  1
  AMAC1 MUTATED    5  2
  AMAC1 WILD-TYPE 46 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMAC1 MUTATED      5    2
  AMAC1 WILD-TYPE   46   73
        clus
vv       AMAC1 MUTATED AMAC1 WILD-TYPE
  FEMALE             5              46
  MALE               2              73
[1] 2 2
[1] FALSE
D453V8, binary
                 cls
clus               0  1
  AMAC1 MUTATED    6  1
  AMAC1 WILD-TYPE 82 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMAC1 MUTATED      6    1
  AMAC1 WILD-TYPE   82   29
     clus
vv    AMAC1 MUTATED AMAC1 WILD-TYPE
  NO              6              82
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMAC1 MUTATED                                     6
  AMAC1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMAC1 MUTATED                                       1
  AMAC1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMAC1 MUTATED                                                  0
  AMAC1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AMAC1 MUTATED                                     0
  AMAC1 WILD-TYPE                                   1
D453V9, multiclass
                                                  clus
vv                                                 AMAC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 AMAC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V10, continuous
[1] "Remove cluster labels:" "AMAC1 MUTATED"         
clus
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-YY-A8LH 
"AMAC1 WILD-TYPE" 
D453V11, continuous
[1] "Remove cluster labels:" "AMAC1 MUTATED"         
clus
  AMAC1 MUTATED AMAC1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" "AMAC1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  AMAC1 MUTATED    7  0  0  0
  AMAC1 WILD-TYPE 73 35  4  2
D453V12, multiclass
    clus
vv   AMAC1 MUTATED AMAC1 WILD-TYPE
  R0             7              73
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMAC1 MUTATED       0                         0     7
  AMAC1 WILD-TYPE     6                         5   107
D453V14, multiclass
                           clus
vv                          AMAC1 MUTATED AMAC1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V15, binary
                 cls
clus               0  1
  AMAC1 MUTATED    1  5
  AMAC1 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMAC1 MUTATED      1    5
  AMAC1 WILD-TYPE    4   86
                        clus
vv                       AMAC1 MUTATED AMAC1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(454) Variable = NFATC2 MUTATION ANALYSIS
D454V1, survival
                  sevent
clus2               0  1
  NFATC2 MUTATED    3  3
  NFATC2 WILD-TYPE 60 59
  NFATC2 MUTATED NFATC2 WILD-TYPE 
               6              119 
  NFATC2 MUTATED NFATC2 WILD-TYPE 
               3               59 
$`NFATC2 MUTATED`
TCGA-2J-AABP TCGA-FB-A5VM TCGA-FB-A78T TCGA-HZ-A77P TCGA-IB-7651 TCGA-XN-A8T5 
       15.22        16.37        12.33        10.85        19.82        23.67 

$`NFATC2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       19.46         3.12        17.00        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        11.51        12.76        66.28        15.35 

  NFATC2 MUTATED NFATC2 WILD-TYPE 
           10.85             0.23 
  NFATC2 MUTATED NFATC2 WILD-TYPE 
           23.67            90.12 
  NFATC2 MUTATED NFATC2 WILD-TYPE 
          15.795           15.190 
[1] "10.8 - 23.7 (15.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1"  
D454V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NFATC2 MUTATED         0        0        2         0         4         0
  NFATC2 WILD-TYPE       1        3       10        19        78         4
                  vv
clus               STAGE IV
  NFATC2 MUTATED          0
  NFATC2 WILD-TYPE        3
D454V3, multiclass
           clus
vv          NFATC2 MUTATED NFATC2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NFATC2 MUTATED    0  2     4
  NFATC2 WILD-TYPE  5 15    98
D454V4, multiclass
       clus
vv      NFATC2 MUTATED NFATC2 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V5, binary
                  cls
clus                0  1
  NFATC2 MUTATED    2  4
  NFATC2 WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC2 MUTATED      2    4
  NFATC2 WILD-TYPE   33   85
   clus
vv  NFATC2 MUTATED NFATC2 WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D454V6, binary
                  cls
clus                0  1
  NFATC2 MUTATED    5  0
  NFATC2 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC2 MUTATED      5    0
  NFATC2 WILD-TYPE   52    3
   clus
vv  NFATC2 MUTATED NFATC2 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D454V7, binary
                  cls
clus                0  1
  NFATC2 MUTATED    4  2
  NFATC2 WILD-TYPE 47 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC2 MUTATED      4    2
  NFATC2 WILD-TYPE   47   73
        clus
vv       NFATC2 MUTATED NFATC2 WILD-TYPE
  FEMALE              4               47
  MALE                2               73
[1] 2 2
[1] FALSE
D454V8, binary
                  cls
clus                0  1
  NFATC2 MUTATED    5  1
  NFATC2 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC2 MUTATED      5    1
  NFATC2 WILD-TYPE   83   29
     clus
vv    NFATC2 MUTATED NFATC2 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFATC2 MUTATED                                     3
  NFATC2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFATC2 MUTATED                                       2
  NFATC2 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFATC2 MUTATED                                                  0
  NFATC2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NFATC2 MUTATED                                     1
  NFATC2 WILD-TYPE                                   0
D454V9, multiclass
                                                  clus
vv                                                 NFATC2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 NFATC2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V10, continuous
D454V11, continuous
                  vv
clus               R0 R1 R2 RX
  NFATC2 MUTATED    5  1  0  0
  NFATC2 WILD-TYPE 75 34  4  2
D454V12, multiclass
    clus
vv   NFATC2 MUTATED NFATC2 WILD-TYPE
  R0              5               75
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFATC2 MUTATED       0                         0     6
  NFATC2 WILD-TYPE     6                         5   108
D454V14, multiclass
                           clus
vv                          NFATC2 MUTATED NFATC2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V15, binary
                  cls
clus                0  1
  NFATC2 MUTATED    1  4
  NFATC2 WILD-TYPE  4 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC2 MUTATED      1    4
  NFATC2 WILD-TYPE    4   87
                        clus
vv                       NFATC2 MUTATED NFATC2 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(455) Variable = RNF128 MUTATION ANALYSIS
D455V1, survival
                  sevent
clus2               0  1
  RNF128 MUTATED    2  3
  RNF128 WILD-TYPE 61 59
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              120 
  RNF128 MUTATED RNF128 WILD-TYPE 
               3               59 
$`RNF128 MUTATED`
TCGA-3A-A9IC TCGA-3A-A9IR TCGA-HZ-8637 TCGA-IB-7651 TCGA-RL-AAAS 
       24.26        50.70        17.00        19.82         0.30 

$`RNF128 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
        7.36        33.57        63.85        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
        8.78        13.68         3.12        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.30             0.23 
  RNF128 MUTATED RNF128 WILD-TYPE 
           50.70            90.12 
  RNF128 MUTATED RNF128 WILD-TYPE 
          19.820           15.155 
[1] "0.3 - 50.7 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D455V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RNF128 MUTATED         0        0        2         0         3         0
  RNF128 WILD-TYPE       1        3       10        19        79         4
                  vv
clus               STAGE IV
  RNF128 MUTATED          0
  RNF128 WILD-TYPE        3
D455V3, multiclass
           clus
vv          RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RNF128 MUTATED    0  2     3
  RNF128 WILD-TYPE  5 15    99
D455V4, multiclass
       clus
vv      RNF128 MUTATED RNF128 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V5, binary
                  cls
clus                0  1
  RNF128 MUTATED    2  3
  RNF128 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      2    3
  RNF128 WILD-TYPE   33   86
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D455V6, binary
                  cls
clus                0  1
  RNF128 MUTATED    2  0
  RNF128 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      2    0
  RNF128 WILD-TYPE   55    3
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D455V7, binary
                  cls
clus                0  1
  RNF128 MUTATED    5  0
  RNF128 WILD-TYPE 46 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      5    0
  RNF128 WILD-TYPE   46   75
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              5               46
  MALE                0               75
[1] 2 2
[1] FALSE
D455V8, binary
                  cls
clus                0  1
  RNF128 MUTATED    3  2
  RNF128 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      3    2
  RNF128 WILD-TYPE   85   28
     clus
vv    RNF128 MUTATED RNF128 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF128 MUTATED                                     4
  RNF128 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF128 MUTATED                                       1
  RNF128 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF128 MUTATED                                                  0
  RNF128 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RNF128 MUTATED                                     0
  RNF128 WILD-TYPE                                   1
D455V9, multiclass
                                                  clus
vv                                                 RNF128 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RNF128 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V10, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
D455V11, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IX 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RNF128 MUTATED    5  0  0  0
  RNF128 WILD-TYPE 75 35  4  2
D455V12, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF128 MUTATED       0                         0     5
  RNF128 WILD-TYPE     6                         5   109
D455V14, multiclass
                           clus
vv                          RNF128 MUTATED RNF128 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V15, binary
                  cls
clus                0  1
  RNF128 MUTATED    1  4
  RNF128 WILD-TYPE  4 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      1    4
  RNF128 WILD-TYPE    4   87
                        clus
vv                       RNF128 MUTATED RNF128 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(456) Variable = PCLO MUTATION ANALYSIS
D456V1, survival
                sevent
clus2             0  1
  PCLO MUTATED    5  3
  PCLO WILD-TYPE 58 59
  PCLO MUTATED PCLO WILD-TYPE 
             8            117 
  PCLO MUTATED PCLO WILD-TYPE 
             3             59 
$`PCLO MUTATED`
TCGA-3A-A9IJ TCGA-HZ-A77Q TCGA-F2-A7TX TCGA-FZ-5921 TCGA-IB-7651 TCGA-IB-7885 
       60.95         1.08         3.12         5.10        19.82        41.33 
TCGA-Q3-A5QY TCGA-YB-A89D 
       13.68        11.51 

$`PCLO WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
       24.36         2.01        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       36.69        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A 
       13.28         7.56        12.46        10.29         8.78         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PCLO MUTATED PCLO WILD-TYPE 
          1.08           0.23 
  PCLO MUTATED PCLO WILD-TYPE 
         60.95          90.12 
  PCLO MUTATED PCLO WILD-TYPE 
        12.595         15.320 
[1] "1.1 - 61.0 (12.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D456V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PCLO MUTATED         0        0        1         0         7         0
  PCLO WILD-TYPE       1        3       11        19        75         4
                vv
clus             STAGE IV
  PCLO MUTATED          0
  PCLO WILD-TYPE        3
D456V3, multiclass
           clus
vv          PCLO MUTATED PCLO WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PCLO MUTATED    0  1     7
  PCLO WILD-TYPE  5 16    95
D456V4, multiclass
       clus
vv      PCLO MUTATED PCLO WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V5, binary
                cls
clus              0  1
  PCLO MUTATED    1  7
  PCLO WILD-TYPE 34 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      1    7
  PCLO WILD-TYPE   34   82
   clus
vv  PCLO MUTATED PCLO WILD-TYPE
  0            1             34
  1            7             82
[1] 2 2
[1] FALSE
D456V6, binary
                cls
clus              0  1
  PCLO MUTATED    4  0
  PCLO WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      4    0
  PCLO WILD-TYPE   53    3
   clus
vv  PCLO MUTATED PCLO WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D456V7, binary
                cls
clus              0  1
  PCLO MUTATED    4  4
  PCLO WILD-TYPE 47 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      4    4
  PCLO WILD-TYPE   47   71
        clus
vv       PCLO MUTATED PCLO WILD-TYPE
  FEMALE            4             47
  MALE              4             71
[1] 2 2
[1] FALSE
D456V8, binary
                cls
clus              0  1
  PCLO MUTATED    5  2
  PCLO WILD-TYPE 83 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      5    2
  PCLO WILD-TYPE   83   28
     clus
vv    PCLO MUTATED PCLO WILD-TYPE
  NO             5             83
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PCLO MUTATED                                     6
  PCLO WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PCLO MUTATED                                       2
  PCLO WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PCLO MUTATED                                                  0
  PCLO WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  PCLO MUTATED                                     0
  PCLO WILD-TYPE                                   1
D456V9, multiclass
                                                  clus
vv                                                 PCLO MUTATED PCLO WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V10, continuous
D456V11, continuous
                vv
clus             R0 R1 R2 RX
  PCLO MUTATED    6  1  0  0
  PCLO WILD-TYPE 74 34  4  2
D456V12, multiclass
    clus
vv   PCLO MUTATED PCLO WILD-TYPE
  R0            6             74
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCLO MUTATED       0                         0     7
  PCLO WILD-TYPE     6                         5   107
D456V14, multiclass
                           clus
vv                          PCLO MUTATED PCLO WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V15, binary
                cls
clus              0  1
  PCLO MUTATED    0  6
  PCLO WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCLO MUTATED      0    6
  PCLO WILD-TYPE    5   85
                        clus
vv                       PCLO MUTATED PCLO WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(457) Variable = NCOA7 MUTATION ANALYSIS
D457V1, survival
                 sevent
clus2              0  1
  NCOA7 MUTATED    3  0
  NCOA7 WILD-TYPE 60 62
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              3             122 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              0              62 
$`NCOA7 MUTATED`
TCGA-IB-8126 TCGA-IB-AAUP TCGA-YH-A8SY 
       15.19        14.17        12.76 

$`NCOA7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
          12.76            0.23 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          15.19           90.12 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
         14.170          15.335 
[1] "12.8 - 15.2 (14.2)" "0.2 - 90.1 (15.3)" 
[1] "hr="     "9300000"
D457V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NCOA7 MUTATED         0        0        0         0         1         2
  NCOA7 WILD-TYPE       1        3       12        19        81         2
                 vv
clus              STAGE IV
  NCOA7 MUTATED          0
  NCOA7 WILD-TYPE        3
D457V3, multiclass
           clus
vv          NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             1              81
  STAGE III             2               2
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NCOA7 MUTATED    0  0     3
  NCOA7 WILD-TYPE  5 17    99
D457V4, multiclass
       clus
vv      NCOA7 MUTATED NCOA7 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V5, binary
                 cls
clus               0  1
  NCOA7 MUTATED    0  3
  NCOA7 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      0    3
  NCOA7 WILD-TYPE   35   86
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D457V6, binary
                 cls
clus               0  1
  NCOA7 MUTATED    2  0
  NCOA7 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      2    0
  NCOA7 WILD-TYPE   55    3
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D457V7, binary
                 cls
clus               0  1
  NCOA7 MUTATED    2  1
  NCOA7 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      2    1
  NCOA7 WILD-TYPE   49   74
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D457V8, binary
                 cls
clus               0  1
  NCOA7 MUTATED    2  1
  NCOA7 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      2    1
  NCOA7 WILD-TYPE   86   29
     clus
vv    NCOA7 MUTATED NCOA7 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NCOA7 MUTATED                                     2
  NCOA7 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NCOA7 MUTATED                                       0
  NCOA7 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NCOA7 MUTATED                                                  0
  NCOA7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NCOA7 MUTATED                                     0
  NCOA7 WILD-TYPE                                   1
D457V9, multiclass
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              2             123 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IV      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FZ-5919      TCGA-FZ-5920      TCGA-FZ-5921      TCGA-FZ-5922 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7651 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-A5SO      TCGA-IB-A5SP 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
D457V10, continuous
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-A6UF 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
D457V11, continuous
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NCOA7 MUTATED    0  2  0  0
  NCOA7 WILD-TYPE 80 33  4  2
D457V12, multiclass
[1] "Remove cluster labels:" "NCOA7 MUTATED"         
clus
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              2             119 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-3A-A9IV      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7651 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-A5SO      TCGA-IB-A5SP 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" "NCOA7 WILD-TYPE" 
D457V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NCOA7 MUTATED       0                         0     3
  NCOA7 WILD-TYPE     6                         5   111
D457V14, multiclass
                           clus
vv                          NCOA7 MUTATED NCOA7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V15, binary
                 cls
clus               0  1
  NCOA7 MUTATED    0  3
  NCOA7 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED      0    3
  NCOA7 WILD-TYPE    5   88
                        clus
vv                       NCOA7 MUTATED NCOA7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(458) Variable = POM121 MUTATION ANALYSIS
D458V1, survival
                  sevent
clus2               0  1
  POM121 MUTATED    2  3
  POM121 WILD-TYPE 61 59
  POM121 MUTATED POM121 WILD-TYPE 
               5              120 
  POM121 MUTATED POM121 WILD-TYPE 
               3               59 
$`POM121 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-A5SQ TCGA-LB-A9Q5 
       22.06        19.82        19.82         7.20        10.29 

$`POM121 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85         0.23        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W 
        7.40         8.05        13.28         7.56        12.46         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  POM121 MUTATED POM121 WILD-TYPE 
            7.20             0.23 
  POM121 MUTATED POM121 WILD-TYPE 
           22.06            90.12 
  POM121 MUTATED POM121 WILD-TYPE 
          19.820           15.205 
[1] "7.2 - 22.1 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D458V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  POM121 MUTATED         0        0        1         1         2         0
  POM121 WILD-TYPE       1        3       11        18        80         4
                  vv
clus               STAGE IV
  POM121 MUTATED          1
  POM121 WILD-TYPE        2
D458V3, multiclass
           clus
vv          POM121 MUTATED POM121 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  POM121 MUTATED    0  1     4
  POM121 WILD-TYPE  5 16    98
D458V4, multiclass
       clus
vv      POM121 MUTATED POM121 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V5, binary
                  cls
clus                0  1
  POM121 MUTATED    3  2
  POM121 WILD-TYPE 32 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      3    2
  POM121 WILD-TYPE   32   87
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              3               32
  1              2               87
[1] 2 2
[1] FALSE
D458V6, binary
                  cls
clus                0  1
  POM121 MUTATED    2  1
  POM121 WILD-TYPE 55  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    1
  POM121 WILD-TYPE   55    2
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              2               55
  1              1                2
[1] 2 2
[1] FALSE
D458V7, binary
                  cls
clus                0  1
  POM121 MUTATED    3  2
  POM121 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      3    2
  POM121 WILD-TYPE   48   73
        clus
vv       POM121 MUTATED POM121 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D458V8, binary
                  cls
clus                0  1
  POM121 MUTATED    4  1
  POM121 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      4    1
  POM121 WILD-TYPE   84   29
     clus
vv    POM121 MUTATED POM121 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POM121 MUTATED                                     3
  POM121 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POM121 MUTATED                                       2
  POM121 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POM121 MUTATED                                                  0
  POM121 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  POM121 MUTATED                                     0
  POM121 WILD-TYPE                                   1
D458V9, multiclass
                                                  clus
vv                                                 POM121 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 POM121 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V10, continuous
D458V11, continuous
                  vv
clus               R0 R1 R2 RX
  POM121 MUTATED    5  0  0  0
  POM121 WILD-TYPE 75 35  4  2
D458V12, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POM121 MUTATED       0                         0     5
  POM121 WILD-TYPE     6                         5   109
D458V14, multiclass
                           clus
vv                          POM121 MUTATED POM121 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V15, binary
                  cls
clus                0  1
  POM121 MUTATED    0  5
  POM121 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      0    5
  POM121 WILD-TYPE    5   86
                        clus
vv                       POM121 MUTATED POM121 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(459) Variable = HIST1H2BK MUTATION ANALYSIS
D459V1, survival
                     sevent
clus2                  0  1
  HIST1H2BK MUTATED    2  2
  HIST1H2BK WILD-TYPE 61 60
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  4                 121 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  2                  60 
$`HIST1H2BK MUTATED`
TCGA-S4-A8RO TCGA-H8-A6C1 TCGA-HZ-8637 TCGA-US-A77G 
       17.26        22.06        17.00         0.39 

$`HIST1H2BK WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
               0.39                0.23 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
              22.06               90.12 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
              17.13               15.19 
[1] "0.4 - 22.1 (17.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D459V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIST1H2BK MUTATED         0        0        0         1         3         0
  HIST1H2BK WILD-TYPE       1        3       12        18        79         4
                     vv
clus                  STAGE IV
  HIST1H2BK MUTATED          0
  HIST1H2BK WILD-TYPE        3
D459V3, multiclass
           clus
vv          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  0                   3
  STAGE IB                  0                  12
  STAGE IIA                 1                  18
  STAGE IIB                 3                  79
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3+T4
  HIST1H2BK MUTATED    0  0     4
  HIST1H2BK WILD-TYPE  5 17    98
D459V4, multiclass
       clus
vv      HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  T1                    0                   5
  T2                    0                  17
  T3+T4                 4                  98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V5, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    1  3
  HIST1H2BK WILD-TYPE 34 86
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      1    3
  HIST1H2BK WILD-TYPE   34   86
   clus
vv  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  0                 1                  34
  1                 3                  86
[1] 2 2
[1] FALSE
D459V6, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    0  0
  HIST1H2BK WILD-TYPE 57  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      0    0
  HIST1H2BK WILD-TYPE   57    3
D459V7, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    2  2
  HIST1H2BK WILD-TYPE 49 73
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      2    2
  HIST1H2BK WILD-TYPE   49   73
        clus
vv       HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  FEMALE                 2                  49
  MALE                   2                  73
[1] 2 2
[1] FALSE
D459V8, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    2  2
  HIST1H2BK WILD-TYPE 86 28
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      2    2
  HIST1H2BK WILD-TYPE   86   28
     clus
vv    HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  NO                  2                  86
  YES                 2                  28
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H2BK MUTATED                                     3
  HIST1H2BK WILD-TYPE                                 102
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H2BK MUTATED                                       1
  HIST1H2BK WILD-TYPE                                    17
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H2BK MUTATED                                                  0
  HIST1H2BK WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIST1H2BK MUTATED                                     0
  HIST1H2BK WILD-TYPE                                   1
D459V9, multiclass
                                                  clus
vv                                                 HIST1H2BK MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 HIST1H2BK WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V10, continuous
[1] "Remove cluster labels:" "HIST1H2BK MUTATED"     
clus
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  1                  38 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2J-AABV 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-2L-AAQA          TCGA-2L-AAQE          TCGA-3A-A9I9 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IX          TCGA-F2-A8YN 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-FB-A5VM          TCGA-FB-A78T          TCGA-FB-AAPQ 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-HV-AA8V          TCGA-HZ-A8P1 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-7651          TCGA-IB-7885          TCGA-IB-8126 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUU 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-AAUV          TCGA-LB-A9Q5          TCGA-OE-A75W 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
D459V11, continuous
[1] "Remove cluster labels:" "HIST1H2BK MUTATED"     
clus
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  1                  32 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABE          TCGA-2J-AABF 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-2J-AABO          TCGA-3A-A9IB          TCGA-3A-A9IR 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-FB-A5VM          TCGA-FB-A78T 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-FB-AAPQ          TCGA-FB-AAPS          TCGA-HZ-A8P1 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-7651          TCGA-IB-7885          TCGA-IB-8126 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XD-AAUI 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"HIST1H2BK WILD-TYPE" "HIST1H2BK WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  HIST1H2BK MUTATED    3  1  0  0
  HIST1H2BK WILD-TYPE 77 34  4  2
D459V12, multiclass
    clus
vv   HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  R0                 3                  77
  R1                 1                  34
  R2                 0                   4
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BK MUTATED       0                         0     4
  HIST1H2BK WILD-TYPE     6                         5   110
D459V14, multiclass
                           clus
vv                          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     4                 110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V15, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    1  3
  HIST1H2BK WILD-TYPE  4 88
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      1    3
  HIST1H2BK WILD-TYPE    4   88
                        clus
vv                       HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  HISPANIC OR LATINO                     1                   4
  NOT HISPANIC OR LATINO                 3                  88
[1] 2 2
[1] FALSE

Clustering(460) Variable = ZHX3 MUTATION ANALYSIS
D460V1, survival
                sevent
clus2             0  1
  ZHX3 MUTATED    2  5
  ZHX3 WILD-TYPE 61 57
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             7            118 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             5             57 
$`ZHX3 MUTATED`
TCGA-2J-AABV TCGA-FZ-5922 TCGA-IB-7651 TCGA-IB-A5SQ TCGA-RB-AA9M TCGA-US-A77G 
       21.44        36.20        19.82         7.20         9.40         0.39 
TCGA-YY-A8LH 
       66.28 

$`ZHX3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  ZHX3 MUTATED ZHX3 WILD-TYPE 
          0.39           0.23 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
         66.28          90.12 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
        19.820         15.205 
[1] "0.4 - 66.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D460V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZHX3 MUTATED         0        0        1         1         5         0
  ZHX3 WILD-TYPE       1        3       11        18        77         4
                vv
clus             STAGE IV
  ZHX3 MUTATED          0
  ZHX3 WILD-TYPE        3
D460V3, multiclass
           clus
vv          ZHX3 MUTATED ZHX3 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  ZHX3 MUTATED    1  1     5
  ZHX3 WILD-TYPE  4 16    97
D460V4, multiclass
       clus
vv      ZHX3 MUTATED ZHX3 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            5             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V5, binary
                cls
clus              0  1
  ZHX3 MUTATED    2  5
  ZHX3 WILD-TYPE 33 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      2    5
  ZHX3 WILD-TYPE   33   84
   clus
vv  ZHX3 MUTATED ZHX3 WILD-TYPE
  0            2             33
  1            5             84
[1] 2 2
[1] FALSE
D460V6, binary
                cls
clus              0  1
  ZHX3 MUTATED    4  0
  ZHX3 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      4    0
  ZHX3 WILD-TYPE   53    3
   clus
vv  ZHX3 MUTATED ZHX3 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D460V7, binary
                cls
clus              0  1
  ZHX3 MUTATED    3  4
  ZHX3 WILD-TYPE 48 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      3    4
  ZHX3 WILD-TYPE   48   71
        clus
vv       ZHX3 MUTATED ZHX3 WILD-TYPE
  FEMALE            3             48
  MALE              4             71
[1] 2 2
[1] FALSE
D460V8, binary
                cls
clus              0  1
  ZHX3 MUTATED    5  2
  ZHX3 WILD-TYPE 83 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      5    2
  ZHX3 WILD-TYPE   83   28
     clus
vv    ZHX3 MUTATED ZHX3 WILD-TYPE
  NO             5             83
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZHX3 MUTATED                                     7
  ZHX3 WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZHX3 MUTATED                                       0
  ZHX3 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZHX3 MUTATED                                                  0
  ZHX3 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZHX3 MUTATED                                     0
  ZHX3 WILD-TYPE                                   1
D460V9, multiclass
                                                  clus
vv                                                 ZHX3 MUTATED ZHX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V10, continuous
D460V11, continuous
[1] "Remove cluster labels:" "ZHX3 MUTATED"          
clus
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5 
"ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" "ZHX3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ZHX3 MUTATED    6  1  0  0
  ZHX3 WILD-TYPE 74 34  4  2
D460V12, multiclass
    clus
vv   ZHX3 MUTATED ZHX3 WILD-TYPE
  R0            6             74
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZHX3 MUTATED       0                         0     7
  ZHX3 WILD-TYPE     6                         5   107
D460V14, multiclass
                           clus
vv                          ZHX3 MUTATED ZHX3 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V15, binary
                cls
clus              0  1
  ZHX3 MUTATED    0  6
  ZHX3 WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      0    6
  ZHX3 WILD-TYPE    5   85
                        clus
vv                       ZHX3 MUTATED ZHX3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(461) Variable = RGPD3 MUTATION ANALYSIS
D461V1, survival
                 sevent
clus2              0  1
  RGPD3 MUTATED    7  1
  RGPD3 WILD-TYPE 56 61
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              8             117 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              1              61 
$`RGPD3 MUTATED`
TCGA-2J-AABO TCGA-3A-A9IS TCGA-3A-A9J0 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8X 
       14.47        32.81        24.43        22.06         8.28        17.49 
TCGA-IB-AAUU TCGA-US-A776 
        8.05        39.98 

$`RGPD3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       32.15        30.25        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RGPD3 MUTATED RGPD3 WILD-TYPE 
           8.05            0.23 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
          39.98           90.12 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
         19.775          15.190 
[1] "8.1 - 40.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "5.3"
D461V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RGPD3 MUTATED         0        0        1         3         4         0
  RGPD3 WILD-TYPE       1        3       11        16        78         4
                 vv
clus              STAGE IV
  RGPD3 MUTATED          0
  RGPD3 WILD-TYPE        3
D461V3, multiclass
           clus
vv          RGPD3 MUTATED RGPD3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             3              16
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RGPD3 MUTATED    0  2     6
  RGPD3 WILD-TYPE  5 15    96
D461V4, multiclass
       clus
vv      RGPD3 MUTATED RGPD3 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V5, binary
                 cls
clus               0  1
  RGPD3 MUTATED    4  4
  RGPD3 WILD-TYPE 31 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      4    4
  RGPD3 WILD-TYPE   31   85
   clus
vv  RGPD3 MUTATED RGPD3 WILD-TYPE
  0             4              31
  1             4              85
[1] 2 2
[1] FALSE
D461V6, binary
                 cls
clus               0  1
  RGPD3 MUTATED    2  0
  RGPD3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      2    0
  RGPD3 WILD-TYPE   55    3
   clus
vv  RGPD3 MUTATED RGPD3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D461V7, binary
                 cls
clus               0  1
  RGPD3 MUTATED    1  7
  RGPD3 WILD-TYPE 50 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      1    7
  RGPD3 WILD-TYPE   50   68
        clus
vv       RGPD3 MUTATED RGPD3 WILD-TYPE
  FEMALE             1              50
  MALE               7              68
[1] 2 2
[1] FALSE
D461V8, binary
                 cls
clus               0  1
  RGPD3 MUTATED    7  1
  RGPD3 WILD-TYPE 81 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      7    1
  RGPD3 WILD-TYPE   81   29
     clus
vv    RGPD3 MUTATED RGPD3 WILD-TYPE
  NO              7              81
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RGPD3 MUTATED                                     5
  RGPD3 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RGPD3 MUTATED                                       2
  RGPD3 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RGPD3 MUTATED                                                  1
  RGPD3 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RGPD3 MUTATED                                     0
  RGPD3 WILD-TYPE                                   1
D461V9, multiclass
                                                  clus
vv                                                 RGPD3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RGPD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V10, continuous
D461V11, continuous
[1] "Remove cluster labels:" "RGPD3 MUTATED"         
clus
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RGPD3 MUTATED    6  0  2  0
  RGPD3 WILD-TYPE 74 35  2  2
D461V12, multiclass
    clus
vv   RGPD3 MUTATED RGPD3 WILD-TYPE
  R0             6              74
  R1             0              35
  R2             2               2
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGPD3 MUTATED       2                         0     6
  RGPD3 WILD-TYPE     4                         5   108
D461V14, multiclass
                           clus
vv                          RGPD3 MUTATED RGPD3 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V15, binary
                 cls
clus               0  1
  RGPD3 MUTATED    0  5
  RGPD3 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      0    5
  RGPD3 WILD-TYPE    5   86
                        clus
vv                       RGPD3 MUTATED RGPD3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(462) Variable = ZNF554 MUTATION ANALYSIS
D462V1, survival
                  sevent
clus2               0  1
  ZNF554 MUTATED    1  2
  ZNF554 WILD-TYPE 62 60
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               3              122 
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               2               60 
$`ZNF554 MUTATED`
TCGA-2J-AAB6 TCGA-FB-AAPP TCGA-XN-A8T5 
        9.63        15.95        23.67 

$`ZNF554 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF554 MUTATED ZNF554 WILD-TYPE 
            9.63             0.23 
  ZNF554 MUTATED ZNF554 WILD-TYPE 
           23.67            90.12 
  ZNF554 MUTATED ZNF554 WILD-TYPE 
          15.950           15.205 
[1] "9.6 - 23.7 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D462V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF554 MUTATED         0        0        1         1         1         0
  ZNF554 WILD-TYPE       1        3       11        18        81         4
                  vv
clus               STAGE IV
  ZNF554 MUTATED          0
  ZNF554 WILD-TYPE        3
D462V3, multiclass
           clus
vv          ZNF554 MUTATED ZNF554 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF554 MUTATED     0   1     2
  ZNF554 WILD-TYPE   5  16   100
D462V4, multiclass
       clus
vv      ZNF554 MUTATED ZNF554 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V5, binary
                  cls
clus                0  1
  ZNF554 MUTATED    2  1
  ZNF554 WILD-TYPE 33 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF554 MUTATED      2    1
  ZNF554 WILD-TYPE   33   88
   clus
vv  ZNF554 MUTATED ZNF554 WILD-TYPE
  0              2               33
  1              1               88
[1] 2 2
[1] FALSE
D462V6, binary
                  cls
clus                0  1
  ZNF554 MUTATED    2  0
  ZNF554 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF554 MUTATED      2    0
  ZNF554 WILD-TYPE   55    3
   clus
vv  ZNF554 MUTATED ZNF554 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D462V7, binary
                  cls
clus                0  1
  ZNF554 MUTATED    1  2
  ZNF554 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF554 MUTATED      1    2
  ZNF554 WILD-TYPE   50   73
        clus
vv       ZNF554 MUTATED ZNF554 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D462V8, binary
                  cls
clus                0  1
  ZNF554 MUTATED    1  2
  ZNF554 WILD-TYPE 87 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF554 MUTATED      1    2
  ZNF554 WILD-TYPE   87   28
     clus
vv    ZNF554 MUTATED ZNF554 WILD-TYPE
  NO               1               87
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF554 MUTATED                                     2
  ZNF554 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF554 MUTATED                                       1
  ZNF554 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF554 MUTATED                                                  0
  ZNF554 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF554 MUTATED                                     0
  ZNF554 WILD-TYPE                                   1
D462V9, multiclass
                                                  clus
vv                                                 ZNF554 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF554 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V10, continuous
[1] "Remove cluster labels:" "ZNF554 MUTATED"        
clus
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-YY-A8LH 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
D462V11, continuous
[1] "Remove cluster labels:" "ZNF554 MUTATED"        
clus
  ZNF554 MUTATED ZNF554 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-YY-A8LH 
"ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" "ZNF554 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF554 MUTATED    2  1  0  0
  ZNF554 WILD-TYPE 78 34  4  2
D462V12, multiclass
    clus
vv   ZNF554 MUTATED ZNF554 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF554 MUTATED       0                         0     3
  ZNF554 WILD-TYPE     6                         5   111
D462V14, multiclass
                           clus
vv                          ZNF554 MUTATED ZNF554 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V15, binary
                  cls
clus                0  1
  ZNF554 MUTATED    1  1
  ZNF554 WILD-TYPE  4 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF554 MUTATED      1    1
  ZNF554 WILD-TYPE    4   90
                        clus
vv                       ZNF554 MUTATED ZNF554 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              1               90
[1] 2 2
[1] FALSE

Clustering(463) Variable = RETN MUTATION ANALYSIS
D463V1, survival
                sevent
clus2             0  1
  RETN MUTATED    2  1
  RETN WILD-TYPE 61 61
  RETN MUTATED RETN WILD-TYPE 
             3            122 
  RETN MUTATED RETN WILD-TYPE 
             1             61 
$`RETN MUTATED`
TCGA-2J-AABU TCGA-HV-A7OL TCGA-Q3-AA2A 
        9.11         8.28         3.12 

$`RETN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RETN MUTATED RETN WILD-TYPE 
          3.12           0.23 
  RETN MUTATED RETN WILD-TYPE 
          9.11          90.12 
  RETN MUTATED RETN WILD-TYPE 
         8.280         15.335 
[1] "3.1 - 9.1 (8.3)"   "0.2 - 90.1 (15.3)"
[1] "hr=" "2.2"
D463V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RETN MUTATED         0        0        1         1         1         0
  RETN WILD-TYPE       1        3       11        18        81         4
                vv
clus             STAGE IV
  RETN MUTATED          0
  RETN WILD-TYPE        3
D463V3, multiclass
           clus
vv          RETN MUTATED RETN WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            1             81
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RETN MUTATED    0  0     3
  RETN WILD-TYPE  5 17    99
D463V4, multiclass
       clus
vv      RETN MUTATED RETN WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V5, binary
                cls
clus              0  1
  RETN MUTATED    1  2
  RETN WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  RETN MUTATED      1    2
  RETN WILD-TYPE   34   87
   clus
vv  RETN MUTATED RETN WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D463V6, binary
                cls
clus              0  1
  RETN MUTATED    1  0
  RETN WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RETN MUTATED      1    0
  RETN WILD-TYPE   56    3
   clus
vv  RETN MUTATED RETN WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D463V7, binary
                cls
clus              0  1
  RETN MUTATED    1  2
  RETN WILD-TYPE 50 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  RETN MUTATED      1    2
  RETN WILD-TYPE   50   73
        clus
vv       RETN MUTATED RETN WILD-TYPE
  FEMALE            1             50
  MALE              2             73
[1] 2 2
[1] FALSE
D463V8, binary
                cls
clus              0  1
  RETN MUTATED    3  0
  RETN WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  RETN MUTATED      3    0
  RETN WILD-TYPE   85   30
     clus
vv    RETN MUTATED RETN WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RETN MUTATED                                     3
  RETN WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RETN MUTATED                                       0
  RETN WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RETN MUTATED                                                  0
  RETN WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RETN MUTATED                                     0
  RETN WILD-TYPE                                   1
D463V9, multiclass
                                                  clus
vv                                                 RETN MUTATED RETN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V10, continuous
D463V11, continuous
                vv
clus             R0 R1 R2 RX
  RETN MUTATED    1  0  1  1
  RETN WILD-TYPE 79 35  3  1
D463V12, multiclass
    clus
vv   RETN MUTATED RETN WILD-TYPE
  R0            1             79
  R1            0             35
  R2            1              3
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V13, continuous
[1] "Remove cluster labels:" "RETN MUTATED"          
clus
  RETN MUTATED RETN WILD-TYPE 
             2            122 
    TCGA-2J-AABR     TCGA-2J-AABT     TCGA-3A-A9I5     TCGA-3A-A9IJ 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-3A-A9IL     TCGA-F2-A44G     TCGA-FB-AAQ6     TCGA-FZ-5924 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-S4-A8RO     TCGA-US-A77E     TCGA-XD-AAUL     TCGA-2J-AAB1 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8     TCGA-2J-AAB9 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABH 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABP     TCGA-2J-AABV 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-2L-AAQI     TCGA-2L-AAQJ 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-2L-AAQL     TCGA-2L-AAQM     TCGA-3A-A9I7     TCGA-3A-A9I9 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IC     TCGA-3A-A9IH     TCGA-3A-A9IR 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-3A-A9IS     TCGA-3A-A9IU     TCGA-3A-A9IV     TCGA-3A-A9IX 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-3A-A9IZ     TCGA-3A-A9J0     TCGA-3E-AAAY     TCGA-3E-AAAZ 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-F2-7273     TCGA-F2-A7TX     TCGA-F2-A8YN     TCGA-FB-A5VM 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPP     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-FB-AAPU     TCGA-FB-AAPZ     TCGA-FB-AAQ0     TCGA-FB-AAQ1 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-FB-AAQ2     TCGA-FB-AAQ3     TCGA-FZ-5919     TCGA-FZ-5920 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-FZ-5921     TCGA-FZ-5922     TCGA-FZ-5923     TCGA-FZ-5926 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-A7OP     TCGA-HV-AA8V     TCGA-HV-AA8X 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-HZ-7918     TCGA-HZ-7925     TCGA-HZ-8637     TCGA-HZ-A49I 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-HZ-A77O     TCGA-HZ-A77P     TCGA-HZ-A8P1     TCGA-HZ-A9TJ 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7652     TCGA-IB-7885     TCGA-IB-8126 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-A5SO     TCGA-IB-A5SP     TCGA-IB-A5SQ     TCGA-IB-A5ST 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7LX     TCGA-IB-A7M4 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-AAUM     TCGA-IB-AAUN     TCGA-IB-AAUO     TCGA-IB-AAUP 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUR     TCGA-IB-AAUS     TCGA-IB-AAUU 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-IB-AAUW     TCGA-LB-A8F3     TCGA-LB-A9Q5 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-OE-A75W     TCGA-Q3-A5QY     TCGA-RB-A7B8     TCGA-RB-AA9M 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-RL-AAAS     TCGA-US-A776     TCGA-US-A779     TCGA-US-A77G 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-US-A77J     TCGA-XD-AAUG     TCGA-XD-AAUH     TCGA-XD-AAUI 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-XN-A8T3     TCGA-XN-A8T5     TCGA-YB-A89D     TCGA-YH-A8SY 
"RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" "RETN WILD-TYPE" 
    TCGA-YY-A8LH     TCGA-Z5-AAPL 
"RETN WILD-TYPE" "RETN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RETN MUTATED       1                         0     2
  RETN WILD-TYPE     5                         5   112
D463V14, multiclass
                           clus
vv                          RETN MUTATED RETN WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V15, binary
                cls
clus              0  1
  RETN MUTATED    0  1
  RETN WILD-TYPE  5 90
[1] "tbl2"
                cls
clus             [,1] [,2]
  RETN MUTATED      0    1
  RETN WILD-TYPE    5   90
                        clus
vv                       RETN MUTATED RETN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            1             90
[1] 2 2
[1] FALSE

Clustering(464) Variable = RSC1A1 MUTATION ANALYSIS
D464V1, survival
                  sevent
clus2               0  1
  RSC1A1 MUTATED    2  1
  RSC1A1 WILD-TYPE 61 61
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               3              122 
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               1               61 
$`RSC1A1 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IH TCGA-IB-7651 
        1.08        33.57        19.82 

$`RSC1A1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
            1.08             0.23 
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
           33.57            90.12 
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
          19.820           15.205 
[1] "1.1 - 33.6 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D464V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RSC1A1 MUTATED         0        1        0         0         2         0
  RSC1A1 WILD-TYPE       1        2       12        19        80         4
                  vv
clus               STAGE IV
  RSC1A1 MUTATED          0
  RSC1A1 WILD-TYPE        3
D464V3, multiclass
           clus
vv          RSC1A1 MUTATED RSC1A1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  RSC1A1 MUTATED     1   0     2
  RSC1A1 WILD-TYPE   4  17   100
D464V4, multiclass
       clus
vv      RSC1A1 MUTATED RSC1A1 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V5, binary
                  cls
clus                0  1
  RSC1A1 MUTATED    1  2
  RSC1A1 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSC1A1 MUTATED      1    2
  RSC1A1 WILD-TYPE   34   87
   clus
vv  RSC1A1 MUTATED RSC1A1 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D464V6, binary
                  cls
clus                0  1
  RSC1A1 MUTATED    1  0
  RSC1A1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSC1A1 MUTATED      1    0
  RSC1A1 WILD-TYPE   56    3
   clus
vv  RSC1A1 MUTATED RSC1A1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D464V7, binary
                  cls
clus                0  1
  RSC1A1 MUTATED    3  0
  RSC1A1 WILD-TYPE 48 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSC1A1 MUTATED      3    0
  RSC1A1 WILD-TYPE   48   75
        clus
vv       RSC1A1 MUTATED RSC1A1 WILD-TYPE
  FEMALE              3               48
  MALE                0               75
[1] 2 2
[1] FALSE
D464V8, binary
                  cls
clus                0  1
  RSC1A1 MUTATED    2  0
  RSC1A1 WILD-TYPE 86 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSC1A1 MUTATED      2    0
  RSC1A1 WILD-TYPE   86   30
     clus
vv    RSC1A1 MUTATED RSC1A1 WILD-TYPE
  NO               2               86
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RSC1A1 MUTATED                                     2
  RSC1A1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RSC1A1 MUTATED                                       1
  RSC1A1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RSC1A1 MUTATED                                                  0
  RSC1A1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RSC1A1 MUTATED                                     0
  RSC1A1 WILD-TYPE                                   1
D464V9, multiclass
                                                  clus
vv                                                 RSC1A1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RSC1A1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V10, continuous
[1] "Remove cluster labels:" "RSC1A1 MUTATED"        
clus
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-YY-A8LH 
"RSC1A1 WILD-TYPE" 
D464V11, continuous
[1] "Remove cluster labels:" "RSC1A1 MUTATED"        
clus
  RSC1A1 MUTATED RSC1A1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" "RSC1A1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RSC1A1 MUTATED    3  0  0  0
  RSC1A1 WILD-TYPE 77 35  4  2
D464V12, multiclass
    clus
vv   RSC1A1 MUTATED RSC1A1 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RSC1A1 MUTATED       0                         0     3
  RSC1A1 WILD-TYPE     6                         5   111
D464V14, multiclass
                           clus
vv                          RSC1A1 MUTATED RSC1A1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V15, binary
                  cls
clus                0  1
  RSC1A1 MUTATED    0  3
  RSC1A1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RSC1A1 MUTATED      0    3
  RSC1A1 WILD-TYPE    5   88
                        clus
vv                       RSC1A1 MUTATED RSC1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(465) Variable = RYR2 MUTATION ANALYSIS
D465V1, survival
                sevent
clus2             0  1
  RYR2 MUTATED    7  7
  RYR2 WILD-TYPE 56 55
  RYR2 MUTATED RYR2 WILD-TYPE 
            14            111 
  RYR2 MUTATED RYR2 WILD-TYPE 
             7             55 
$`RYR2 MUTATED`
TCGA-LB-A7SX TCGA-2J-AAB1 TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABU TCGA-2J-AABV 
       12.92         2.17        42.31        15.91         9.11        21.44 
TCGA-FB-AAPP TCGA-FB-AAPZ TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A7LX TCGA-IB-A7M4 
       15.95        23.54        32.15        19.82         8.22        15.88 
TCGA-IB-AAUU TCGA-Z5-AAPL 
        8.05        15.35 

$`RYR2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABO TCGA-2J-AABP TCGA-2L-AAQA TCGA-2L-AAQE 
       22.22        22.72        14.47        15.22         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-AAUM TCGA-IB-AAUN 
        7.20        20.88        21.90         1.35         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV 
        7.86        14.17         6.02        11.11         7.40        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  RYR2 MUTATED RYR2 WILD-TYPE 
          2.17           0.23 
  RYR2 MUTATED RYR2 WILD-TYPE 
         42.31          90.12 
  RYR2 MUTATED RYR2 WILD-TYPE 
        15.895         15.120 
[1] "2.2 - 42.3 (15.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D465V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RYR2 MUTATED         0        0        0         2        12         0
  RYR2 WILD-TYPE       1        3       12        17        70         4
                vv
clus             STAGE IV
  RYR2 MUTATED          0
  RYR2 WILD-TYPE        3
D465V3, multiclass
           clus
vv          RYR2 MUTATED RYR2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB           12             70
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  RYR2 MUTATED    0  1    13
  RYR2 WILD-TYPE  5 16    89
D465V4, multiclass
       clus
vv      RYR2 MUTATED RYR2 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4           13             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V5, binary
                cls
clus              0  1
  RYR2 MUTATED    2 12
  RYR2 WILD-TYPE 33 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED      2   12
  RYR2 WILD-TYPE   33   77
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0            2             33
  1           12             77
[1] 2 2
[1] FALSE
D465V6, binary
                cls
clus              0  1
  RYR2 MUTATED    9  0
  RYR2 WILD-TYPE 48  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED      9    0
  RYR2 WILD-TYPE   48    3
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0            9             48
  1            0              3
[1] 2 2
[1] FALSE
D465V7, binary
                cls
clus              0  1
  RYR2 MUTATED    3 11
  RYR2 WILD-TYPE 48 64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED      3   11
  RYR2 WILD-TYPE   48   64
        clus
vv       RYR2 MUTATED RYR2 WILD-TYPE
  FEMALE            3             48
  MALE             11             64
[1] 2 2
[1] FALSE
D465V8, binary
                cls
clus              0  1
  RYR2 MUTATED   11  3
  RYR2 WILD-TYPE 77 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     11    3
  RYR2 WILD-TYPE   77   27
     clus
vv    RYR2 MUTATED RYR2 WILD-TYPE
  NO            11             77
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RYR2 MUTATED                                    11
  RYR2 WILD-TYPE                                  94
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RYR2 MUTATED                                       3
  RYR2 WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RYR2 MUTATED                                                  0
  RYR2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  RYR2 MUTATED                                     0
  RYR2 WILD-TYPE                                   1
D465V9, multiclass
                                                  clus
vv                                                 RYR2 MUTATED RYR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        11             94
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V10, continuous
D465V11, continuous
                vv
clus             R0 R1 R2 RX
  RYR2 MUTATED   11  3  0  0
  RYR2 WILD-TYPE 69 32  4  2
D465V12, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  R0           11             69
  R1            3             32
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RYR2 MUTATED       1                         1    12
  RYR2 WILD-TYPE     5                         4   102
D465V14, multiclass
                           clus
vv                          RYR2 MUTATED RYR2 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               12            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V15, binary
                cls
clus              0  1
  RYR2 MUTATED    0  8
  RYR2 WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED      0    8
  RYR2 WILD-TYPE    5   83
                        clus
vv                       RYR2 MUTATED RYR2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(466) Variable = HNRNPCL1 MUTATION ANALYSIS
D466V1, survival
                    sevent
clus2                 0  1
  HNRNPCL1 MUTATED    4  2
  HNRNPCL1 WILD-TYPE 59 60
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 6                119 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 2                 60 
$`HNRNPCL1 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABO TCGA-3A-A9J0 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-AAUW 
       23.97        14.47        24.43        19.82        19.82         7.56 

$`HNRNPCL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        13.28        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
              7.56               0.23 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             24.43              90.12 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             19.82              15.19 
[1] "7.6 - 24.4 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D466V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HNRNPCL1 MUTATED         0        0        0         0         5         0
  HNRNPCL1 WILD-TYPE       1        3       12        19        77         4
                    vv
clus                 STAGE IV
  HNRNPCL1 MUTATED          1
  HNRNPCL1 WILD-TYPE        2
D466V3, multiclass
           clus
vv          HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                0                  4
  STAGE IV                 1                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  HNRNPCL1 MUTATED    0  1     5
  HNRNPCL1 WILD-TYPE  5 16    97
D466V4, multiclass
       clus
vv      HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V5, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    1  5
  HNRNPCL1 WILD-TYPE 34 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      1    5
  HNRNPCL1 WILD-TYPE   34   84
   clus
vv  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  0                1                 34
  1                5                 84
[1] 2 2
[1] FALSE
D466V6, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    4  1
  HNRNPCL1 WILD-TYPE 53  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      4    1
  HNRNPCL1 WILD-TYPE   53    2
   clus
vv  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  0                4                 53
  1                1                  2
[1] 2 2
[1] FALSE
D466V7, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    2  4
  HNRNPCL1 WILD-TYPE 49 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      2    4
  HNRNPCL1 WILD-TYPE   49   71
        clus
vv       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  FEMALE                2                 49
  MALE                  4                 71
[1] 2 2
[1] FALSE
D466V8, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    5  1
  HNRNPCL1 WILD-TYPE 83 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      5    1
  HNRNPCL1 WILD-TYPE   83   29
     clus
vv    HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  NO                 5                 83
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HNRNPCL1 MUTATED                                     4
  HNRNPCL1 WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HNRNPCL1 MUTATED                                       2
  HNRNPCL1 WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HNRNPCL1 MUTATED                                                  0
  HNRNPCL1 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  HNRNPCL1 MUTATED                                     0
  HNRNPCL1 WILD-TYPE                                   1
D466V9, multiclass
                                                  clus
vv                                                 HNRNPCL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 HNRNPCL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V10, continuous
[1] "Remove cluster labels:" "HNRNPCL1 MUTATED"      
clus
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABV         TCGA-2L-AAQA 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-YY-A8LH 
"HNRNPCL1 WILD-TYPE" 
D466V11, continuous
[1] "Remove cluster labels:" "HNRNPCL1 MUTATED"      
clus
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" "HNRNPCL1 WILD-TYPE" 
        TCGA-YY-A8LH 
"HNRNPCL1 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  HNRNPCL1 MUTATED    6  0  0  0
  HNRNPCL1 WILD-TYPE 74 35  4  2
D466V12, multiclass
    clus
vv   HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  R0                6                 74
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HNRNPCL1 MUTATED       0                         0     6
  HNRNPCL1 WILD-TYPE     6                         5   108
D466V14, multiclass
                           clus
vv                          HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    6                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V15, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    0  4
  HNRNPCL1 WILD-TYPE  5 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      0    4
  HNRNPCL1 WILD-TYPE    5   87
                        clus
vv                       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                4                 87
[1] 2 2
[1] FALSE

Clustering(467) Variable = SEPHS2 MUTATION ANALYSIS
D467V1, survival
                  sevent
clus2               0  1
  SEPHS2 MUTATED    2  3
  SEPHS2 WILD-TYPE 61 59
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              120 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               3               59 
$`SEPHS2 MUTATED`
TCGA-IB-A5SS TCGA-3A-A9IX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-RB-A7B8 
       15.12        34.09        17.00        16.37        15.32 

$`SEPHS2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
        3.12        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           15.12             0.23 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           34.09            90.12 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
          16.370           15.125 
[1] "15.1 - 34.1 (16.4)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.1"
D467V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SEPHS2 MUTATED         0        1        1         1         2         0
  SEPHS2 WILD-TYPE       1        2       11        18        80         4
                  vv
clus               STAGE IV
  SEPHS2 MUTATED          0
  SEPHS2 WILD-TYPE        3
D467V3, multiclass
           clus
vv          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SEPHS2 MUTATED    1  1     3
  SEPHS2 WILD-TYPE  4 16    99
D467V4, multiclass
       clus
vv      SEPHS2 MUTATED SEPHS2 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V5, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    3  2
  SEPHS2 WILD-TYPE 32 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    2
  SEPHS2 WILD-TYPE   32   87
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               32
  1              2               87
[1] 2 2
[1] FALSE
D467V6, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    3  0
  SEPHS2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    0
  SEPHS2 WILD-TYPE   54    3
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D467V7, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    2  3
  SEPHS2 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      2    3
  SEPHS2 WILD-TYPE   49   72
        clus
vv       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D467V8, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    4  1
  SEPHS2 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      4    1
  SEPHS2 WILD-TYPE   84   29
     clus
vv    SEPHS2 MUTATED SEPHS2 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEPHS2 MUTATED                                     4
  SEPHS2 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEPHS2 MUTATED                                       1
  SEPHS2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEPHS2 MUTATED                                                  0
  SEPHS2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SEPHS2 MUTATED                                     0
  SEPHS2 WILD-TYPE                                   1
D467V9, multiclass
                                                  clus
vv                                                 SEPHS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SEPHS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V10, continuous
D467V11, continuous
                  vv
clus               R0 R1 R2 RX
  SEPHS2 MUTATED    4  1  0  0
  SEPHS2 WILD-TYPE 76 34  4  2
D467V12, multiclass
    clus
vv   SEPHS2 MUTATED SEPHS2 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEPHS2 MUTATED       0                         0     5
  SEPHS2 WILD-TYPE     6                         5   109
D467V14, multiclass
                           clus
vv                          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V15, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    0  5
  SEPHS2 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      0    5
  SEPHS2 WILD-TYPE    5   86
                        clus
vv                       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(468) Variable = KIAA0020 MUTATION ANALYSIS
D468V1, survival
                    sevent
clus2                 0  1
  KIAA0020 MUTATED    1  1
  KIAA0020 WILD-TYPE 62 61
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 2                123 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 1                 61 
$`KIAA0020 MUTATED`
TCGA-IB-AAUR TCGA-US-A77J 
       11.11        18.67 

$`KIAA0020 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86        14.17         6.02         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
             11.11               0.23 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
             18.67              90.12 
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
             14.89              15.22 
[1] "11.1 - 18.7 (14.9)" "0.2 - 90.1 (15.2)" 
[1] "Remove cluster labels:" "KIAA0020 MUTATED"      
D468V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA0020 MUTATED         0        0        0         0         3         0
  KIAA0020 WILD-TYPE       1        3       12        19        79         4
                    vv
clus                 STAGE IV
  KIAA0020 MUTATED          0
  KIAA0020 WILD-TYPE        3
D468V3, multiclass
           clus
vv          KIAA0020 MUTATED KIAA0020 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA0020 MUTATED    0  0     3
  KIAA0020 WILD-TYPE  5 17    99
D468V4, multiclass
       clus
vv      KIAA0020 MUTATED KIAA0020 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V5, binary
                    cls
clus                  0  1
  KIAA0020 MUTATED    0  3
  KIAA0020 WILD-TYPE 35 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      0    3
  KIAA0020 WILD-TYPE   35   86
   clus
vv  KIAA0020 MUTATED KIAA0020 WILD-TYPE
  0                0                 35
  1                3                 86
[1] 2 2
[1] FALSE
D468V6, binary
                    cls
clus                  0  1
  KIAA0020 MUTATED    1  0
  KIAA0020 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      1    0
  KIAA0020 WILD-TYPE   56    3
   clus
vv  KIAA0020 MUTATED KIAA0020 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D468V7, binary
                    cls
clus                  0  1
  KIAA0020 MUTATED    1  2
  KIAA0020 WILD-TYPE 50 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      1    2
  KIAA0020 WILD-TYPE   50   73
        clus
vv       KIAA0020 MUTATED KIAA0020 WILD-TYPE
  FEMALE                1                 50
  MALE                  2                 73
[1] 2 2
[1] FALSE
D468V8, binary
                    cls
clus                  0  1
  KIAA0020 MUTATED    1  0
  KIAA0020 WILD-TYPE 87 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      1    0
  KIAA0020 WILD-TYPE   87   30
     clus
vv    KIAA0020 MUTATED KIAA0020 WILD-TYPE
  NO                 1                 87
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0020 MUTATED                                     3
  KIAA0020 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0020 MUTATED                                       0
  KIAA0020 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0020 MUTATED                                                  0
  KIAA0020 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA0020 MUTATED                                     0
  KIAA0020 WILD-TYPE                                   1
D468V9, multiclass
                                                  clus
vv                                                 KIAA0020 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 KIAA0020 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V10, continuous
[1] "Remove cluster labels:" "KIAA0020 MUTATED"      
clus
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-IB-A5SS 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-XD-AAUL         TCGA-2J-AAB1 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
D468V11, continuous
[1] "Remove cluster labels:" "KIAA0020 MUTATED"      
clus
  KIAA0020 MUTATED KIAA0020 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-IB-A5SS 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-XD-AAUL         TCGA-2J-AAB1 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"KIAA0020 WILD-TYPE" "KIAA0020 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  KIAA0020 MUTATED    2  1  0  0
  KIAA0020 WILD-TYPE 78 34  4  2
D468V12, multiclass
    clus
vv   KIAA0020 MUTATED KIAA0020 WILD-TYPE
  R0                2                 78
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0020 MUTATED       0                         0     3
  KIAA0020 WILD-TYPE     6                         5   111
D468V14, multiclass
                           clus
vv                          KIAA0020 MUTATED KIAA0020 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V15, binary
                    cls
clus                  0  1
  KIAA0020 MUTATED    0  3
  KIAA0020 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0020 MUTATED      0    3
  KIAA0020 WILD-TYPE    5   88
                        clus
vv                       KIAA0020 MUTATED KIAA0020 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(469) Variable = ACVR2A MUTATION ANALYSIS
D469V1, survival
                  sevent
clus2               0  1
  ACVR2A MUTATED    2  1
  ACVR2A WILD-TYPE 61 61
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               3              122 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               1               61 
$`ACVR2A MUTATED`
TCGA-HZ-A77Q TCGA-IB-7651 TCGA-RL-AAAS 
        1.08        19.82         0.30 

$`ACVR2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ACVR2A MUTATED ACVR2A WILD-TYPE 
            0.30             0.23 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
           19.82            90.12 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
            1.08            15.27 
[1] "0.3 - 19.8 (1.1)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D469V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ACVR2A MUTATED         0        0        1         0         2         0
  ACVR2A WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  ACVR2A MUTATED          0
  ACVR2A WILD-TYPE        3
D469V3, multiclass
           clus
vv          ACVR2A MUTATED ACVR2A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ACVR2A MUTATED     0   1     2
  ACVR2A WILD-TYPE   5  16   100
D469V4, multiclass
       clus
vv      ACVR2A MUTATED ACVR2A WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V5, binary
                  cls
clus                0  1
  ACVR2A MUTATED    1  2
  ACVR2A WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      1    2
  ACVR2A WILD-TYPE   34   87
   clus
vv  ACVR2A MUTATED ACVR2A WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D469V6, binary
                  cls
clus                0  1
  ACVR2A MUTATED    2  0
  ACVR2A WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      2    0
  ACVR2A WILD-TYPE   55    3
   clus
vv  ACVR2A MUTATED ACVR2A WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D469V7, binary
                  cls
clus                0  1
  ACVR2A MUTATED    3  0
  ACVR2A WILD-TYPE 48 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      3    0
  ACVR2A WILD-TYPE   48   75
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  FEMALE              3               48
  MALE                0               75
[1] 2 2
[1] FALSE
D469V8, binary
                  cls
clus                0  1
  ACVR2A MUTATED    2  0
  ACVR2A WILD-TYPE 86 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      2    0
  ACVR2A WILD-TYPE   86   30
     clus
vv    ACVR2A MUTATED ACVR2A WILD-TYPE
  NO               2               86
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACVR2A MUTATED                                     2
  ACVR2A WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACVR2A MUTATED                                       1
  ACVR2A WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACVR2A MUTATED                                                  0
  ACVR2A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ACVR2A MUTATED                                     0
  ACVR2A WILD-TYPE                                   1
D469V9, multiclass
                                                  clus
vv                                                 ACVR2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ACVR2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V10, continuous
[1] "Remove cluster labels:" "ACVR2A MUTATED"        
clus
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-YY-A8LH 
"ACVR2A WILD-TYPE" 
D469V11, continuous
[1] "Remove cluster labels:" "ACVR2A MUTATED"        
clus
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ACVR2A MUTATED    3  0  0  0
  ACVR2A WILD-TYPE 77 35  4  2
D469V12, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACVR2A MUTATED       0                         0     3
  ACVR2A WILD-TYPE     6                         5   111
D469V14, multiclass
                           clus
vv                          ACVR2A MUTATED ACVR2A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V15, binary
                  cls
clus                0  1
  ACVR2A MUTATED    0  3
  ACVR2A WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      0    3
  ACVR2A WILD-TYPE    5   88
                        clus
vv                       ACVR2A MUTATED ACVR2A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(470) Variable = CCDC158 MUTATION ANALYSIS
D470V1, survival
                   sevent
clus2                0  1
  CCDC158 MUTATED    0  4
  CCDC158 WILD-TYPE 63 58
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                4               121 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                4                58 
$`CCDC158 MUTATED`
TCGA-3E-AAAZ TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A5SO 
       71.74         5.26        19.82        12.00 

$`CCDC158 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        15.19        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CCDC158 MUTATED CCDC158 WILD-TYPE 
             5.26              0.23 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
            71.74             90.12 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
            15.91             15.22 
[1] "5.3 - 71.7 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D470V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC158 MUTATED         0        0        0         1         3         0
  CCDC158 WILD-TYPE       1        3       12        18        79         4
                   vv
clus                STAGE IV
  CCDC158 MUTATED          0
  CCDC158 WILD-TYPE        3
D470V3, multiclass
           clus
vv          CCDC158 MUTATED CCDC158 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC158 MUTATED    0  1     3
  CCDC158 WILD-TYPE  5 16    99
D470V4, multiclass
       clus
vv      CCDC158 MUTATED CCDC158 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V5, binary
                   cls
clus                 0  1
  CCDC158 MUTATED    1  3
  CCDC158 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      1    3
  CCDC158 WILD-TYPE   34   86
   clus
vv  CCDC158 MUTATED CCDC158 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D470V6, binary
                   cls
clus                 0  1
  CCDC158 MUTATED    2  0
  CCDC158 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      2    0
  CCDC158 WILD-TYPE   55    3
   clus
vv  CCDC158 MUTATED CCDC158 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D470V7, binary
                   cls
clus                 0  1
  CCDC158 MUTATED    2  2
  CCDC158 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      2    2
  CCDC158 WILD-TYPE   49   73
        clus
vv       CCDC158 MUTATED CCDC158 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D470V8, binary
                   cls
clus                 0  1
  CCDC158 MUTATED    3  0
  CCDC158 WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      3    0
  CCDC158 WILD-TYPE   85   30
     clus
vv    CCDC158 MUTATED CCDC158 WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC158 MUTATED                                     4
  CCDC158 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC158 MUTATED                                       0
  CCDC158 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC158 MUTATED                                                  0
  CCDC158 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC158 MUTATED                                     0
  CCDC158 WILD-TYPE                                   1
D470V9, multiclass
                                                  clus
vv                                                 CCDC158 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC158 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V10, continuous
[1] "Remove cluster labels:" "CCDC158 MUTATED"       
clus
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
D470V11, continuous
[1] "Remove cluster labels:" "CCDC158 MUTATED"       
clus
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" "CCDC158 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC158 MUTATED    3  0  0  0
  CCDC158 WILD-TYPE 77 35  4  2
D470V12, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC158 MUTATED       0                         0     4
  CCDC158 WILD-TYPE     6                         5   110
D470V14, multiclass
                           clus
vv                          CCDC158 MUTATED CCDC158 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V15, binary
                   cls
clus                 0  1
  CCDC158 MUTATED    1  2
  CCDC158 WILD-TYPE  4 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      1    2
  CCDC158 WILD-TYPE    4   89
                        clus
vv                       CCDC158 MUTATED CCDC158 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(471) Variable = FTH1 MUTATION ANALYSIS
D471V1, survival
                sevent
clus2             0  1
  FTH1 MUTATED    0  3
  FTH1 WILD-TYPE 63 59
  FTH1 MUTATED FTH1 WILD-TYPE 
             3            122 
  FTH1 MUTATED FTH1 WILD-TYPE 
             3             59 
$`FTH1 MUTATED`
TCGA-2L-AAQE TCGA-IB-A5SQ TCGA-US-A77J 
       22.49         7.20        18.67 

$`FTH1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00        15.85        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
        9.40         0.30        39.98        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FTH1 MUTATED FTH1 WILD-TYPE 
          7.20           0.23 
  FTH1 MUTATED FTH1 WILD-TYPE 
         22.49          90.12 
  FTH1 MUTATED FTH1 WILD-TYPE 
        18.670         15.205 
[1] "7.2 - 22.5 (18.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D471V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FTH1 MUTATED         0        0        1         0         2         0
  FTH1 WILD-TYPE       1        3       11        19        80         4
                vv
clus             STAGE IV
  FTH1 MUTATED          0
  FTH1 WILD-TYPE        3
D471V3, multiclass
           clus
vv          FTH1 MUTATED FTH1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  FTH1 MUTATED     0   1     2
  FTH1 WILD-TYPE   5  16   100
D471V4, multiclass
       clus
vv      FTH1 MUTATED FTH1 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V5, binary
                cls
clus              0  1
  FTH1 MUTATED    1  2
  FTH1 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      1    2
  FTH1 WILD-TYPE   34   87
   clus
vv  FTH1 MUTATED FTH1 WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D471V6, binary
                cls
clus              0  1
  FTH1 MUTATED    2  0
  FTH1 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    0
  FTH1 WILD-TYPE   55    3
   clus
vv  FTH1 MUTATED FTH1 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D471V7, binary
                cls
clus              0  1
  FTH1 MUTATED    2  1
  FTH1 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    1
  FTH1 WILD-TYPE   49   74
        clus
vv       FTH1 MUTATED FTH1 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D471V8, binary
                cls
clus              0  1
  FTH1 MUTATED    2  0
  FTH1 WILD-TYPE 86 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      2    0
  FTH1 WILD-TYPE   86   30
     clus
vv    FTH1 MUTATED FTH1 WILD-TYPE
  NO             2             86
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FTH1 MUTATED                                     3
  FTH1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FTH1 MUTATED                                       0
  FTH1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FTH1 MUTATED                                                  0
  FTH1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  FTH1 MUTATED                                     0
  FTH1 WILD-TYPE                                   1
D471V9, multiclass
                                                  clus
vv                                                 FTH1 MUTATED FTH1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V10, continuous
[1] "Remove cluster labels:" "FTH1 MUTATED"          
clus
  FTH1 MUTATED FTH1 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"FTH1 WILD-TYPE" "FTH1 WILD-TYPE" 
D471V11, continuous
                vv
clus             R0 R1 R2 RX
  FTH1 MUTATED    3  0  0  0
  FTH1 WILD-TYPE 77 35  4  2
D471V12, multiclass
    clus
vv   FTH1 MUTATED FTH1 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FTH1 MUTATED       0                         0     3
  FTH1 WILD-TYPE     6                         5   111
D471V14, multiclass
                           clus
vv                          FTH1 MUTATED FTH1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V15, binary
                cls
clus              0  1
  FTH1 MUTATED    0  2
  FTH1 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  FTH1 MUTATED      0    2
  FTH1 WILD-TYPE    5   89
                        clus
vv                       FTH1 MUTATED FTH1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(472) Variable = BCKDHA MUTATION ANALYSIS
D472V1, survival
                  sevent
clus2               0  1
  BCKDHA MUTATED    1  2
  BCKDHA WILD-TYPE 62 60
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               3              122 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               2               60 
$`BCKDHA MUTATED`
TCGA-2J-AAB6 TCGA-2L-AAQA TCGA-IB-A6UF 
        9.63         4.70        21.90 

$`BCKDHA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  BCKDHA MUTATED BCKDHA WILD-TYPE 
            4.70             0.23 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
           21.90            90.12 
  BCKDHA MUTATED BCKDHA WILD-TYPE 
            9.63            15.27 
[1] "4.7 - 21.9 (9.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D472V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BCKDHA MUTATED         0        0        0         1         2         0
  BCKDHA WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  BCKDHA MUTATED          0
  BCKDHA WILD-TYPE        3
D472V3, multiclass
           clus
vv          BCKDHA MUTATED BCKDHA WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  BCKDHA MUTATED    0  0     3
  BCKDHA WILD-TYPE  5 17    99
D472V4, multiclass
       clus
vv      BCKDHA MUTATED BCKDHA WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V5, binary
                  cls
clus                0  1
  BCKDHA MUTATED    1  2
  BCKDHA WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      1    2
  BCKDHA WILD-TYPE   34   87
   clus
vv  BCKDHA MUTATED BCKDHA WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D472V6, binary
                  cls
clus                0  1
  BCKDHA MUTATED    2  0
  BCKDHA WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      2    0
  BCKDHA WILD-TYPE   55    3
   clus
vv  BCKDHA MUTATED BCKDHA WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D472V7, binary
                  cls
clus                0  1
  BCKDHA MUTATED    0  3
  BCKDHA WILD-TYPE 51 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      0    3
  BCKDHA WILD-TYPE   51   72
        clus
vv       BCKDHA MUTATED BCKDHA WILD-TYPE
  FEMALE              0               51
  MALE                3               72
[1] 2 2
[1] FALSE
D472V8, binary
                  cls
clus                0  1
  BCKDHA MUTATED    3  0
  BCKDHA WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      3    0
  BCKDHA WILD-TYPE   85   30
     clus
vv    BCKDHA MUTATED BCKDHA WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCKDHA MUTATED                                     3
  BCKDHA WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCKDHA MUTATED                                       0
  BCKDHA WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCKDHA MUTATED                                                  0
  BCKDHA WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  BCKDHA MUTATED                                     0
  BCKDHA WILD-TYPE                                   1
D472V9, multiclass
                                                  clus
vv                                                 BCKDHA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 BCKDHA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V10, continuous
[1] "Remove cluster labels:" "BCKDHA MUTATED"        
clus
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UG 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-YY-A8LH 
"BCKDHA WILD-TYPE" 
D472V11, continuous
[1] "Remove cluster labels:" "BCKDHA MUTATED"        
clus
  BCKDHA MUTATED BCKDHA WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UG       TCGA-IB-A7M4 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" "BCKDHA WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  BCKDHA MUTATED    1  2  0  0
  BCKDHA WILD-TYPE 79 33  4  2
D472V12, multiclass
    clus
vv   BCKDHA MUTATED BCKDHA WILD-TYPE
  R0              1               79
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCKDHA MUTATED       0                         0     3
  BCKDHA WILD-TYPE     6                         5   111
D472V14, multiclass
                           clus
vv                          BCKDHA MUTATED BCKDHA WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V15, binary
                  cls
clus                0  1
  BCKDHA MUTATED    0  1
  BCKDHA WILD-TYPE  5 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCKDHA MUTATED      0    1
  BCKDHA WILD-TYPE    5   90
                        clus
vv                       BCKDHA MUTATED BCKDHA WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              1               90
[1] 2 2
[1] FALSE

Clustering(473) Variable = SLC34A2 MUTATION ANALYSIS
D473V1, survival
                   sevent
clus2                0  1
  SLC34A2 MUTATED    3  2
  SLC34A2 WILD-TYPE 60 60
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                5               120 
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                2                60 
$`SLC34A2 MUTATED`
TCGA-2J-AABO TCGA-2L-AAQM TCGA-HV-A7OL TCGA-IB-7651 TCGA-RB-A7B8 
       14.47        45.47         8.28        19.82        15.32 

$`SLC34A2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
             8.28              0.23 
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
            45.47             90.12 
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
           15.320            15.205 
[1] "8.3 - 45.5 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D473V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC34A2 MUTATED         0        0        0         1         4         0
  SLC34A2 WILD-TYPE       1        3       12        18        78         4
                   vv
clus                STAGE IV
  SLC34A2 MUTATED          0
  SLC34A2 WILD-TYPE        3
D473V3, multiclass
           clus
vv          SLC34A2 MUTATED SLC34A2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC34A2 MUTATED    0  0     5
  SLC34A2 WILD-TYPE  5 17    97
D473V4, multiclass
       clus
vv      SLC34A2 MUTATED SLC34A2 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V5, binary
                   cls
clus                 0  1
  SLC34A2 MUTATED    1  4
  SLC34A2 WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A2 MUTATED      1    4
  SLC34A2 WILD-TYPE   34   85
   clus
vv  SLC34A2 MUTATED SLC34A2 WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D473V6, binary
                   cls
clus                 0  1
  SLC34A2 MUTATED    2  0
  SLC34A2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A2 MUTATED      2    0
  SLC34A2 WILD-TYPE   55    3
   clus
vv  SLC34A2 MUTATED SLC34A2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D473V7, binary
                   cls
clus                 0  1
  SLC34A2 MUTATED    2  3
  SLC34A2 WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A2 MUTATED      2    3
  SLC34A2 WILD-TYPE   49   72
        clus
vv       SLC34A2 MUTATED SLC34A2 WILD-TYPE
  FEMALE               2                49
  MALE                 3                72
[1] 2 2
[1] FALSE
D473V8, binary
                   cls
clus                 0  1
  SLC34A2 MUTATED    4  1
  SLC34A2 WILD-TYPE 84 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A2 MUTATED      4    1
  SLC34A2 WILD-TYPE   84   29
     clus
vv    SLC34A2 MUTATED SLC34A2 WILD-TYPE
  NO                4                84
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC34A2 MUTATED                                     3
  SLC34A2 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC34A2 MUTATED                                       2
  SLC34A2 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC34A2 MUTATED                                                  0
  SLC34A2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC34A2 MUTATED                                     0
  SLC34A2 WILD-TYPE                                   1
D473V9, multiclass
                                                  clus
vv                                                 SLC34A2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC34A2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V10, continuous
[1] "Remove cluster labels:" "SLC34A2 MUTATED"       
clus
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABV        TCGA-2L-AAQA 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC34A2 WILD-TYPE" 
D473V11, continuous
[1] "Remove cluster labels:" "SLC34A2 MUTATED"       
clus
  SLC34A2 MUTATED SLC34A2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" "SLC34A2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC34A2 MUTATED    3  1  1  0
  SLC34A2 WILD-TYPE 77 34  3  2
D473V12, multiclass
    clus
vv   SLC34A2 MUTATED SLC34A2 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC34A2 MUTATED       1                         0     4
  SLC34A2 WILD-TYPE     5                         5   110
D473V14, multiclass
                           clus
vv                          SLC34A2 MUTATED SLC34A2 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V15, binary
                   cls
clus                 0  1
  SLC34A2 MUTATED    0  2
  SLC34A2 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC34A2 MUTATED      0    2
  SLC34A2 WILD-TYPE    5   89
                        clus
vv                       SLC34A2 MUTATED SLC34A2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(474) Variable = RAB11FIP5 MUTATION ANALYSIS
D474V1, survival
                     sevent
clus2                  0  1
  RAB11FIP5 MUTATED    1  2
  RAB11FIP5 WILD-TYPE 62 60
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  3                 122 
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  2                  60 
$`RAB11FIP5 MUTATED`
TCGA-2L-AAQA TCGA-3E-AAAZ TCGA-H8-A6C1 
        4.70        71.74        22.06 

$`RAB11FIP5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
               4.70                0.23 
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
              71.74               90.12 
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
             22.060              15.205 
[1] "4.7 - 71.7 (22.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D474V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RAB11FIP5 MUTATED         0        0        0         2         1         0
  RAB11FIP5 WILD-TYPE       1        3       12        17        81         4
                     vv
clus                  STAGE IV
  RAB11FIP5 MUTATED          0
  RAB11FIP5 WILD-TYPE        3
D474V3, multiclass
           clus
vv          RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  0                   3
  STAGE IB                  0                  12
  STAGE IIA                 2                  17
  STAGE IIB                 1                  81
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3+T4
  RAB11FIP5 MUTATED    0  0     3
  RAB11FIP5 WILD-TYPE  5 17    99
D474V4, multiclass
       clus
vv      RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  T1                    0                   5
  T2                    0                  17
  T3+T4                 3                  99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V5, binary
                     cls
clus                   0  1
  RAB11FIP5 MUTATED    2  1
  RAB11FIP5 WILD-TYPE 33 88
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP5 MUTATED      2    1
  RAB11FIP5 WILD-TYPE   33   88
   clus
vv  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  0                 2                  33
  1                 1                  88
[1] 2 2
[1] FALSE
D474V6, binary
                     cls
clus                   0  1
  RAB11FIP5 MUTATED    0  0
  RAB11FIP5 WILD-TYPE 57  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP5 MUTATED      0    0
  RAB11FIP5 WILD-TYPE   57    3
D474V7, binary
                     cls
clus                   0  1
  RAB11FIP5 MUTATED    0  3
  RAB11FIP5 WILD-TYPE 51 72
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP5 MUTATED      0    3
  RAB11FIP5 WILD-TYPE   51   72
        clus
vv       RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  FEMALE                 0                  51
  MALE                   3                  72
[1] 2 2
[1] FALSE
D474V8, binary
                     cls
clus                   0  1
  RAB11FIP5 MUTATED    2  0
  RAB11FIP5 WILD-TYPE 86 30
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP5 MUTATED      2    0
  RAB11FIP5 WILD-TYPE   86   30
     clus
vv    RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  NO                  2                  86
  YES                 0                  30
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RAB11FIP5 MUTATED                                     2
  RAB11FIP5 WILD-TYPE                                 103
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RAB11FIP5 MUTATED                                       1
  RAB11FIP5 WILD-TYPE                                    17
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RAB11FIP5 MUTATED                                                  0
  RAB11FIP5 WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  RAB11FIP5 MUTATED                                     0
  RAB11FIP5 WILD-TYPE                                   1
D474V9, multiclass
                                                  clus
vv                                                 RAB11FIP5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 RAB11FIP5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V10, continuous
[1] "Remove cluster labels:" "RAB11FIP5 MUTATED"     
clus
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  2                  37 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2J-AABV 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2L-AAQE          TCGA-3A-A9I9          TCGA-3A-A9IB 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-F2-A8YN          TCGA-FB-A5VM 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-A78T          TCGA-FB-AAPQ          TCGA-FB-AAPS 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HV-AA8V          TCGA-HZ-A8P1          TCGA-IB-7651 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-7885          TCGA-IB-8126          TCGA-IB-A6UF 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A6UG          TCGA-IB-A7M4          TCGA-IB-AAUQ 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-AAUS          TCGA-IB-AAUU          TCGA-IB-AAUV 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XN-A8T5 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-YY-A8LH 
"RAB11FIP5 WILD-TYPE" 
D474V11, continuous
[1] "Remove cluster labels:" "RAB11FIP5 MUTATED"     
clus
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  1                  32 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABE          TCGA-2J-AABF 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AABO          TCGA-3A-A9IB          TCGA-3A-A9IR 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-FB-A5VM          TCGA-FB-A78T 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-AAPQ          TCGA-FB-AAPS          TCGA-HZ-A8P1 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-7651          TCGA-IB-7885          TCGA-IB-8126 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XD-AAUI 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  RAB11FIP5 MUTATED    1  1  0  0
  RAB11FIP5 WILD-TYPE 79 34  4  2
D474V12, multiclass
[1] "Remove cluster labels:" "RAB11FIP5 MUTATED"     
clus
  RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE 
                  2                 119 
         TCGA-2J-AABR          TCGA-2J-AABT          TCGA-3A-A9I5 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IJ          TCGA-3A-A9IL          TCGA-F2-A44G 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-AAQ6          TCGA-FZ-5924          TCGA-HZ-A77Q 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HZ-A8P0          TCGA-IB-A5SS          TCGA-LB-A7SX 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-S4-A8RO          TCGA-US-A77E          TCGA-XD-AAUL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AAB4          TCGA-2J-AAB6 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AAB8          TCGA-2J-AAB9          TCGA-2J-AABA 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AABE          TCGA-2J-AABF          TCGA-2J-AABH 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AABK          TCGA-2J-AABO          TCGA-2J-AABP 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2J-AABU          TCGA-2J-AABV          TCGA-2L-AAQE 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2L-AAQI          TCGA-2L-AAQJ          TCGA-2L-AAQL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-2L-AAQM          TCGA-3A-A9I7          TCGA-3A-A9I9 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IC          TCGA-3A-A9IH 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IO          TCGA-3A-A9IR          TCGA-3A-A9IS 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IU          TCGA-3A-A9IV          TCGA-3A-A9IX 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-3A-A9IZ          TCGA-3A-A9J0          TCGA-F2-7273 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-F2-A7TX          TCGA-F2-A8YN          TCGA-FB-A5VM 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-A78T          TCGA-FB-AAPP          TCGA-FB-AAPQ 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-FB-AAPU          TCGA-FB-AAPZ 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-AAQ0          TCGA-FB-AAQ1          TCGA-FB-AAQ2 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FB-AAQ3          TCGA-FZ-5920          TCGA-FZ-5922 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-FZ-5923          TCGA-FZ-5926          TCGA-HV-A7OL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HV-A7OP          TCGA-HV-AA8V          TCGA-HV-AA8X 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HZ-7918          TCGA-HZ-7925          TCGA-HZ-8637 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HZ-A49I          TCGA-HZ-A77O          TCGA-HZ-A77P 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-HZ-A9TJ          TCGA-IB-7651 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-7652          TCGA-IB-7885          TCGA-IB-8126 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A5SO          TCGA-IB-A5SP          TCGA-IB-A5SQ 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A5ST          TCGA-IB-A6UF          TCGA-IB-A6UG 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-A7LX          TCGA-IB-A7M4          TCGA-IB-AAUM 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-AAUN          TCGA-IB-AAUO          TCGA-IB-AAUP 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUR          TCGA-IB-AAUS 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-IB-AAUU          TCGA-IB-AAUV          TCGA-IB-AAUW 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-LB-A8F3          TCGA-LB-A9Q5          TCGA-OE-A75W 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-Q3-A5QY          TCGA-Q3-AA2A          TCGA-RB-A7B8 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-RB-AA9M          TCGA-RL-AAAS          TCGA-US-A776 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-US-A779          TCGA-US-A77G          TCGA-US-A77J 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-XD-AAUG          TCGA-XD-AAUH          TCGA-XD-AAUI 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-XN-A8T3          TCGA-XN-A8T5          TCGA-YB-A89D 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
         TCGA-YY-A8LH          TCGA-Z5-AAPL 
"RAB11FIP5 WILD-TYPE" "RAB11FIP5 WILD-TYPE" 
D474V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAB11FIP5 MUTATED       0                         0     3
  RAB11FIP5 WILD-TYPE     6                         5   111
D474V14, multiclass
                           clus
vv                          RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     3                 111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V15, binary
                     cls
clus                   0  1
  RAB11FIP5 MUTATED    1  1
  RAB11FIP5 WILD-TYPE  4 90
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  RAB11FIP5 MUTATED      1    1
  RAB11FIP5 WILD-TYPE    4   90
                        clus
vv                       RAB11FIP5 MUTATED RAB11FIP5 WILD-TYPE
  HISPANIC OR LATINO                     1                   4
  NOT HISPANIC OR LATINO                 1                  90
[1] 2 2
[1] FALSE

Clustering(475) Variable = ATP6V1A MUTATION ANALYSIS
D475V1, survival
                   sevent
clus2                0  1
  ATP6V1A MUTATED    3  0
  ATP6V1A WILD-TYPE 60 62
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                3               122 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                0                62 
$`ATP6V1A MUTATED`
TCGA-HZ-A77Q TCGA-HV-A7OP TCGA-YB-A89D 
        1.08        32.15        11.51 

$`ATP6V1A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
             1.08              0.23 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
            32.15             90.12 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
            11.51             15.27 
[1] "1.1 - 32.1 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr="     "9200000"
D475V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP6V1A MUTATED         0        0        0         0         3         0
  ATP6V1A WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  ATP6V1A MUTATED          0
  ATP6V1A WILD-TYPE        3
D475V3, multiclass
           clus
vv          ATP6V1A MUTATED ATP6V1A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ATP6V1A MUTATED    0  0     3
  ATP6V1A WILD-TYPE  5 17    99
D475V4, multiclass
       clus
vv      ATP6V1A MUTATED ATP6V1A WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V5, binary
                   cls
clus                 0  1
  ATP6V1A MUTATED    0  3
  ATP6V1A WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      0    3
  ATP6V1A WILD-TYPE   35   86
   clus
vv  ATP6V1A MUTATED ATP6V1A WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D475V6, binary
                   cls
clus                 0  1
  ATP6V1A MUTATED    1  0
  ATP6V1A WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      1    0
  ATP6V1A WILD-TYPE   56    3
   clus
vv  ATP6V1A MUTATED ATP6V1A WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D475V7, binary
                   cls
clus                 0  1
  ATP6V1A MUTATED    1  2
  ATP6V1A WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      1    2
  ATP6V1A WILD-TYPE   50   73
        clus
vv       ATP6V1A MUTATED ATP6V1A WILD-TYPE
  FEMALE               1                50
  MALE                 2                73
[1] 2 2
[1] FALSE
D475V8, binary
                   cls
clus                 0  1
  ATP6V1A MUTATED    0  2
  ATP6V1A WILD-TYPE 88 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      0    2
  ATP6V1A WILD-TYPE   88   28
     clus
vv    ATP6V1A MUTATED ATP6V1A WILD-TYPE
  NO                0                88
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP6V1A MUTATED                                     1
  ATP6V1A WILD-TYPE                                 104
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP6V1A MUTATED                                       2
  ATP6V1A WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP6V1A MUTATED                                                  0
  ATP6V1A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP6V1A MUTATED                                     0
  ATP6V1A WILD-TYPE                                   1
D475V9, multiclass
                                                  clus
vv                                                 ATP6V1A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ATP6V1A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V10, continuous
[1] "Remove cluster labels:" "ATP6V1A MUTATED"       
clus
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
D475V11, continuous
[1] "Remove cluster labels:" "ATP6V1A MUTATED"       
clus
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" "ATP6V1A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ATP6V1A MUTATED    3  0  0  0
  ATP6V1A WILD-TYPE 77 35  4  2
D475V12, multiclass
    clus
vv   ATP6V1A MUTATED ATP6V1A WILD-TYPE
  R0               3                77
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1A MUTATED       1                         0     2
  ATP6V1A WILD-TYPE     5                         5   112
D475V14, multiclass
                           clus
vv                          ATP6V1A MUTATED ATP6V1A WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   2               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V15, binary
                   cls
clus                 0  1
  ATP6V1A MUTATED    0  2
  ATP6V1A WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      0    2
  ATP6V1A WILD-TYPE    5   89
                        clus
vv                       ATP6V1A MUTATED ATP6V1A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(476) Variable = TMEM41B MUTATION ANALYSIS
D476V1, survival
                   sevent
clus2                0  1
  TMEM41B MUTATED    2  1
  TMEM41B WILD-TYPE 61 61
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                3               122 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                1                61 
$`TMEM41B MUTATED`
TCGA-2J-AABO TCGA-FB-AAQ1 TCGA-US-A776 
       14.47         4.04        39.98 

$`TMEM41B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             4.04              0.23 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            39.98             90.12 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            14.47             15.27 
[1] "4.0 - 40.0 (14.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D476V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TMEM41B MUTATED         0        0        0         1         2         0
  TMEM41B WILD-TYPE       1        3       12        18        80         4
                   vv
clus                STAGE IV
  TMEM41B MUTATED          0
  TMEM41B WILD-TYPE        3
D476V3, multiclass
           clus
vv          TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               2                80
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TMEM41B MUTATED    0  0     3
  TMEM41B WILD-TYPE  5 17    99
D476V4, multiclass
       clus
vv      TMEM41B MUTATED TMEM41B WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V5, binary
                   cls
clus                 0  1
  TMEM41B MUTATED    1  2
  TMEM41B WILD-TYPE 34 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      1    2
  TMEM41B WILD-TYPE   34   87
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               1                34
  1               2                87
[1] 2 2
[1] FALSE
D476V6, binary
                   cls
clus                 0  1
  TMEM41B MUTATED    1  0
  TMEM41B WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      1    0
  TMEM41B WILD-TYPE   56    3
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D476V7, binary
                   cls
clus                 0  1
  TMEM41B MUTATED    0  3
  TMEM41B WILD-TYPE 51 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      0    3
  TMEM41B WILD-TYPE   51   72
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               0                51
  MALE                 3                72
[1] 2 2
[1] FALSE
D476V8, binary
                   cls
clus                 0  1
  TMEM41B MUTATED    2  1
  TMEM41B WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    1
  TMEM41B WILD-TYPE   86   29
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM41B MUTATED                                     2
  TMEM41B WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM41B MUTATED                                       0
  TMEM41B WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM41B MUTATED                                                  1
  TMEM41B WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TMEM41B MUTATED                                     0
  TMEM41B WILD-TYPE                                   1
D476V9, multiclass
                                                  clus
vv                                                 TMEM41B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TMEM41B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V10, continuous
[1] "Remove cluster labels:" "TMEM41B MUTATED"       
clus
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABV        TCGA-2L-AAQA 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
D476V11, continuous
[1] "Remove cluster labels:" "TMEM41B MUTATED"       
clus
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-2J-AABF        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7651        TCGA-IB-7885 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" "TMEM41B WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TMEM41B MUTATED    2  1  0  0
  TMEM41B WILD-TYPE 78 34  4  2
D476V12, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM41B MUTATED       0                         0     3
  TMEM41B WILD-TYPE     6                         5   111
D476V14, multiclass
                           clus
vv                          TMEM41B MUTATED TMEM41B WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V15, binary
                   cls
clus                 0  1
  TMEM41B MUTATED    0  2
  TMEM41B WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      0    2
  TMEM41B WILD-TYPE    5   89
                        clus
vv                       TMEM41B MUTATED TMEM41B WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(477) Variable = GIGYF1 MUTATION ANALYSIS
D477V1, survival
                  sevent
clus2               0  1
  GIGYF1 MUTATED    1  2
  GIGYF1 WILD-TYPE 62 60
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               3              122 
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               2               60 
$`GIGYF1 MUTATED`
TCGA-2J-AABU TCGA-IB-7651 TCGA-XN-A8T3 
        9.11        19.82        31.27 

$`GIGYF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
            9.11             0.23 
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
           31.27            90.12 
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
          19.820           15.205 
[1] "9.1 - 31.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D477V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GIGYF1 MUTATED         0        0        1         0         2         0
  GIGYF1 WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  GIGYF1 MUTATED          0
  GIGYF1 WILD-TYPE        3
D477V3, multiclass
           clus
vv          GIGYF1 MUTATED GIGYF1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  GIGYF1 MUTATED     0   1     2
  GIGYF1 WILD-TYPE   5  16   100
D477V4, multiclass
       clus
vv      GIGYF1 MUTATED GIGYF1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V5, binary
                  cls
clus                0  1
  GIGYF1 MUTATED    1  2
  GIGYF1 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF1 MUTATED      1    2
  GIGYF1 WILD-TYPE   34   87
   clus
vv  GIGYF1 MUTATED GIGYF1 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D477V6, binary
                  cls
clus                0  1
  GIGYF1 MUTATED    3  0
  GIGYF1 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF1 MUTATED      3    0
  GIGYF1 WILD-TYPE   54    3
   clus
vv  GIGYF1 MUTATED GIGYF1 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D477V7, binary
                  cls
clus                0  1
  GIGYF1 MUTATED    1  2
  GIGYF1 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF1 MUTATED      1    2
  GIGYF1 WILD-TYPE   50   73
        clus
vv       GIGYF1 MUTATED GIGYF1 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D477V8, binary
                  cls
clus                0  1
  GIGYF1 MUTATED    2  1
  GIGYF1 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF1 MUTATED      2    1
  GIGYF1 WILD-TYPE   86   29
     clus
vv    GIGYF1 MUTATED GIGYF1 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GIGYF1 MUTATED                                     3
  GIGYF1 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GIGYF1 MUTATED                                       0
  GIGYF1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GIGYF1 MUTATED                                                  0
  GIGYF1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GIGYF1 MUTATED                                     0
  GIGYF1 WILD-TYPE                                   1
D477V9, multiclass
                                                  clus
vv                                                 GIGYF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GIGYF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V10, continuous
[1] "Remove cluster labels:" "GIGYF1 MUTATED"        
clus
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
D477V11, continuous
[1] "Remove cluster labels:" "GIGYF1 MUTATED"        
clus
  GIGYF1 MUTATED GIGYF1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" "GIGYF1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GIGYF1 MUTATED    2  1  0  0
  GIGYF1 WILD-TYPE 78 34  4  2
D477V12, multiclass
    clus
vv   GIGYF1 MUTATED GIGYF1 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GIGYF1 MUTATED       0                         0     3
  GIGYF1 WILD-TYPE     6                         5   111
D477V14, multiclass
                           clus
vv                          GIGYF1 MUTATED GIGYF1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V15, binary
                  cls
clus                0  1
  GIGYF1 MUTATED    1  1
  GIGYF1 WILD-TYPE  4 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF1 MUTATED      1    1
  GIGYF1 WILD-TYPE    4   90
                        clus
vv                       GIGYF1 MUTATED GIGYF1 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              1               90
[1] 2 2
[1] FALSE

Clustering(478) Variable = EPB41L4B MUTATION ANALYSIS
D478V1, survival
                    sevent
clus2                 0  1
  EPB41L4B MUTATED    0  4
  EPB41L4B WILD-TYPE 63 58
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 4                121 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 4                 58 
$`EPB41L4B MUTATED`
TCGA-2J-AAB1 TCGA-FB-AAPU TCGA-FZ-5920 TCGA-IB-7651 
        2.17        12.53         2.01        19.82 

$`EPB41L4B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
              2.01               0.23 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
             19.82              90.12 
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
              7.35              15.32 
[1] "2.0 - 19.8 (7.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.2"
D478V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EPB41L4B MUTATED         0        0        0         1         3         0
  EPB41L4B WILD-TYPE       1        3       12        18        79         4
                    vv
clus                 STAGE IV
  EPB41L4B MUTATED          0
  EPB41L4B WILD-TYPE        3
D478V3, multiclass
           clus
vv          EPB41L4B MUTATED EPB41L4B WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  EPB41L4B MUTATED    0  0     4
  EPB41L4B WILD-TYPE  5 17    98
D478V4, multiclass
       clus
vv      EPB41L4B MUTATED EPB41L4B WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V5, binary
                    cls
clus                  0  1
  EPB41L4B MUTATED    1  3
  EPB41L4B WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      1    3
  EPB41L4B WILD-TYPE   34   86
   clus
vv  EPB41L4B MUTATED EPB41L4B WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D478V6, binary
                    cls
clus                  0  1
  EPB41L4B MUTATED    3  0
  EPB41L4B WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      3    0
  EPB41L4B WILD-TYPE   54    3
   clus
vv  EPB41L4B MUTATED EPB41L4B WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D478V7, binary
                    cls
clus                  0  1
  EPB41L4B MUTATED    2  2
  EPB41L4B WILD-TYPE 49 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      2    2
  EPB41L4B WILD-TYPE   49   73
        clus
vv       EPB41L4B MUTATED EPB41L4B WILD-TYPE
  FEMALE                2                 49
  MALE                  2                 73
[1] 2 2
[1] FALSE
D478V8, binary
                    cls
clus                  0  1
  EPB41L4B MUTATED    4  0
  EPB41L4B WILD-TYPE 84 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      4    0
  EPB41L4B WILD-TYPE   84   30
     clus
vv    EPB41L4B MUTATED EPB41L4B WILD-TYPE
  NO                 4                 84
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EPB41L4B MUTATED                                     3
  EPB41L4B WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EPB41L4B MUTATED                                       1
  EPB41L4B WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EPB41L4B MUTATED                                                  0
  EPB41L4B WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  EPB41L4B MUTATED                                     0
  EPB41L4B WILD-TYPE                                   1
D478V9, multiclass
                                                  clus
vv                                                 EPB41L4B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 EPB41L4B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V10, continuous
[1] "Remove cluster labels:" "EPB41L4B MUTATED"      
clus
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-YY-A8LH 
"EPB41L4B WILD-TYPE" 
D478V11, continuous
[1] "Remove cluster labels:" "EPB41L4B MUTATED"      
clus
  EPB41L4B MUTATED EPB41L4B WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" "EPB41L4B WILD-TYPE" 
        TCGA-YY-A8LH 
"EPB41L4B WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  EPB41L4B MUTATED    3  1  0  0
  EPB41L4B WILD-TYPE 77 34  4  2
D478V12, multiclass
    clus
vv   EPB41L4B MUTATED EPB41L4B WILD-TYPE
  R0                3                 77
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPB41L4B MUTATED       1                         1     2
  EPB41L4B WILD-TYPE     5                         4   112
D478V14, multiclass
                           clus
vv                          EPB41L4B MUTATED EPB41L4B WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    2                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V15, binary
                    cls
clus                  0  1
  EPB41L4B MUTATED    0  3
  EPB41L4B WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4B MUTATED      0    3
  EPB41L4B WILD-TYPE    5   88
                        clus
vv                       EPB41L4B MUTATED EPB41L4B WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(479) Variable = EPHX1 MUTATION ANALYSIS
D479V1, survival
                 sevent
clus2              0  1
  EPHX1 MUTATED    1  3
  EPHX1 WILD-TYPE 62 59
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              4             121 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              3              59 
$`EPHX1 MUTATED`
TCGA-2J-AABA TCGA-3A-A9IB TCGA-IB-7651 TCGA-RL-AAAS 
       19.96         7.36        19.82         0.30 

$`EPHX1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  EPHX1 MUTATED EPHX1 WILD-TYPE 
           0.30            0.23 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
          19.96           90.12 
  EPHX1 MUTATED EPHX1 WILD-TYPE 
          13.59           15.22 
[1] "0.3 - 20.0 (13.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.2"
D479V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EPHX1 MUTATED         0        0        1         0         3         0
  EPHX1 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  EPHX1 MUTATED          0
  EPHX1 WILD-TYPE        3
D479V3, multiclass
           clus
vv          EPHX1 MUTATED EPHX1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  EPHX1 MUTATED    0  1     3
  EPHX1 WILD-TYPE  5 16    99
D479V4, multiclass
       clus
vv      EPHX1 MUTATED EPHX1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V5, binary
                 cls
clus               0  1
  EPHX1 MUTATED    1  3
  EPHX1 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      1    3
  EPHX1 WILD-TYPE   34   86
   clus
vv  EPHX1 MUTATED EPHX1 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D479V6, binary
                 cls
clus               0  1
  EPHX1 MUTATED    3  0
  EPHX1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      3    0
  EPHX1 WILD-TYPE   54    3
   clus
vv  EPHX1 MUTATED EPHX1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D479V7, binary
                 cls
clus               0  1
  EPHX1 MUTATED    3  1
  EPHX1 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      3    1
  EPHX1 WILD-TYPE   48   74
        clus
vv       EPHX1 MUTATED EPHX1 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D479V8, binary
                 cls
clus               0  1
  EPHX1 MUTATED    4  0
  EPHX1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      4    0
  EPHX1 WILD-TYPE   84   30
     clus
vv    EPHX1 MUTATED EPHX1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EPHX1 MUTATED                                     4
  EPHX1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EPHX1 MUTATED                                       0
  EPHX1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EPHX1 MUTATED                                                  0
  EPHX1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EPHX1 MUTATED                                     0
  EPHX1 WILD-TYPE                                   1
D479V9, multiclass
                                                  clus
vv                                                 EPHX1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 EPHX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V10, continuous
D479V11, continuous
[1] "Remove cluster labels:" "EPHX1 MUTATED"         
clus
  EPHX1 MUTATED EPHX1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IR      TCGA-3A-A9IX 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" "EPHX1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  EPHX1 MUTATED    3  1  0  0
  EPHX1 WILD-TYPE 77 34  4  2
D479V12, multiclass
    clus
vv   EPHX1 MUTATED EPHX1 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPHX1 MUTATED       0                         0     4
  EPHX1 WILD-TYPE     6                         5   110
D479V14, multiclass
                           clus
vv                          EPHX1 MUTATED EPHX1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V15, binary
                 cls
clus               0  1
  EPHX1 MUTATED    0  3
  EPHX1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHX1 MUTATED      0    3
  EPHX1 WILD-TYPE    5   88
                        clus
vv                       EPHX1 MUTATED EPHX1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(480) Variable = LUZP1 MUTATION ANALYSIS
D480V1, survival
                 sevent
clus2              0  1
  LUZP1 MUTATED    2  1
  LUZP1 WILD-TYPE 61 61
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              3             122 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              1              61 
$`LUZP1 MUTATED`
TCGA-HV-A7OL TCGA-IB-A6UF TCGA-OE-A75W 
        8.28        21.90         8.78 

$`LUZP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG 
       15.19        12.00        15.85         7.20        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
           8.28            0.23 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
          21.90           90.12 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
           8.78           15.27 
[1] "8.3 - 21.9 (8.8)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D480V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LUZP1 MUTATED         0        0        0         2         1         0
  LUZP1 WILD-TYPE       1        3       12        17        81         4
                 vv
clus              STAGE IV
  LUZP1 MUTATED          0
  LUZP1 WILD-TYPE        3
D480V3, multiclass
           clus
vv          LUZP1 MUTATED LUZP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LUZP1 MUTATED    0  0     3
  LUZP1 WILD-TYPE  5 17    99
D480V4, multiclass
       clus
vv      LUZP1 MUTATED LUZP1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V5, binary
                 cls
clus               0  1
  LUZP1 MUTATED    2  1
  LUZP1 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      2    1
  LUZP1 WILD-TYPE   33   88
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D480V6, binary
                 cls
clus               0  1
  LUZP1 MUTATED    2  0
  LUZP1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      2    0
  LUZP1 WILD-TYPE   55    3
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D480V7, binary
                 cls
clus               0  1
  LUZP1 MUTATED    0  3
  LUZP1 WILD-TYPE 51 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      0    3
  LUZP1 WILD-TYPE   51   72
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  FEMALE             0              51
  MALE               3              72
[1] 2 2
[1] FALSE
D480V8, binary
                 cls
clus               0  1
  LUZP1 MUTATED    2  1
  LUZP1 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      2    1
  LUZP1 WILD-TYPE   86   29
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LUZP1 MUTATED                                     3
  LUZP1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LUZP1 MUTATED                                       0
  LUZP1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LUZP1 MUTATED                                                  0
  LUZP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LUZP1 MUTATED                                     0
  LUZP1 WILD-TYPE                                   1
D480V9, multiclass
                                                  clus
vv                                                 LUZP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LUZP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V10, continuous
[1] "Remove cluster labels:" "LUZP1 MUTATED"         
clus
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-XN-A8T5 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-YY-A8LH 
"LUZP1 WILD-TYPE" 
D480V11, continuous
[1] "Remove cluster labels:" "LUZP1 MUTATED"         
clus
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG      TCGA-IB-A7M4 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  LUZP1 MUTATED    1  1  1  0
  LUZP1 WILD-TYPE 79 34  3  2
D480V12, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  R0             1              79
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V13, continuous
[1] "Remove cluster labels:" "LUZP1 MUTATED"         
clus
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5919 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FZ-5920      TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OP      TCGA-HV-AA8V 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77G 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D      TCGA-YH-A8SY 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LUZP1 MUTATED       1                         0     2
  LUZP1 WILD-TYPE     5                         5   112
D480V14, multiclass
                           clus
vv                          LUZP1 MUTATED LUZP1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V15, binary
                 cls
clus               0  1
  LUZP1 MUTATED    0  2
  LUZP1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      0    2
  LUZP1 WILD-TYPE    5   89
                        clus
vv                       LUZP1 MUTATED LUZP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(481) Variable = ZHX1 MUTATION ANALYSIS
D481V1, survival
                sevent
clus2             0  1
  ZHX1 MUTATED    2  1
  ZHX1 WILD-TYPE 61 61
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             3            122 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             1             61 
$`ZHX1 MUTATED`
TCGA-3A-A9I9 TCGA-HZ-7918 TCGA-IB-A6UF 
       20.84        31.86        21.90 

$`ZHX1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZHX1 MUTATED ZHX1 WILD-TYPE 
         20.84           0.23 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
         31.86          90.12 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
        21.900         15.155 
[1] "20.8 - 31.9 (21.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.5"
D481V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZHX1 MUTATED         0        0        0         1         2         0
  ZHX1 WILD-TYPE       1        3       12        18        80         4
                vv
clus             STAGE IV
  ZHX1 MUTATED          0
  ZHX1 WILD-TYPE        3
D481V3, multiclass
           clus
vv          ZHX1 MUTATED ZHX1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  ZHX1 MUTATED    0  0     3
  ZHX1 WILD-TYPE  5 17    99
D481V4, multiclass
       clus
vv      ZHX1 MUTATED ZHX1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V5, binary
                cls
clus              0  1
  ZHX1 MUTATED    1  2
  ZHX1 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      1    2
  ZHX1 WILD-TYPE   34   87
   clus
vv  ZHX1 MUTATED ZHX1 WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D481V6, binary
                cls
clus              0  1
  ZHX1 MUTATED    2  0
  ZHX1 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      2    0
  ZHX1 WILD-TYPE   55    3
   clus
vv  ZHX1 MUTATED ZHX1 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D481V7, binary
                cls
clus              0  1
  ZHX1 MUTATED    0  3
  ZHX1 WILD-TYPE 51 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      0    3
  ZHX1 WILD-TYPE   51   72
        clus
vv       ZHX1 MUTATED ZHX1 WILD-TYPE
  FEMALE            0             51
  MALE              3             72
[1] 2 2
[1] FALSE
D481V8, binary
                cls
clus              0  1
  ZHX1 MUTATED    1  2
  ZHX1 WILD-TYPE 87 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      1    2
  ZHX1 WILD-TYPE   87   28
     clus
vv    ZHX1 MUTATED ZHX1 WILD-TYPE
  NO             1             87
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZHX1 MUTATED                                     3
  ZHX1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZHX1 MUTATED                                       0
  ZHX1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZHX1 MUTATED                                                  0
  ZHX1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZHX1 MUTATED                                     0
  ZHX1 WILD-TYPE                                   1
D481V9, multiclass
                                                  clus
vv                                                 ZHX1 MUTATED ZHX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V10, continuous
[1] "Remove cluster labels:" "ZHX1 MUTATED"          
clus
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9IB     TCGA-3A-A9IX 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UG 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-YY-A8LH 
"ZHX1 WILD-TYPE" 
D481V11, continuous
[1] "Remove cluster labels:" "ZHX1 MUTATED"          
clus
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UG     TCGA-IB-A7M4 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" "ZHX1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ZHX1 MUTATED    2  1  0  0
  ZHX1 WILD-TYPE 78 34  4  2
D481V12, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZHX1 MUTATED       0                         0     3
  ZHX1 WILD-TYPE     6                         5   111
D481V14, multiclass
                           clus
vv                          ZHX1 MUTATED ZHX1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V15, binary
                cls
clus              0  1
  ZHX1 MUTATED    0  3
  ZHX1 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      0    3
  ZHX1 WILD-TYPE    5   88
                        clus
vv                       ZHX1 MUTATED ZHX1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(482) Variable = GNAL MUTATION ANALYSIS
D482V1, survival
                sevent
clus2             0  1
  GNAL MUTATED    1  2
  GNAL WILD-TYPE 62 60
  GNAL MUTATED GNAL WILD-TYPE 
             3            122 
  GNAL MUTATED GNAL WILD-TYPE 
             2             60 
$`GNAL MUTATED`
TCGA-FB-A5VM TCGA-FB-AAQ0 TCGA-IB-A6UF 
       16.37        15.55        21.90 

$`GNAL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        23.54         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  GNAL MUTATED GNAL WILD-TYPE 
         15.55           0.23 
  GNAL MUTATED GNAL WILD-TYPE 
         21.90          90.12 
  GNAL MUTATED GNAL WILD-TYPE 
        16.370         15.155 
[1] "15.6 - 21.9 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D482V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GNAL MUTATED         0        0        1         1         1         0
  GNAL WILD-TYPE       1        3       11        18        81         4
                vv
clus             STAGE IV
  GNAL MUTATED          0
  GNAL WILD-TYPE        3
D482V3, multiclass
           clus
vv          GNAL MUTATED GNAL WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            1             81
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  GNAL MUTATED     0   1     2
  GNAL WILD-TYPE   5  16   100
D482V4, multiclass
       clus
vv      GNAL MUTATED GNAL WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V5, binary
                cls
clus              0  1
  GNAL MUTATED    2  1
  GNAL WILD-TYPE 33 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAL MUTATED      2    1
  GNAL WILD-TYPE   33   88
   clus
vv  GNAL MUTATED GNAL WILD-TYPE
  0            2             33
  1            1             88
[1] 2 2
[1] FALSE
D482V6, binary
                cls
clus              0  1
  GNAL MUTATED    2  0
  GNAL WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAL MUTATED      2    0
  GNAL WILD-TYPE   55    3
   clus
vv  GNAL MUTATED GNAL WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D482V7, binary
                cls
clus              0  1
  GNAL MUTATED    0  3
  GNAL WILD-TYPE 51 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAL MUTATED      0    3
  GNAL WILD-TYPE   51   72
        clus
vv       GNAL MUTATED GNAL WILD-TYPE
  FEMALE            0             51
  MALE              3             72
[1] 2 2
[1] FALSE
D482V8, binary
                cls
clus              0  1
  GNAL MUTATED    3  0
  GNAL WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAL MUTATED      3    0
  GNAL WILD-TYPE   85   30
     clus
vv    GNAL MUTATED GNAL WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNAL MUTATED                                     3
  GNAL WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNAL MUTATED                                       0
  GNAL WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNAL MUTATED                                                  0
  GNAL WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  GNAL MUTATED                                     0
  GNAL WILD-TYPE                                   1
D482V9, multiclass
                                                  clus
vv                                                 GNAL MUTATED GNAL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V10, continuous
[1] "Remove cluster labels:" "GNAL MUTATED"          
clus
  GNAL MUTATED GNAL WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A78T     TCGA-FB-AAPQ 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UG 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-YY-A8LH 
"GNAL WILD-TYPE" 
D482V11, continuous
[1] "Remove cluster labels:" "GNAL MUTATED"          
clus
  GNAL MUTATED GNAL WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"GNAL WILD-TYPE" "GNAL WILD-TYPE" "GNAL WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  GNAL MUTATED    2  1  0  0
  GNAL WILD-TYPE 78 34  4  2
D482V12, multiclass
    clus
vv   GNAL MUTATED GNAL WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNAL MUTATED       0                         0     3
  GNAL WILD-TYPE     6                         5   111
D482V14, multiclass
                           clus
vv                          GNAL MUTATED GNAL WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V15, binary
                cls
clus              0  1
  GNAL MUTATED    0  3
  GNAL WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAL MUTATED      0    3
  GNAL WILD-TYPE    5   88
                        clus
vv                       GNAL MUTATED GNAL WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(483) Variable = DOCK10 MUTATION ANALYSIS
D483V1, survival
                  sevent
clus2               0  1
  DOCK10 MUTATED    2  4
  DOCK10 WILD-TYPE 61 58
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               6              119 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               4               58 
$`DOCK10 MUTATED`
TCGA-US-A77E TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-AAUU 
       14.14        19.46        19.82         7.20        21.90         8.05 

$`DOCK10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       15.85        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  DOCK10 MUTATED DOCK10 WILD-TYPE 
            7.20             0.23 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
           21.90            90.12 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
           16.80            15.22 
[1] "7.2 - 21.9 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D483V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DOCK10 MUTATED         0        0        1         0         5         0
  DOCK10 WILD-TYPE       1        3       11        19        77         4
                  vv
clus               STAGE IV
  DOCK10 MUTATED          0
  DOCK10 WILD-TYPE        3
D483V3, multiclass
           clus
vv          DOCK10 MUTATED DOCK10 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  DOCK10 MUTATED    0  1     5
  DOCK10 WILD-TYPE  5 16    97
D483V4, multiclass
       clus
vv      DOCK10 MUTATED DOCK10 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V5, binary
                  cls
clus                0  1
  DOCK10 MUTATED    1  5
  DOCK10 WILD-TYPE 34 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED      1    5
  DOCK10 WILD-TYPE   34   84
   clus
vv  DOCK10 MUTATED DOCK10 WILD-TYPE
  0              1               34
  1              5               84
[1] 2 2
[1] FALSE
D483V6, binary
                  cls
clus                0  1
  DOCK10 MUTATED    5  0
  DOCK10 WILD-TYPE 52  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED      5    0
  DOCK10 WILD-TYPE   52    3
   clus
vv  DOCK10 MUTATED DOCK10 WILD-TYPE
  0              5               52
  1              0                3
[1] 2 2
[1] FALSE
D483V7, binary
                  cls
clus                0  1
  DOCK10 MUTATED    2  4
  DOCK10 WILD-TYPE 49 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED      2    4
  DOCK10 WILD-TYPE   49   71
        clus
vv       DOCK10 MUTATED DOCK10 WILD-TYPE
  FEMALE              2               49
  MALE                4               71
[1] 2 2
[1] FALSE
D483V8, binary
                  cls
clus                0  1
  DOCK10 MUTATED    5  1
  DOCK10 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED      5    1
  DOCK10 WILD-TYPE   83   29
     clus
vv    DOCK10 MUTATED DOCK10 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DOCK10 MUTATED                                     5
  DOCK10 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DOCK10 MUTATED                                       1
  DOCK10 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DOCK10 MUTATED                                                  0
  DOCK10 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  DOCK10 MUTATED                                     0
  DOCK10 WILD-TYPE                                   1
D483V9, multiclass
                                                  clus
vv                                                 DOCK10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 DOCK10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V10, continuous
D483V11, continuous
[1] "Remove cluster labels:" "DOCK10 MUTATED"        
clus
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" "DOCK10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  DOCK10 MUTATED    3  3  0  0
  DOCK10 WILD-TYPE 77 32  4  2
D483V12, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  R0              3               77
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOCK10 MUTATED       0                         1     5
  DOCK10 WILD-TYPE     6                         4   109
D483V14, multiclass
                           clus
vv                          DOCK10 MUTATED DOCK10 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V15, binary
                  cls
clus                0  1
  DOCK10 MUTATED    0  6
  DOCK10 WILD-TYPE  5 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED      0    6
  DOCK10 WILD-TYPE    5   85
                        clus
vv                       DOCK10 MUTATED DOCK10 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(484) Variable = CDC25A MUTATION ANALYSIS
D484V1, survival
                  sevent
clus2               0  1
  CDC25A MUTATED    1  2
  CDC25A WILD-TYPE 62 60
  CDC25A MUTATED CDC25A WILD-TYPE 
               3              122 
  CDC25A MUTATED CDC25A WILD-TYPE 
               2               60 
$`CDC25A MUTATED`
TCGA-2J-AAB6 TCGA-HZ-A77P TCGA-LB-A9Q5 
        9.63        10.85        10.29 

$`CDC25A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CDC25A MUTATED CDC25A WILD-TYPE 
            9.63             0.23 
  CDC25A MUTATED CDC25A WILD-TYPE 
           10.85            90.12 
  CDC25A MUTATED CDC25A WILD-TYPE 
          10.290           15.335 
[1] "9.6 - 10.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.7"
D484V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDC25A MUTATED         0        0        0         1         2         0
  CDC25A WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  CDC25A MUTATED          0
  CDC25A WILD-TYPE        3
D484V3, multiclass
           clus
vv          CDC25A MUTATED CDC25A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  CDC25A MUTATED    0  0     3
  CDC25A WILD-TYPE  5 17    99
D484V4, multiclass
       clus
vv      CDC25A MUTATED CDC25A WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V5, binary
                  cls
clus                0  1
  CDC25A MUTATED    1  2
  CDC25A WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25A MUTATED      1    2
  CDC25A WILD-TYPE   34   87
   clus
vv  CDC25A MUTATED CDC25A WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D484V6, binary
                  cls
clus                0  1
  CDC25A MUTATED    1  0
  CDC25A WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25A MUTATED      1    0
  CDC25A WILD-TYPE   56    3
   clus
vv  CDC25A MUTATED CDC25A WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D484V7, binary
                  cls
clus                0  1
  CDC25A MUTATED    1  2
  CDC25A WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25A MUTATED      1    2
  CDC25A WILD-TYPE   50   73
        clus
vv       CDC25A MUTATED CDC25A WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D484V8, binary
                  cls
clus                0  1
  CDC25A MUTATED    2  1
  CDC25A WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25A MUTATED      2    1
  CDC25A WILD-TYPE   86   29
     clus
vv    CDC25A MUTATED CDC25A WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC25A MUTATED                                     2
  CDC25A WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC25A MUTATED                                       1
  CDC25A WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC25A MUTATED                                                  0
  CDC25A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDC25A MUTATED                                     0
  CDC25A WILD-TYPE                                   1
D484V9, multiclass
                                                  clus
vv                                                 CDC25A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CDC25A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V10, continuous
[1] "Remove cluster labels:" "CDC25A MUTATED"        
clus
  CDC25A MUTATED CDC25A WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-OE-A75W 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
D484V11, continuous
[1] "Remove cluster labels:" "CDC25A MUTATED"        
clus
  CDC25A MUTATED CDC25A WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" "CDC25A WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CDC25A MUTATED    3  0  0  0
  CDC25A WILD-TYPE 77 35  4  2
D484V12, multiclass
    clus
vv   CDC25A MUTATED CDC25A WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC25A MUTATED       0                         0     3
  CDC25A WILD-TYPE     6                         5   111
D484V14, multiclass
                           clus
vv                          CDC25A MUTATED CDC25A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V15, binary
                  cls
clus                0  1
  CDC25A MUTATED    0  2
  CDC25A WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDC25A MUTATED      0    2
  CDC25A WILD-TYPE    5   89
                        clus
vv                       CDC25A MUTATED CDC25A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(485) Variable = VPS24 MUTATION ANALYSIS
D485V1, survival
                 sevent
clus2              0  1
  VPS24 MUTATED    0  3
  VPS24 WILD-TYPE 63 59
  VPS24 MUTATED VPS24 WILD-TYPE 
              3             122 
  VPS24 MUTATED VPS24 WILD-TYPE 
              3              59 
$`VPS24 MUTATED`
TCGA-FB-A78T TCGA-OE-A75W TCGA-US-A779 
       12.33         8.78        16.80 

$`VPS24 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46        10.29        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        39.98         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  VPS24 MUTATED VPS24 WILD-TYPE 
           8.78            0.23 
  VPS24 MUTATED VPS24 WILD-TYPE 
          16.80           90.12 
  VPS24 MUTATED VPS24 WILD-TYPE 
          12.33           15.27 
[1] "8.8 - 16.8 (12.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "3.1"
D485V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  VPS24 MUTATED         0        0        0         1         2         0
  VPS24 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  VPS24 MUTATED          0
  VPS24 WILD-TYPE        3
D485V3, multiclass
           clus
vv          VPS24 MUTATED VPS24 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  VPS24 MUTATED    0  0     3
  VPS24 WILD-TYPE  5 17    99
D485V4, multiclass
       clus
vv      VPS24 MUTATED VPS24 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V5, binary
                 cls
clus               0  1
  VPS24 MUTATED    1  2
  VPS24 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS24 MUTATED      1    2
  VPS24 WILD-TYPE   34   87
   clus
vv  VPS24 MUTATED VPS24 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D485V6, binary
                 cls
clus               0  1
  VPS24 MUTATED    2  0
  VPS24 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS24 MUTATED      2    0
  VPS24 WILD-TYPE   55    3
   clus
vv  VPS24 MUTATED VPS24 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D485V7, binary
                 cls
clus               0  1
  VPS24 MUTATED    2  1
  VPS24 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS24 MUTATED      2    1
  VPS24 WILD-TYPE   49   74
        clus
vv       VPS24 MUTATED VPS24 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D485V8, binary
                 cls
clus               0  1
  VPS24 MUTATED    1  1
  VPS24 WILD-TYPE 87 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS24 MUTATED      1    1
  VPS24 WILD-TYPE   87   29
     clus
vv    VPS24 MUTATED VPS24 WILD-TYPE
  NO              1              87
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VPS24 MUTATED                                     3
  VPS24 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VPS24 MUTATED                                       0
  VPS24 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VPS24 MUTATED                                                  0
  VPS24 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  VPS24 MUTATED                                     0
  VPS24 WILD-TYPE                                   1
D485V9, multiclass
                                                  clus
vv                                                 VPS24 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 VPS24 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V10, continuous
[1] "Remove cluster labels:" "VPS24 MUTATED"         
clus
  VPS24 MUTATED VPS24 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-AAPQ 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-XN-A8T5 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-YY-A8LH 
"VPS24 WILD-TYPE" 
D485V11, continuous
[1] "Remove cluster labels:" "VPS24 MUTATED"         
clus
  VPS24 MUTATED VPS24 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"VPS24 WILD-TYPE" "VPS24 WILD-TYPE" "VPS24 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  VPS24 MUTATED    3  0  0  0
  VPS24 WILD-TYPE 77 35  4  2
D485V12, multiclass
    clus
vv   VPS24 MUTATED VPS24 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VPS24 MUTATED       0                         0     3
  VPS24 WILD-TYPE     6                         5   111
D485V14, multiclass
                           clus
vv                          VPS24 MUTATED VPS24 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V15, binary
                 cls
clus               0  1
  VPS24 MUTATED    0  3
  VPS24 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS24 MUTATED      0    3
  VPS24 WILD-TYPE    5   88
                        clus
vv                       VPS24 MUTATED VPS24 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(486) Variable = F5 MUTATION ANALYSIS
D486V1, survival
              sevent
clus2           0  1
  F5 MUTATED    2  8
  F5 WILD-TYPE 61 54
  F5 MUTATED F5 WILD-TYPE 
          10          115 
  F5 MUTATED F5 WILD-TYPE 
           8           54 
$`F5 MUTATED`
TCGA-FB-AAQ6 TCGA-IB-A5SS TCGA-US-A77E TCGA-2J-AAB9 TCGA-FB-A5VM TCGA-FB-AAPU 
        8.02        15.12        14.14        20.61        16.37        12.53 
TCGA-IB-7651 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-YY-A8LH 
       19.82         8.78        13.68        66.28 

$`F5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-XD-AAUL TCGA-2J-AAB1 
       15.78         1.08        12.92        17.26        16.37         2.17 
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF 
       23.97         9.63         2.63        19.96        22.22        22.72 
TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV 
       42.31        15.91        14.47        15.22         9.11        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 
       12.33        15.95        37.15         7.50        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
        7.56        12.46        10.29         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  F5 MUTATED F5 WILD-TYPE 
        8.02         0.23 
  F5 MUTATED F5 WILD-TYPE 
       66.28        90.12 
  F5 MUTATED F5 WILD-TYPE 
       14.63        15.32 
[1] "8.0 - 66.3 (14.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D486V2, continuous
              vv
clus           STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  F5 MUTATED         0        1        1         2         7         0        0
  F5 WILD-TYPE       1        2       11        17        75         4        3
D486V3, multiclass
           clus
vv          F5 MUTATED F5 WILD-TYPE
  STAGE I            0            1
  STAGE IA           1            2
  STAGE IB           1           11
  STAGE IIA          2           17
  STAGE IIB          7           75
  STAGE III          0            4
  STAGE IV           0            3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T1 T2 T3+T4
  F5 MUTATED    1  1     9
  F5 WILD-TYPE  4 16    93
D486V4, multiclass
       clus
vv      F5 MUTATED F5 WILD-TYPE
  T1             1            4
  T2             1           16
  T3+T4          9           93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V5, binary
              cls
clus            0  1
  F5 MUTATED    4  7
  F5 WILD-TYPE 31 82
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      4    7
  F5 WILD-TYPE   31   82
   clus
vv  F5 MUTATED F5 WILD-TYPE
  0          4           31
  1          7           82
[1] 2 2
[1] FALSE
D486V6, binary
              cls
clus            0  1
  F5 MUTATED    5  0
  F5 WILD-TYPE 52  3
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      5    0
  F5 WILD-TYPE   52    3
   clus
vv  F5 MUTATED F5 WILD-TYPE
  0          5           52
  1          0            3
[1] 2 2
[1] FALSE
D486V7, binary
              cls
clus            0  1
  F5 MUTATED    5  6
  F5 WILD-TYPE 46 69
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      5    6
  F5 WILD-TYPE   46   69
        clus
vv       F5 MUTATED F5 WILD-TYPE
  FEMALE          5           46
  MALE            6           69
[1] 2 2
[1] FALSE
D486V8, binary
              cls
clus            0  1
  F5 MUTATED    7  3
  F5 WILD-TYPE 81 27
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      7    3
  F5 WILD-TYPE   81   27
     clus
vv    F5 MUTATED F5 WILD-TYPE
  NO           7           81
  YES          3           27
[1] 2 2
[1] FALSE
              vv
clus           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  F5 MUTATED                                    10
  F5 WILD-TYPE                                  95
              vv
clus           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  F5 MUTATED                                       1
  F5 WILD-TYPE                                    17
              vv
clus           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  F5 MUTATED                                                  0
  F5 WILD-TYPE                                                1
              vv
clus           PANCREAS-UNDIFFERENTIATED CARCINOMA
  F5 MUTATED                                     0
  F5 WILD-TYPE                                   1
D486V9, multiclass
                                                  clus
vv                                                 F5 MUTATED F5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                      10           95
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                     1           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA          0            1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                       0            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V10, continuous
D486V11, continuous
              vv
clus           R0 R1 R2 RX
  F5 MUTATED    9  2  0  0
  F5 WILD-TYPE 71 33  4  2
D486V12, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  R0          9           71
  R1          2           33
  R2          0            4
  RX          0            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V13, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  F5 MUTATED       1                         0    10
  F5 WILD-TYPE     5                         5   104
D486V14, multiclass
                           clus
vv                          F5 MUTATED F5 WILD-TYPE
  ASIAN                              1            5
  BLACK OR AFRICAN AMERICAN          0            5
  WHITE                             10          104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V15, binary
              cls
clus            0  1
  F5 MUTATED    0 10
  F5 WILD-TYPE  5 81
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      0   10
  F5 WILD-TYPE    5   81
                        clus
vv                       F5 MUTATED F5 WILD-TYPE
  HISPANIC OR LATINO              0            5
  NOT HISPANIC OR LATINO         10           81
[1] 2 2
[1] FALSE

Clustering(487) Variable = AFF2 MUTATION ANALYSIS
D487V1, survival
                sevent
clus2             0  1
  AFF2 MUTATED    4  2
  AFF2 WILD-TYPE 59 60
  AFF2 MUTATED AFF2 WILD-TYPE 
             6            119 
  AFF2 MUTATED AFF2 WILD-TYPE 
             2             60 
$`AFF2 MUTATED`
TCGA-3A-A9IX TCGA-FB-AAQ2 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SP TCGA-RL-AAAS 
       34.09         5.03        19.82        41.33        15.85         0.30 

$`AFF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ 
        0.23        19.82        36.69        15.19        12.00         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         9.40        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  AFF2 MUTATED AFF2 WILD-TYPE 
          0.30           0.23 
  AFF2 MUTATED AFF2 WILD-TYPE 
         41.33          90.12 
  AFF2 MUTATED AFF2 WILD-TYPE 
        17.835         15.190 
[1] "0.3 - 41.3 (17.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D487V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AFF2 MUTATED         0        1        1         1         3         0
  AFF2 WILD-TYPE       1        2       11        18        79         4
                vv
clus             STAGE IV
  AFF2 MUTATED          0
  AFF2 WILD-TYPE        3
D487V3, multiclass
           clus
vv          AFF2 MUTATED AFF2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  AFF2 MUTATED    1  1     4
  AFF2 WILD-TYPE  4 16    98
D487V4, multiclass
       clus
vv      AFF2 MUTATED AFF2 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V5, binary
                cls
clus              0  1
  AFF2 MUTATED    3  3
  AFF2 WILD-TYPE 32 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF2 MUTATED      3    3
  AFF2 WILD-TYPE   32   86
   clus
vv  AFF2 MUTATED AFF2 WILD-TYPE
  0            3             32
  1            3             86
[1] 2 2
[1] FALSE
D487V6, binary
                cls
clus              0  1
  AFF2 MUTATED    4  0
  AFF2 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF2 MUTATED      4    0
  AFF2 WILD-TYPE   53    3
   clus
vv  AFF2 MUTATED AFF2 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D487V7, binary
                cls
clus              0  1
  AFF2 MUTATED    4  2
  AFF2 WILD-TYPE 47 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF2 MUTATED      4    2
  AFF2 WILD-TYPE   47   73
        clus
vv       AFF2 MUTATED AFF2 WILD-TYPE
  FEMALE            4             47
  MALE              2             73
[1] 2 2
[1] FALSE
D487V8, binary
                cls
clus              0  1
  AFF2 MUTATED    5  1
  AFF2 WILD-TYPE 83 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF2 MUTATED      5    1
  AFF2 WILD-TYPE   83   29
     clus
vv    AFF2 MUTATED AFF2 WILD-TYPE
  NO             5             83
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AFF2 MUTATED                                     6
  AFF2 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AFF2 MUTATED                                       0
  AFF2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AFF2 MUTATED                                                  0
  AFF2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  AFF2 MUTATED                                     0
  AFF2 WILD-TYPE                                   1
D487V9, multiclass
                                                  clus
vv                                                 AFF2 MUTATED AFF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V10, continuous
D487V11, continuous
                vv
clus             R0 R1 R2 RX
  AFF2 MUTATED    4  2  0  0
  AFF2 WILD-TYPE 76 33  4  2
D487V12, multiclass
    clus
vv   AFF2 MUTATED AFF2 WILD-TYPE
  R0            4             76
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AFF2 MUTATED       0                         0     6
  AFF2 WILD-TYPE     6                         5   108
D487V14, multiclass
                           clus
vv                          AFF2 MUTATED AFF2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V15, binary
                cls
clus              0  1
  AFF2 MUTATED    0  5
  AFF2 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF2 MUTATED      0    5
  AFF2 WILD-TYPE    5   86
                        clus
vv                       AFF2 MUTATED AFF2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(488) Variable = ZFHX3 MUTATION ANALYSIS
D488V1, survival
                 sevent
clus2              0  1
  ZFHX3 MUTATED    3  7
  ZFHX3 WILD-TYPE 60 55
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             10             115 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              7              55 
$`ZFHX3 MUTATED`
TCGA-2J-AABP TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FZ-5923 TCGA-HZ-7925 
       15.22        12.33        15.95         7.50        20.35        20.19 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        19.82        19.82 

$`ZFHX3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPQ TCGA-FB-AAPU 
       19.46         3.12        17.00        16.37        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        2.01         5.10        36.20        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A77P 
       32.15        30.25        17.49        31.86        17.00        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
           5.26            0.23 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          20.35           90.12 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         15.585          15.190 
[1] "5.3 - 20.4 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D488V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZFHX3 MUTATED         0        0        0         0         8         0
  ZFHX3 WILD-TYPE       1        3       12        19        74         4
                 vv
clus              STAGE IV
  ZFHX3 MUTATED          2
  ZFHX3 WILD-TYPE        1
D488V3, multiclass
           clus
vv          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              2               1
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ZFHX3 MUTATED    0  2     8
  ZFHX3 WILD-TYPE  5 15    94
D488V4, multiclass
       clus
vv      ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V5, binary
                 cls
clus               0  1
  ZFHX3 MUTATED    1  9
  ZFHX3 WILD-TYPE 34 80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      1    9
  ZFHX3 WILD-TYPE   34   80
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0             1              34
  1             9              80
[1] 2 2
[1] FALSE
D488V6, binary
                 cls
clus               0  1
  ZFHX3 MUTATED    3  2
  ZFHX3 WILD-TYPE 54  1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      3    2
  ZFHX3 WILD-TYPE   54    1
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0             3              54
  1             2               1
[1] 2 2
[1] FALSE
D488V7, binary
                 cls
clus               0  1
  ZFHX3 MUTATED    5  5
  ZFHX3 WILD-TYPE 46 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      5    5
  ZFHX3 WILD-TYPE   46   70
        clus
vv       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  FEMALE             5              46
  MALE               5              70
[1] 2 2
[1] FALSE
D488V8, binary
                 cls
clus               0  1
  ZFHX3 MUTATED    7  3
  ZFHX3 WILD-TYPE 81 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      7    3
  ZFHX3 WILD-TYPE   81   27
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO              7              81
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZFHX3 MUTATED                                     8
  ZFHX3 WILD-TYPE                                  97
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZFHX3 MUTATED                                       1
  ZFHX3 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZFHX3 MUTATED                                                  0
  ZFHX3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZFHX3 MUTATED                                     1
  ZFHX3 WILD-TYPE                                   0
D488V9, multiclass
                                                  clus
vv                                                 ZFHX3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 ZFHX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V10, continuous
D488V11, continuous
                 vv
clus              R0 R1 R2 RX
  ZFHX3 MUTATED    9  1  0  0
  ZFHX3 WILD-TYPE 71 34  4  2
D488V12, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0             9              71
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFHX3 MUTATED       0                         0    10
  ZFHX3 WILD-TYPE     6                         5   104
D488V14, multiclass
                           clus
vv                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                10             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V15, binary
                 cls
clus               0  1
  ZFHX3 MUTATED    0  9
  ZFHX3 WILD-TYPE  5 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      0    9
  ZFHX3 WILD-TYPE    5   82
                        clus
vv                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9              82
[1] 2 2
[1] FALSE

Clustering(489) Variable = RNF168 MUTATION ANALYSIS
D489V1, survival
                  sevent
clus2               0  1
  RNF168 MUTATED    2  2
  RNF168 WILD-TYPE 61 60
  RNF168 MUTATED RNF168 WILD-TYPE 
               4              121 
  RNF168 MUTATED RNF168 WILD-TYPE 
               2               60 
$`RNF168 MUTATED`
TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-HZ-A49I TCGA-IB-7651 
        1.08        17.26        10.13        19.82 

$`RNF168 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        15.12        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RNF168 MUTATED RNF168 WILD-TYPE 
            1.08             0.23 
  RNF168 MUTATED RNF168 WILD-TYPE 
           19.82            90.12 
  RNF168 MUTATED RNF168 WILD-TYPE 
          13.695           15.220 
[1] "1.1 - 19.8 (13.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D489V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RNF168 MUTATED         0        0        0         0         4         0
  RNF168 WILD-TYPE       1        3       12        19        78         4
                  vv
clus               STAGE IV
  RNF168 MUTATED          0
  RNF168 WILD-TYPE        3
D489V3, multiclass
           clus
vv          RNF168 MUTATED RNF168 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  RNF168 MUTATED    0  0     4
  RNF168 WILD-TYPE  5 17    98
D489V4, multiclass
       clus
vv      RNF168 MUTATED RNF168 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V5, binary
                  cls
clus                0  1
  RNF168 MUTATED    0  4
  RNF168 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF168 MUTATED      0    4
  RNF168 WILD-TYPE   35   85
   clus
vv  RNF168 MUTATED RNF168 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D489V6, binary
                  cls
clus                0  1
  RNF168 MUTATED    1  0
  RNF168 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF168 MUTATED      1    0
  RNF168 WILD-TYPE   56    3
   clus
vv  RNF168 MUTATED RNF168 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D489V7, binary
                  cls
clus                0  1
  RNF168 MUTATED    3  1
  RNF168 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF168 MUTATED      3    1
  RNF168 WILD-TYPE   48   74
        clus
vv       RNF168 MUTATED RNF168 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D489V8, binary
                  cls
clus                0  1
  RNF168 MUTATED    1  2
  RNF168 WILD-TYPE 87 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF168 MUTATED      1    2
  RNF168 WILD-TYPE   87   28
     clus
vv    RNF168 MUTATED RNF168 WILD-TYPE
  NO               1               87
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF168 MUTATED                                     3
  RNF168 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF168 MUTATED                                       1
  RNF168 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF168 MUTATED                                                  0
  RNF168 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RNF168 MUTATED                                     0
  RNF168 WILD-TYPE                                   1
D489V9, multiclass
                                                  clus
vv                                                 RNF168 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RNF168 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V10, continuous
[1] "Remove cluster labels:" "RNF168 MUTATED"        
clus
  RNF168 MUTATED RNF168 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-YY-A8LH 
"RNF168 WILD-TYPE" 
D489V11, continuous
[1] "Remove cluster labels:" "RNF168 MUTATED"        
clus
  RNF168 MUTATED RNF168 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"RNF168 WILD-TYPE" "RNF168 WILD-TYPE" "RNF168 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  RNF168 MUTATED    2  2  0  0
  RNF168 WILD-TYPE 78 33  4  2
D489V12, multiclass
    clus
vv   RNF168 MUTATED RNF168 WILD-TYPE
  R0              2               78
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF168 MUTATED       0                         0     4
  RNF168 WILD-TYPE     6                         5   110
D489V14, multiclass
                           clus
vv                          RNF168 MUTATED RNF168 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V15, binary
                  cls
clus                0  1
  RNF168 MUTATED    0  4
  RNF168 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF168 MUTATED      0    4
  RNF168 WILD-TYPE    5   87
                        clus
vv                       RNF168 MUTATED RNF168 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(490) Variable = TGFBI MUTATION ANALYSIS
D490V1, survival
                 sevent
clus2              0  1
  TGFBI MUTATED    4  2
  TGFBI WILD-TYPE 59 60
  TGFBI MUTATED TGFBI WILD-TYPE 
              6             119 
  TGFBI MUTATED TGFBI WILD-TYPE 
              2              60 
$`TGFBI MUTATED`
TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-RL-AAAS TCGA-Z5-AAPL 
       12.33        22.06        19.82        19.82         0.30        15.35 

$`TGFBI WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
        8.78        13.68         3.12        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       31.27        23.67        11.51        12.76        66.28 

  TGFBI MUTATED TGFBI WILD-TYPE 
           0.30            0.23 
  TGFBI MUTATED TGFBI WILD-TYPE 
          22.06           90.12 
  TGFBI MUTATED TGFBI WILD-TYPE 
         17.585          15.190 
[1] "0.3 - 22.1 (17.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D490V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TGFBI MUTATED         0        0        1         2         2         0
  TGFBI WILD-TYPE       1        3       11        17        80         4
                 vv
clus              STAGE IV
  TGFBI MUTATED          1
  TGFBI WILD-TYPE        2
D490V3, multiclass
           clus
vv          TGFBI MUTATED TGFBI WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TGFBI MUTATED    0  1     5
  TGFBI WILD-TYPE  5 16    97
D490V4, multiclass
       clus
vv      TGFBI MUTATED TGFBI WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V5, binary
                 cls
clus               0  1
  TGFBI MUTATED    4  2
  TGFBI WILD-TYPE 31 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGFBI MUTATED      4    2
  TGFBI WILD-TYPE   31   87
   clus
vv  TGFBI MUTATED TGFBI WILD-TYPE
  0             4              31
  1             2              87
[1] 2 2
[1] FALSE
D490V6, binary
                 cls
clus               0  1
  TGFBI MUTATED    4  1
  TGFBI WILD-TYPE 53  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGFBI MUTATED      4    1
  TGFBI WILD-TYPE   53    2
   clus
vv  TGFBI MUTATED TGFBI WILD-TYPE
  0             4              53
  1             1               2
[1] 2 2
[1] FALSE
D490V7, binary
                 cls
clus               0  1
  TGFBI MUTATED    4  2
  TGFBI WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGFBI MUTATED      4    2
  TGFBI WILD-TYPE   47   73
        clus
vv       TGFBI MUTATED TGFBI WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D490V8, binary
                 cls
clus               0  1
  TGFBI MUTATED    6  0
  TGFBI WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGFBI MUTATED      6    0
  TGFBI WILD-TYPE   82   30
     clus
vv    TGFBI MUTATED TGFBI WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBI MUTATED                                     4
  TGFBI WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBI MUTATED                                       2
  TGFBI WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBI MUTATED                                                  0
  TGFBI WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TGFBI MUTATED                                     0
  TGFBI WILD-TYPE                                   1
D490V9, multiclass
                                                  clus
vv                                                 TGFBI MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TGFBI WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V10, continuous
D490V11, continuous
                 vv
clus              R0 R1 R2 RX
  TGFBI MUTATED    6  0  0  0
  TGFBI WILD-TYPE 74 35  4  2
D490V12, multiclass
    clus
vv   TGFBI MUTATED TGFBI WILD-TYPE
  R0             6              74
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBI MUTATED       0                         0     6
  TGFBI WILD-TYPE     6                         5   108
D490V14, multiclass
                           clus
vv                          TGFBI MUTATED TGFBI WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V15, binary
                 cls
clus               0  1
  TGFBI MUTATED    0  6
  TGFBI WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGFBI MUTATED      0    6
  TGFBI WILD-TYPE    5   85
                        clus
vv                       TGFBI MUTATED TGFBI WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(491) Variable = KLK13 MUTATION ANALYSIS
D491V1, survival
                 sevent
clus2              0  1
  KLK13 MUTATED    1  4
  KLK13 WILD-TYPE 62 58
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             120 
  KLK13 MUTATED KLK13 WILD-TYPE 
              4              58 
$`KLK13 MUTATED`
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-2L-AAQE TCGA-FB-A78T TCGA-IB-7651 
        1.08        15.12        22.49        12.33        19.82 

$`KLK13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KLK13 MUTATED KLK13 WILD-TYPE 
           1.08            0.23 
  KLK13 MUTATED KLK13 WILD-TYPE 
          22.49           90.12 
  KLK13 MUTATED KLK13 WILD-TYPE 
          15.12           15.27 
[1] "1.1 - 22.5 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D491V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KLK13 MUTATED         0        0        0         0         5         0
  KLK13 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  KLK13 MUTATED          0
  KLK13 WILD-TYPE        3
D491V3, multiclass
           clus
vv          KLK13 MUTATED KLK13 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KLK13 MUTATED    0  0     5
  KLK13 WILD-TYPE  5 17    97
D491V4, multiclass
       clus
vv      KLK13 MUTATED KLK13 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V5, binary
                 cls
clus               0  1
  KLK13 MUTATED    0  5
  KLK13 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    5
  KLK13 WILD-TYPE   35   84
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D491V6, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  0
  KLK13 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    0
  KLK13 WILD-TYPE   53    3
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D491V7, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  1
  KLK13 WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    1
  KLK13 WILD-TYPE   47   74
        clus
vv       KLK13 MUTATED KLK13 WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D491V8, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  0
  KLK13 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    0
  KLK13 WILD-TYPE   84   30
     clus
vv    KLK13 MUTATED KLK13 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK13 MUTATED                                     4
  KLK13 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK13 MUTATED                                       1
  KLK13 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK13 MUTATED                                                  0
  KLK13 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KLK13 MUTATED                                     0
  KLK13 WILD-TYPE                                   1
D491V9, multiclass
                                                  clus
vv                                                 KLK13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KLK13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V10, continuous
D491V11, continuous
                 vv
clus              R0 R1 R2 RX
  KLK13 MUTATED    5  0  0  0
  KLK13 WILD-TYPE 75 35  4  2
D491V12, multiclass
    clus
vv   KLK13 MUTATED KLK13 WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK13 MUTATED       0                         0     5
  KLK13 WILD-TYPE     6                         5   109
D491V14, multiclass
                           clus
vv                          KLK13 MUTATED KLK13 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V15, binary
                 cls
clus               0  1
  KLK13 MUTATED    0  4
  KLK13 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    4
  KLK13 WILD-TYPE    5   87
                        clus
vv                       KLK13 MUTATED KLK13 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(492) Variable = ASS1 MUTATION ANALYSIS
D492V1, survival
                sevent
clus2             0  1
  ASS1 MUTATED    3  1
  ASS1 WILD-TYPE 60 61
  ASS1 MUTATED ASS1 WILD-TYPE 
             4            121 
  ASS1 MUTATED ASS1 WILD-TYPE 
             1             61 
$`ASS1 MUTATED`
TCGA-2J-AAB1 TCGA-2L-AAQM TCGA-3A-A9IO TCGA-YY-A8LH 
        2.17        45.47        63.85        66.28 

$`ASS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       33.57        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  ASS1 MUTATED ASS1 WILD-TYPE 
          2.17           0.23 
  ASS1 MUTATED ASS1 WILD-TYPE 
         66.28          90.12 
  ASS1 MUTATED ASS1 WILD-TYPE 
         54.66          15.19 
[1] "2.2 - 66.3 (54.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.4"
D492V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ASS1 MUTATED         0        0        0         0         3         0
  ASS1 WILD-TYPE       1        3       12        19        79         4
                vv
clus             STAGE IV
  ASS1 MUTATED          0
  ASS1 WILD-TYPE        3
D492V3, multiclass
           clus
vv          ASS1 MUTATED ASS1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  ASS1 MUTATED    0  0     3
  ASS1 WILD-TYPE  5 17    99
D492V4, multiclass
       clus
vv      ASS1 MUTATED ASS1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V5, binary
                cls
clus              0  1
  ASS1 MUTATED    0  3
  ASS1 WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASS1 MUTATED      0    3
  ASS1 WILD-TYPE   35   86
   clus
vv  ASS1 MUTATED ASS1 WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D492V6, binary
                cls
clus              0  1
  ASS1 MUTATED    1  0
  ASS1 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASS1 MUTATED      1    0
  ASS1 WILD-TYPE   56    3
   clus
vv  ASS1 MUTATED ASS1 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D492V7, binary
                cls
clus              0  1
  ASS1 MUTATED    1  3
  ASS1 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASS1 MUTATED      1    3
  ASS1 WILD-TYPE   50   72
        clus
vv       ASS1 MUTATED ASS1 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D492V8, binary
                cls
clus              0  1
  ASS1 MUTATED    3  1
  ASS1 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASS1 MUTATED      3    1
  ASS1 WILD-TYPE   85   29
     clus
vv    ASS1 MUTATED ASS1 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASS1 MUTATED                                     1
  ASS1 WILD-TYPE                                 104
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASS1 MUTATED                                       3
  ASS1 WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASS1 MUTATED                                                  0
  ASS1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  ASS1 MUTATED                                     0
  ASS1 WILD-TYPE                                   1
D492V9, multiclass
                                                  clus
vv                                                 ASS1 MUTATED ASS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         1            104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V10, continuous
[1] "Remove cluster labels:" "ASS1 MUTATED"          
clus
  ASS1 MUTATED ASS1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABA     TCGA-2J-AABE 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-XN-A8T5 
"ASS1 WILD-TYPE" 
D492V11, continuous
[1] "Remove cluster labels:" "ASS1 MUTATED"          
clus
  ASS1 MUTATED ASS1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5 
"ASS1 WILD-TYPE" "ASS1 WILD-TYPE" "ASS1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ASS1 MUTATED    3  1  0  0
  ASS1 WILD-TYPE 77 34  4  2
D492V12, multiclass
    clus
vv   ASS1 MUTATED ASS1 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASS1 MUTATED       0                         0     4
  ASS1 WILD-TYPE     6                         5   110
D492V14, multiclass
                           clus
vv                          ASS1 MUTATED ASS1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V15, binary
                cls
clus              0  1
  ASS1 MUTATED    0  2
  ASS1 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASS1 MUTATED      0    2
  ASS1 WILD-TYPE    5   89
                        clus
vv                       ASS1 MUTATED ASS1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(493) Variable = FOXD4 MUTATION ANALYSIS
D493V1, survival
                 sevent
clus2              0  1
  FOXD4 MUTATED    4  2
  FOXD4 WILD-TYPE 59 60
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              6             119 
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              2              60 
$`FOXD4 MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ2 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-IB-7651 TCGA-RB-AA9M 
       23.54         5.03        32.15        30.25        19.82         9.40 

$`FOXD4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       17.79        22.06         8.28        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  FOXD4 MUTATED FOXD4 WILD-TYPE 
           5.03            0.23 
  FOXD4 MUTATED FOXD4 WILD-TYPE 
          32.15           90.12 
  FOXD4 MUTATED FOXD4 WILD-TYPE 
          21.68           15.19 
[1] "5.0 - 32.1 (21.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D493V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FOXD4 MUTATED         0        0        0         0         6         0
  FOXD4 WILD-TYPE       1        3       12        19        76         4
                 vv
clus              STAGE IV
  FOXD4 MUTATED          0
  FOXD4 WILD-TYPE        3
D493V3, multiclass
           clus
vv          FOXD4 MUTATED FOXD4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FOXD4 MUTATED    1  1     4
  FOXD4 WILD-TYPE  4 16    98
D493V4, multiclass
       clus
vv      FOXD4 MUTATED FOXD4 WILD-TYPE
  T1                1               4
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V5, binary
                 cls
clus               0  1
  FOXD4 MUTATED    0  6
  FOXD4 WILD-TYPE 35 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD4 MUTATED      0    6
  FOXD4 WILD-TYPE   35   83
   clus
vv  FOXD4 MUTATED FOXD4 WILD-TYPE
  0             0              35
  1             6              83
[1] 2 2
[1] FALSE
D493V6, binary
                 cls
clus               0  1
  FOXD4 MUTATED    2  0
  FOXD4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD4 MUTATED      2    0
  FOXD4 WILD-TYPE   55    3
   clus
vv  FOXD4 MUTATED FOXD4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D493V7, binary
                 cls
clus               0  1
  FOXD4 MUTATED    2  4
  FOXD4 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD4 MUTATED      2    4
  FOXD4 WILD-TYPE   49   71
        clus
vv       FOXD4 MUTATED FOXD4 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D493V8, binary
                 cls
clus               0  1
  FOXD4 MUTATED    4  2
  FOXD4 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD4 MUTATED      4    2
  FOXD4 WILD-TYPE   84   28
     clus
vv    FOXD4 MUTATED FOXD4 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FOXD4 MUTATED                                     5
  FOXD4 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FOXD4 MUTATED                                       1
  FOXD4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FOXD4 MUTATED                                                  0
  FOXD4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FOXD4 MUTATED                                     0
  FOXD4 WILD-TYPE                                   1
D493V9, multiclass
                                                  clus
vv                                                 FOXD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FOXD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V10, continuous
[1] "Remove cluster labels:" "FOXD4 MUTATED"         
clus
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-YY-A8LH 
"FOXD4 WILD-TYPE" 
D493V11, continuous
[1] "Remove cluster labels:" "FOXD4 MUTATED"         
clus
  FOXD4 MUTATED FOXD4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" "FOXD4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  FOXD4 MUTATED    4  1  1  0
  FOXD4 WILD-TYPE 76 34  3  2
D493V12, multiclass
    clus
vv   FOXD4 MUTATED FOXD4 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXD4 MUTATED       2                         0     4
  FOXD4 WILD-TYPE     4                         5   110
D493V14, multiclass
                           clus
vv                          FOXD4 MUTATED FOXD4 WILD-TYPE
  ASIAN                                 2               4
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V15, binary
                 cls
clus               0  1
  FOXD4 MUTATED    0  4
  FOXD4 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD4 MUTATED      0    4
  FOXD4 WILD-TYPE    5   87
                        clus
vv                       FOXD4 MUTATED FOXD4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(494) Variable = PVRL4 MUTATION ANALYSIS
D494V1, survival
                 sevent
clus2              0  1
  PVRL4 MUTATED    0  3
  PVRL4 WILD-TYPE 63 59
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              3             122 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              3              59 
$`PVRL4 MUTATED`
TCGA-FB-AAPQ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       37.15        15.55         5.03 

$`PVRL4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ3 
       15.95         7.50        12.53        23.54         4.04         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PVRL4 MUTATED PVRL4 WILD-TYPE 
           5.03            0.23 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
          37.15           90.12 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         15.550          15.205 
[1] "5.0 - 37.1 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D494V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PVRL4 MUTATED         0        0        0         1         2         0
  PVRL4 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  PVRL4 MUTATED          0
  PVRL4 WILD-TYPE        3
D494V3, multiclass
           clus
vv          PVRL4 MUTATED PVRL4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PVRL4 MUTATED    0  0     3
  PVRL4 WILD-TYPE  5 17    99
D494V4, multiclass
       clus
vv      PVRL4 MUTATED PVRL4 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V5, binary
                 cls
clus               0  1
  PVRL4 MUTATED    1  2
  PVRL4 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      1    2
  PVRL4 WILD-TYPE   34   87
   clus
vv  PVRL4 MUTATED PVRL4 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D494V6, binary
                 cls
clus               0  1
  PVRL4 MUTATED    0  0
  PVRL4 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      0    0
  PVRL4 WILD-TYPE   57    3
D494V7, binary
                 cls
clus               0  1
  PVRL4 MUTATED    1  2
  PVRL4 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      1    2
  PVRL4 WILD-TYPE   50   73
        clus
vv       PVRL4 MUTATED PVRL4 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D494V8, binary
                 cls
clus               0  1
  PVRL4 MUTATED    3  0
  PVRL4 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      3    0
  PVRL4 WILD-TYPE   85   30
     clus
vv    PVRL4 MUTATED PVRL4 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PVRL4 MUTATED                                     3
  PVRL4 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PVRL4 MUTATED                                       0
  PVRL4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PVRL4 MUTATED                                                  0
  PVRL4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PVRL4 MUTATED                                     0
  PVRL4 WILD-TYPE                                   1
D494V9, multiclass
                                                  clus
vv                                                 PVRL4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PVRL4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V10, continuous
[1] "Remove cluster labels:" "PVRL4 MUTATED"         
clus
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
D494V11, continuous
[1] "Remove cluster labels:" "PVRL4 MUTATED"         
clus
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" "PVRL4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PVRL4 MUTATED    2  1  0  0
  PVRL4 WILD-TYPE 78 34  4  2
D494V12, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PVRL4 MUTATED       0                         0     3
  PVRL4 WILD-TYPE     6                         5   111
D494V14, multiclass
                           clus
vv                          PVRL4 MUTATED PVRL4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V15, binary
                 cls
clus               0  1
  PVRL4 MUTATED    0  3
  PVRL4 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      0    3
  PVRL4 WILD-TYPE    5   88
                        clus
vv                       PVRL4 MUTATED PVRL4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(495) Variable = NBEA MUTATION ANALYSIS
D495V1, survival
                sevent
clus2             0  1
  NBEA MUTATED    1  2
  NBEA WILD-TYPE 62 60
  NBEA MUTATED NBEA WILD-TYPE 
             3            122 
  NBEA MUTATED NBEA WILD-TYPE 
             2             60 
$`NBEA MUTATED`
TCGA-3A-A9IU TCGA-HV-A7OP TCGA-IB-7651 
       15.06        32.15        19.82 

$`NBEA WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NBEA MUTATED NBEA WILD-TYPE 
         15.06           0.23 
  NBEA MUTATED NBEA WILD-TYPE 
         32.15          90.12 
  NBEA MUTATED NBEA WILD-TYPE 
        19.820         15.205 
[1] "15.1 - 32.1 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1"  
D495V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NBEA MUTATED         0        0        0         0         3         0
  NBEA WILD-TYPE       1        3       12        19        79         4
                vv
clus             STAGE IV
  NBEA MUTATED          0
  NBEA WILD-TYPE        3
D495V3, multiclass
           clus
vv          NBEA MUTATED NBEA WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  NBEA MUTATED    0  0     3
  NBEA WILD-TYPE  5 17    99
D495V4, multiclass
       clus
vv      NBEA MUTATED NBEA WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V5, binary
                cls
clus              0  1
  NBEA MUTATED    0  3
  NBEA WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      0    3
  NBEA WILD-TYPE   35   86
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D495V6, binary
                cls
clus              0  1
  NBEA MUTATED    2  0
  NBEA WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      2    0
  NBEA WILD-TYPE   55    3
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D495V7, binary
                cls
clus              0  1
  NBEA MUTATED    1  2
  NBEA WILD-TYPE 50 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      1    2
  NBEA WILD-TYPE   50   73
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  FEMALE            1             50
  MALE              2             73
[1] 2 2
[1] FALSE
D495V8, binary
                cls
clus              0  1
  NBEA MUTATED    2  1
  NBEA WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      2    1
  NBEA WILD-TYPE   86   29
     clus
vv    NBEA MUTATED NBEA WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBEA MUTATED                                     2
  NBEA WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBEA MUTATED                                       1
  NBEA WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBEA MUTATED                                                  0
  NBEA WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NBEA MUTATED                                     0
  NBEA WILD-TYPE                                   1
D495V9, multiclass
                                                  clus
vv                                                 NBEA MUTATED NBEA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V10, continuous
[1] "Remove cluster labels:" "NBEA MUTATED"          
clus
  NBEA MUTATED NBEA WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" 
D495V11, continuous
[1] "Remove cluster labels:" "NBEA MUTATED"          
clus
  NBEA MUTATED NBEA WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" "NBEA WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  NBEA MUTATED    3  0  0  0
  NBEA WILD-TYPE 77 35  4  2
D495V12, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBEA MUTATED       1                         0     2
  NBEA WILD-TYPE     5                         5   112
D495V14, multiclass
                           clus
vv                          NBEA MUTATED NBEA WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V15, binary
                cls
clus              0  1
  NBEA MUTATED    0  2
  NBEA WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      0    2
  NBEA WILD-TYPE    5   89
                        clus
vv                       NBEA MUTATED NBEA WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(496) Variable = ZNF737 MUTATION ANALYSIS
D496V1, survival
                  sevent
clus2               0  1
  ZNF737 MUTATED    3  2
  ZNF737 WILD-TYPE 60 60
  ZNF737 MUTATED ZNF737 WILD-TYPE 
               5              120 
  ZNF737 MUTATED ZNF737 WILD-TYPE 
               2               60 
$`ZNF737 MUTATED`
TCGA-2J-AABR TCGA-FB-AAQ6 TCGA-3A-A9IV TCGA-FB-AAQ1 TCGA-HV-A7OL 
       14.40         8.02        36.26         4.04         8.28 

$`ZNF737 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FZ-5924 
       10.49        58.98        60.95        90.12         7.66        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54        15.55         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 
       10.13         5.26        10.85         0.23        19.82        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ZNF737 MUTATED ZNF737 WILD-TYPE 
            4.04             0.23 
  ZNF737 MUTATED ZNF737 WILD-TYPE 
           36.26            90.12 
  ZNF737 MUTATED ZNF737 WILD-TYPE 
           8.280           15.335 
[1] "4.0 - 36.3 (8.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D496V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF737 MUTATED         0        1        1         2         1         0
  ZNF737 WILD-TYPE       1        2       11        17        81         4
                  vv
clus               STAGE IV
  ZNF737 MUTATED          0
  ZNF737 WILD-TYPE        3
D496V3, multiclass
           clus
vv          ZNF737 MUTATED ZNF737 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               1               11
  STAGE IIA              2               17
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF737 MUTATED    1  1     3
  ZNF737 WILD-TYPE  4 16    99
D496V4, multiclass
       clus
vv      ZNF737 MUTATED ZNF737 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V5, binary
                  cls
clus                0  1
  ZNF737 MUTATED    4  1
  ZNF737 WILD-TYPE 31 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF737 MUTATED      4    1
  ZNF737 WILD-TYPE   31   88
   clus
vv  ZNF737 MUTATED ZNF737 WILD-TYPE
  0              4               31
  1              1               88
[1] 2 2
[1] FALSE
D496V6, binary
                  cls
clus                0  1
  ZNF737 MUTATED    1  0
  ZNF737 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF737 MUTATED      1    0
  ZNF737 WILD-TYPE   56    3
   clus
vv  ZNF737 MUTATED ZNF737 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D496V7, binary
                  cls
clus                0  1
  ZNF737 MUTATED    2  3
  ZNF737 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF737 MUTATED      2    3
  ZNF737 WILD-TYPE   49   72
        clus
vv       ZNF737 MUTATED ZNF737 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D496V8, binary
                  cls
clus                0  1
  ZNF737 MUTATED    5  0
  ZNF737 WILD-TYPE 83 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF737 MUTATED      5    0
  ZNF737 WILD-TYPE   83   30
     clus
vv    ZNF737 MUTATED ZNF737 WILD-TYPE
  NO               5               83
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF737 MUTATED                                     4
  ZNF737 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF737 MUTATED                                       1
  ZNF737 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF737 MUTATED                                                  0
  ZNF737 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF737 MUTATED                                     0
  ZNF737 WILD-TYPE                                   1
D496V9, multiclass
                                                  clus
vv                                                 ZNF737 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF737 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V10, continuous
D496V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF737 MUTATED    3  1  1  0
  ZNF737 WILD-TYPE 77 34  3  2
D496V12, multiclass
    clus
vv   ZNF737 MUTATED ZNF737 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF737 MUTATED       1                         0     4
  ZNF737 WILD-TYPE     5                         5   110
D496V14, multiclass
                           clus
vv                          ZNF737 MUTATED ZNF737 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V15, binary
                  cls
clus                0  1
  ZNF737 MUTATED    0  3
  ZNF737 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF737 MUTATED      0    3
  ZNF737 WILD-TYPE    5   88
                        clus
vv                       ZNF737 MUTATED ZNF737 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(497) Variable = CPVL MUTATION ANALYSIS
D497V1, survival
                sevent
clus2             0  1
  CPVL MUTATED    1  2
  CPVL WILD-TYPE 62 60
  CPVL MUTATED CPVL WILD-TYPE 
             3            122 
  CPVL MUTATED CPVL WILD-TYPE 
             2             60 
$`CPVL MUTATED`
TCGA-2J-AABE TCGA-3E-AAAZ TCGA-OE-A75W 
       22.22        71.74         8.78 

$`CPVL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CPVL MUTATED CPVL WILD-TYPE 
          8.78           0.23 
  CPVL MUTATED CPVL WILD-TYPE 
         71.74          90.12 
  CPVL MUTATED CPVL WILD-TYPE 
        22.220         15.205 
[1] "8.8 - 71.7 (22.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D497V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CPVL MUTATED         0        0        0         3         0         0
  CPVL WILD-TYPE       1        3       12        16        82         4
                vv
clus             STAGE IV
  CPVL MUTATED          0
  CPVL WILD-TYPE        3
D497V3, multiclass
           clus
vv          CPVL MUTATED CPVL WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            3             16
  STAGE IIB            0             82
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CPVL MUTATED    0  0     3
  CPVL WILD-TYPE  5 17    99
D497V4, multiclass
       clus
vv      CPVL MUTATED CPVL WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V5, binary
                cls
clus              0  1
  CPVL MUTATED    3  0
  CPVL WILD-TYPE 32 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPVL MUTATED      3    0
  CPVL WILD-TYPE   32   89
   clus
vv  CPVL MUTATED CPVL WILD-TYPE
  0            3             32
  1            0             89
[1] 2 2
[1] FALSE
D497V6, binary
                cls
clus              0  1
  CPVL MUTATED    2  0
  CPVL WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPVL MUTATED      2    0
  CPVL WILD-TYPE   55    3
   clus
vv  CPVL MUTATED CPVL WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D497V7, binary
                cls
clus              0  1
  CPVL MUTATED    0  3
  CPVL WILD-TYPE 51 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPVL MUTATED      0    3
  CPVL WILD-TYPE   51   72
        clus
vv       CPVL MUTATED CPVL WILD-TYPE
  FEMALE            0             51
  MALE              3             72
[1] 2 2
[1] FALSE
D497V8, binary
                cls
clus              0  1
  CPVL MUTATED    0  2
  CPVL WILD-TYPE 88 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPVL MUTATED      0    2
  CPVL WILD-TYPE   88   28
     clus
vv    CPVL MUTATED CPVL WILD-TYPE
  NO             0             88
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CPVL MUTATED                                     3
  CPVL WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CPVL MUTATED                                       0
  CPVL WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CPVL MUTATED                                                  0
  CPVL WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CPVL MUTATED                                     0
  CPVL WILD-TYPE                                   1
D497V9, multiclass
                                                  clus
vv                                                 CPVL MUTATED CPVL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V10, continuous
[1] "Remove cluster labels:" "CPVL MUTATED"          
clus
  CPVL MUTATED CPVL WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-XN-A8T5 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-YY-A8LH 
"CPVL WILD-TYPE" 
D497V11, continuous
[1] "Remove cluster labels:" "CPVL MUTATED"          
clus
  CPVL MUTATED CPVL WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABF 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CPVL MUTATED    2  0  0  0
  CPVL WILD-TYPE 78 35  4  2
D497V12, multiclass
[1] "Remove cluster labels:" "CPVL MUTATED"          
clus
  CPVL MUTATED CPVL WILD-TYPE 
             2            119 
    TCGA-2J-AABR     TCGA-2J-AABT     TCGA-3A-A9I5     TCGA-3A-A9IJ 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-3A-A9IL     TCGA-F2-A44G     TCGA-FB-AAQ6     TCGA-FZ-5924 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-S4-A8RO     TCGA-US-A77E     TCGA-XD-AAUL     TCGA-2J-AAB1 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8     TCGA-2J-AAB9 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2J-AABA     TCGA-2J-AABF     TCGA-2J-AABH     TCGA-2J-AABK 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABP     TCGA-2J-AABU     TCGA-2J-AABV 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-2L-AAQI     TCGA-2L-AAQJ 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-2L-AAQL     TCGA-2L-AAQM     TCGA-3A-A9I7     TCGA-3A-A9I9 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IC     TCGA-3A-A9IH     TCGA-3A-A9IO 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-3A-A9IR     TCGA-3A-A9IS     TCGA-3A-A9IU     TCGA-3A-A9IV 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-3A-A9IZ     TCGA-3A-A9J0     TCGA-F2-7273 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-F2-A7TX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FB-AAPP     TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-FB-AAPU 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FB-AAPZ     TCGA-FB-AAQ0     TCGA-FB-AAQ1     TCGA-FB-AAQ2 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FB-AAQ3     TCGA-FZ-5920     TCGA-FZ-5922     TCGA-FZ-5923 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-FZ-5926     TCGA-H8-A6C1     TCGA-HV-A7OL     TCGA-HV-A7OP 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-HV-AA8V     TCGA-HV-AA8X     TCGA-HZ-7918     TCGA-HZ-7925 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-HZ-8637     TCGA-HZ-A49I     TCGA-HZ-A77O     TCGA-HZ-A77P 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-HZ-A9TJ     TCGA-IB-7651     TCGA-IB-7652 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SO     TCGA-IB-A5SP 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-A5SQ     TCGA-IB-A5ST     TCGA-IB-A6UF     TCGA-IB-A6UG 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-A7LX     TCGA-IB-A7M4     TCGA-IB-AAUM     TCGA-IB-AAUN 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-AAUO     TCGA-IB-AAUP     TCGA-IB-AAUQ     TCGA-IB-AAUR 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-IB-AAUW 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-LB-A8F3     TCGA-LB-A9Q5     TCGA-Q3-A5QY     TCGA-Q3-AA2A 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-RB-A7B8     TCGA-RB-AA9M     TCGA-RL-AAAS     TCGA-US-A776 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-US-A779     TCGA-US-A77G     TCGA-US-A77J     TCGA-XD-AAUG 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-XD-AAUH     TCGA-XD-AAUI     TCGA-XN-A8T3     TCGA-XN-A8T5 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
    TCGA-YB-A89D     TCGA-YY-A8LH     TCGA-Z5-AAPL 
"CPVL WILD-TYPE" "CPVL WILD-TYPE" "CPVL WILD-TYPE" 
D497V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPVL MUTATED       0                         0     3
  CPVL WILD-TYPE     6                         5   111
D497V14, multiclass
                           clus
vv                          CPVL MUTATED CPVL WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V15, binary
                cls
clus              0  1
  CPVL MUTATED    1  1
  CPVL WILD-TYPE  4 90
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPVL MUTATED      1    1
  CPVL WILD-TYPE    4   90
                        clus
vv                       CPVL MUTATED CPVL WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            1             90
[1] 2 2
[1] FALSE

Clustering(498) Variable = AGAP6 MUTATION ANALYSIS
D498V1, survival
                 sevent
clus2              0  1
  AGAP6 MUTATED    2  3
  AGAP6 WILD-TYPE 61 59
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             120 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              3              59 
$`AGAP6 MUTATED`
TCGA-2J-AABR TCGA-IB-A5SS TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A6UF 
       14.40        15.12         5.26        19.82        21.90 

$`AGAP6 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
           5.26            0.23 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          21.90           90.12 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          15.12           15.27 
[1] "5.3 - 21.9 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D498V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AGAP6 MUTATED         0        0        0         1         4         0
  AGAP6 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  AGAP6 MUTATED          0
  AGAP6 WILD-TYPE        3
D498V3, multiclass
           clus
vv          AGAP6 MUTATED AGAP6 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  AGAP6 MUTATED    0  1     4
  AGAP6 WILD-TYPE  5 16    98
D498V4, multiclass
       clus
vv      AGAP6 MUTATED AGAP6 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V5, binary
                 cls
clus               0  1
  AGAP6 MUTATED    1  4
  AGAP6 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      1    4
  AGAP6 WILD-TYPE   34   85
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D498V6, binary
                 cls
clus               0  1
  AGAP6 MUTATED    4  0
  AGAP6 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    0
  AGAP6 WILD-TYPE   53    3
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D498V7, binary
                 cls
clus               0  1
  AGAP6 MUTATED    4  1
  AGAP6 WILD-TYPE 47 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    1
  AGAP6 WILD-TYPE   47   74
        clus
vv       AGAP6 MUTATED AGAP6 WILD-TYPE
  FEMALE             4              47
  MALE               1              74
[1] 2 2
[1] FALSE
D498V8, binary
                 cls
clus               0  1
  AGAP6 MUTATED    5  0
  AGAP6 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      5    0
  AGAP6 WILD-TYPE   83   30
     clus
vv    AGAP6 MUTATED AGAP6 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AGAP6 MUTATED                                     5
  AGAP6 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AGAP6 MUTATED                                       0
  AGAP6 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AGAP6 MUTATED                                                  0
  AGAP6 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  AGAP6 MUTATED                                     0
  AGAP6 WILD-TYPE                                   1
D498V9, multiclass
                                                  clus
vv                                                 AGAP6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 AGAP6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V10, continuous
D498V11, continuous
                 vv
clus              R0 R1 R2 RX
  AGAP6 MUTATED    4  1  0  0
  AGAP6 WILD-TYPE 76 34  4  2
D498V12, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AGAP6 MUTATED       0                         0     5
  AGAP6 WILD-TYPE     6                         5   109
D498V14, multiclass
                           clus
vv                          AGAP6 MUTATED AGAP6 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V15, binary
                 cls
clus               0  1
  AGAP6 MUTATED    0  4
  AGAP6 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      0    4
  AGAP6 WILD-TYPE    5   87
                        clus
vv                       AGAP6 MUTATED AGAP6 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(499) Variable = MMP13 MUTATION ANALYSIS
D499V1, survival
                 sevent
clus2              0  1
  MMP13 MUTATED    1  3
  MMP13 WILD-TYPE 62 59
  MMP13 MUTATED MMP13 WILD-TYPE 
              4             121 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3              59 
$`MMP13 MUTATED`
TCGA-2J-AABP TCGA-3A-A9IB TCGA-FB-AAQ1 TCGA-IB-7651 
       15.22         7.36         4.04        19.82 

$`MMP13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        23.54        15.55         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MMP13 MUTATED MMP13 WILD-TYPE 
           4.04            0.23 
  MMP13 MUTATED MMP13 WILD-TYPE 
          19.82           90.12 
  MMP13 MUTATED MMP13 WILD-TYPE 
          11.29           15.32 
[1] "4.0 - 19.8 (11.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.5"
D499V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MMP13 MUTATED         0        0        0         0         4         0
  MMP13 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  MMP13 MUTATED          0
  MMP13 WILD-TYPE        3
D499V3, multiclass
           clus
vv          MMP13 MUTATED MMP13 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MMP13 MUTATED    0  0     4
  MMP13 WILD-TYPE  5 17    98
D499V4, multiclass
       clus
vv      MMP13 MUTATED MMP13 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V5, binary
                 cls
clus               0  1
  MMP13 MUTATED    0  4
  MMP13 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    4
  MMP13 WILD-TYPE   35   85
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D499V6, binary
                 cls
clus               0  1
  MMP13 MUTATED    2  0
  MMP13 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      2    0
  MMP13 WILD-TYPE   55    3
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D499V7, binary
                 cls
clus               0  1
  MMP13 MUTATED    3  1
  MMP13 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      3    1
  MMP13 WILD-TYPE   48   74
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D499V8, binary
                 cls
clus               0  1
  MMP13 MUTATED    4  0
  MMP13 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      4    0
  MMP13 WILD-TYPE   84   30
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP13 MUTATED                                     3
  MMP13 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP13 MUTATED                                       0
  MMP13 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP13 MUTATED                                                  0
  MMP13 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MMP13 MUTATED                                     1
  MMP13 WILD-TYPE                                   0
D499V9, multiclass
                                                  clus
vv                                                 MMP13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          1
                                                  clus
vv                                                 MMP13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V10, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IX 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-YY-A8LH 
"MMP13 WILD-TYPE" 
D499V11, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IR      TCGA-3A-A9IX 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MMP13 MUTATED    3  1  0  0
  MMP13 WILD-TYPE 77 34  4  2
D499V12, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED       0                         0     4
  MMP13 WILD-TYPE     6                         5   110
D499V14, multiclass
                           clus
vv                          MMP13 MUTATED MMP13 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V15, binary
                 cls
clus               0  1
  MMP13 MUTATED    0  3
  MMP13 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    3
  MMP13 WILD-TYPE    5   88
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(500) Variable = BCL11A MUTATION ANALYSIS
D500V1, survival
                  sevent
clus2               0  1
  BCL11A MUTATED    1  5
  BCL11A WILD-TYPE 62 57
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              119 
  BCL11A MUTATED BCL11A WILD-TYPE 
               5               57 
$`BCL11A MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9IZ TCGA-F2-7273 TCGA-HZ-7918 TCGA-IB-A6UG TCGA-IB-AAUO 
       12.95        10.13        19.46        31.86         1.35         7.86 

$`BCL11A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       36.26        34.09        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        17.49        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88        21.90         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  BCL11A MUTATED BCL11A WILD-TYPE 
            1.35             0.23 
  BCL11A MUTATED BCL11A WILD-TYPE 
           31.86            90.12 
  BCL11A MUTATED BCL11A WILD-TYPE 
           11.54            15.32 
[1] "1.4 - 31.9 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.3"
D500V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BCL11A MUTATED         0        0        0         0         5         1
  BCL11A WILD-TYPE       1        3       12        19        77         3
                  vv
clus               STAGE IV
  BCL11A MUTATED          0
  BCL11A WILD-TYPE        3
D500V3, multiclass
           clus
vv          BCL11A MUTATED BCL11A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              5               77
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  BCL11A MUTATED    0  0     6
  BCL11A WILD-TYPE  5 17    96
D500V4, multiclass
       clus
vv      BCL11A MUTATED BCL11A WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V5, binary
                  cls
clus                0  1
  BCL11A MUTATED    1  5
  BCL11A WILD-TYPE 34 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      1    5
  BCL11A WILD-TYPE   34   84
   clus
vv  BCL11A MUTATED BCL11A WILD-TYPE
  0              1               34
  1              5               84
[1] 2 2
[1] FALSE
D500V6, binary
                  cls
clus                0  1
  BCL11A MUTATED    4  0
  BCL11A WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      4    0
  BCL11A WILD-TYPE   53    3
   clus
vv  BCL11A MUTATED BCL11A WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D500V7, binary
                  cls
clus                0  1
  BCL11A MUTATED    2  4
  BCL11A WILD-TYPE 49 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      2    4
  BCL11A WILD-TYPE   49   71
        clus
vv       BCL11A MUTATED BCL11A WILD-TYPE
  FEMALE              2               49
  MALE                4               71
[1] 2 2
[1] FALSE
D500V8, binary
                  cls
clus                0  1
  BCL11A MUTATED    4  2
  BCL11A WILD-TYPE 84 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      4    2
  BCL11A WILD-TYPE   84   28
     clus
vv    BCL11A MUTATED BCL11A WILD-TYPE
  NO               4               84
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCL11A MUTATED                                     6
  BCL11A WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCL11A MUTATED                                       0
  BCL11A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCL11A MUTATED                                                  0
  BCL11A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  BCL11A MUTATED                                     0
  BCL11A WILD-TYPE                                   1
D500V9, multiclass
                                                  clus
vv                                                 BCL11A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 BCL11A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V10, continuous
[1] "Remove cluster labels:" "BCL11A MUTATED"        
clus
  BCL11A MUTATED BCL11A WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
D500V11, continuous
[1] "Remove cluster labels:" "BCL11A MUTATED"        
clus
  BCL11A MUTATED BCL11A WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A7M4 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" "BCL11A WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  BCL11A MUTATED    1  5  0  0
  BCL11A WILD-TYPE 79 30  4  2
D500V12, multiclass
    clus
vv   BCL11A MUTATED BCL11A WILD-TYPE
  R0              1               79
  R1              5               30
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL11A MUTATED       0                         1     5
  BCL11A WILD-TYPE     6                         4   109
D500V14, multiclass
                           clus
vv                          BCL11A MUTATED BCL11A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V15, binary
                  cls
clus                0  1
  BCL11A MUTATED    1  4
  BCL11A WILD-TYPE  4 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      1    4
  BCL11A WILD-TYPE    4   87
                        clus
vv                       BCL11A MUTATED BCL11A WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(501) Variable = ZNF207 MUTATION ANALYSIS
D501V1, survival
                  sevent
clus2               0  1
  ZNF207 MUTATED    3  1
  ZNF207 WILD-TYPE 60 61
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               4              121 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               1               61 
$`ZNF207 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABP TCGA-IB-7651 TCGA-Z5-AAPL 
       23.97        15.22        19.82        15.35 

$`ZNF207 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  ZNF207 MUTATED ZNF207 WILD-TYPE 
           15.22             0.23 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
           23.97            90.12 
  ZNF207 MUTATED ZNF207 WILD-TYPE 
          17.585           15.120 
[1] "15.2 - 24.0 (17.6)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "2.3"
D501V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF207 MUTATED         0        0        0         1         3         0
  ZNF207 WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  ZNF207 MUTATED          0
  ZNF207 WILD-TYPE        3
D501V3, multiclass
           clus
vv          ZNF207 MUTATED ZNF207 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF207 MUTATED    0  1     3
  ZNF207 WILD-TYPE  5 16    99
D501V4, multiclass
       clus
vv      ZNF207 MUTATED ZNF207 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V5, binary
                  cls
clus                0  1
  ZNF207 MUTATED    1  3
  ZNF207 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      1    3
  ZNF207 WILD-TYPE   34   86
   clus
vv  ZNF207 MUTATED ZNF207 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D501V6, binary
                  cls
clus                0  1
  ZNF207 MUTATED    4  0
  ZNF207 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      4    0
  ZNF207 WILD-TYPE   53    3
   clus
vv  ZNF207 MUTATED ZNF207 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D501V7, binary
                  cls
clus                0  1
  ZNF207 MUTATED    3  1
  ZNF207 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      3    1
  ZNF207 WILD-TYPE   48   74
        clus
vv       ZNF207 MUTATED ZNF207 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D501V8, binary
                  cls
clus                0  1
  ZNF207 MUTATED    4  0
  ZNF207 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      4    0
  ZNF207 WILD-TYPE   84   30
     clus
vv    ZNF207 MUTATED ZNF207 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF207 MUTATED                                     2
  ZNF207 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF207 MUTATED                                       1
  ZNF207 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF207 MUTATED                                                  0
  ZNF207 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF207 MUTATED                                     1
  ZNF207 WILD-TYPE                                   0
D501V9, multiclass
                                                  clus
vv                                                 ZNF207 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           1
                                                  clus
vv                                                 ZNF207 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V10, continuous
[1] "Remove cluster labels:" "ZNF207 MUTATED"        
clus
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
D501V11, continuous
[1] "Remove cluster labels:" "ZNF207 MUTATED"        
clus
  ZNF207 MUTATED ZNF207 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" "ZNF207 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF207 MUTATED    4  0  0  0
  ZNF207 WILD-TYPE 76 35  4  2
D501V12, multiclass
    clus
vv   ZNF207 MUTATED ZNF207 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF207 MUTATED       0                         0     4
  ZNF207 WILD-TYPE     6                         5   110
D501V14, multiclass
                           clus
vv                          ZNF207 MUTATED ZNF207 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V15, binary
                  cls
clus                0  1
  ZNF207 MUTATED    0  2
  ZNF207 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF207 MUTATED      0    2
  ZNF207 WILD-TYPE    5   89
                        clus
vv                       ZNF207 MUTATED ZNF207 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(502) Variable = CCDC55 MUTATION ANALYSIS
D502V1, survival
                  sevent
clus2               0  1
  CCDC55 MUTATED    1  2
  CCDC55 WILD-TYPE 62 60
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               3              122 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               2               60 
$`CCDC55 MUTATED`
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-HZ-A77O 
       15.06        36.26         5.26 

$`CCDC55 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CCDC55 MUTATED CCDC55 WILD-TYPE 
            5.26             0.23 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           36.26            90.12 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           15.06            15.27 
[1] "5.3 - 36.3 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D502V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC55 MUTATED         0        0        1         0         2         0
  CCDC55 WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  CCDC55 MUTATED          0
  CCDC55 WILD-TYPE        3
D502V3, multiclass
           clus
vv          CCDC55 MUTATED CCDC55 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CCDC55 MUTATED     0   2     1
  CCDC55 WILD-TYPE   5  15   101
D502V4, multiclass
       clus
vv      CCDC55 MUTATED CCDC55 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              1              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V5, binary
                  cls
clus                0  1
  CCDC55 MUTATED    1  2
  CCDC55 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      1    2
  CCDC55 WILD-TYPE   34   87
   clus
vv  CCDC55 MUTATED CCDC55 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D502V6, binary
                  cls
clus                0  1
  CCDC55 MUTATED    0  0
  CCDC55 WILD-TYPE 57  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      0    0
  CCDC55 WILD-TYPE   57    3
D502V7, binary
                  cls
clus                0  1
  CCDC55 MUTATED    2  1
  CCDC55 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      2    1
  CCDC55 WILD-TYPE   49   74
        clus
vv       CCDC55 MUTATED CCDC55 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D502V8, binary
                  cls
clus                0  1
  CCDC55 MUTATED    3  0
  CCDC55 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      3    0
  CCDC55 WILD-TYPE   85   30
     clus
vv    CCDC55 MUTATED CCDC55 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC55 MUTATED                                     2
  CCDC55 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC55 MUTATED                                       1
  CCDC55 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC55 MUTATED                                                  0
  CCDC55 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC55 MUTATED                                     0
  CCDC55 WILD-TYPE                                   1
D502V9, multiclass
                                                  clus
vv                                                 CCDC55 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CCDC55 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V10, continuous
D502V11, continuous
                  vv
clus               R0 R1 R2 RX
  CCDC55 MUTATED    3  0  0  0
  CCDC55 WILD-TYPE 77 35  4  2
D502V12, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC55 MUTATED       0                         0     3
  CCDC55 WILD-TYPE     6                         5   111
D502V14, multiclass
                           clus
vv                          CCDC55 MUTATED CCDC55 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V15, binary
                  cls
clus                0  1
  CCDC55 MUTATED    0  3
  CCDC55 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      0    3
  CCDC55 WILD-TYPE    5   88
                        clus
vv                       CCDC55 MUTATED CCDC55 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(503) Variable = ORAI3 MUTATION ANALYSIS
D503V1, survival
                 sevent
clus2              0  1
  ORAI3 MUTATED    1  2
  ORAI3 WILD-TYPE 62 60
  ORAI3 MUTATED ORAI3 WILD-TYPE 
              3             122 
  ORAI3 MUTATED ORAI3 WILD-TYPE 
              2              60 
$`ORAI3 MUTATED`
TCGA-3E-AAAZ TCGA-IB-A5SQ TCGA-YB-A89D 
       71.74         7.20        11.51 

$`ORAI3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00        15.85        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ORAI3 MUTATED ORAI3 WILD-TYPE 
           7.20            0.23 
  ORAI3 MUTATED ORAI3 WILD-TYPE 
          71.74           90.12 
  ORAI3 MUTATED ORAI3 WILD-TYPE 
          11.51           15.27 
[1] "7.2 - 71.7 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D503V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ORAI3 MUTATED         0        0        1         1         1         0
  ORAI3 WILD-TYPE       1        3       11        18        81         4
                 vv
clus              STAGE IV
  ORAI3 MUTATED          0
  ORAI3 WILD-TYPE        3
D503V3, multiclass
           clus
vv          ORAI3 MUTATED ORAI3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ORAI3 MUTATED     0   1     2
  ORAI3 WILD-TYPE   5  16   100
D503V4, multiclass
       clus
vv      ORAI3 MUTATED ORAI3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V5, binary
                 cls
clus               0  1
  ORAI3 MUTATED    2  1
  ORAI3 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORAI3 MUTATED      2    1
  ORAI3 WILD-TYPE   33   88
   clus
vv  ORAI3 MUTATED ORAI3 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D503V6, binary
                 cls
clus               0  1
  ORAI3 MUTATED    1  0
  ORAI3 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORAI3 MUTATED      1    0
  ORAI3 WILD-TYPE   56    3
   clus
vv  ORAI3 MUTATED ORAI3 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D503V7, binary
                 cls
clus               0  1
  ORAI3 MUTATED    1  2
  ORAI3 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORAI3 MUTATED      1    2
  ORAI3 WILD-TYPE   50   73
        clus
vv       ORAI3 MUTATED ORAI3 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D503V8, binary
                 cls
clus               0  1
  ORAI3 MUTATED    1  1
  ORAI3 WILD-TYPE 87 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORAI3 MUTATED      1    1
  ORAI3 WILD-TYPE   87   29
     clus
vv    ORAI3 MUTATED ORAI3 WILD-TYPE
  NO              1              87
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ORAI3 MUTATED                                     3
  ORAI3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ORAI3 MUTATED                                       0
  ORAI3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ORAI3 MUTATED                                                  0
  ORAI3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ORAI3 MUTATED                                     0
  ORAI3 WILD-TYPE                                   1
D503V9, multiclass
                                                  clus
vv                                                 ORAI3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ORAI3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V10, continuous
D503V11, continuous
                 vv
clus              R0 R1 R2 RX
  ORAI3 MUTATED    2  0  0  0
  ORAI3 WILD-TYPE 78 35  4  2
D503V12, multiclass
[1] "Remove cluster labels:" "ORAI3 MUTATED"         
clus
  ORAI3 MUTATED ORAI3 WILD-TYPE 
              2             119 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-3A-A9IV      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7651 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-US-A776      TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" "ORAI3 WILD-TYPE" 
D503V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ORAI3 MUTATED       0                         0     3
  ORAI3 WILD-TYPE     6                         5   111
D503V14, multiclass
                           clus
vv                          ORAI3 MUTATED ORAI3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V15, binary
                 cls
clus               0  1
  ORAI3 MUTATED    1  2
  ORAI3 WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORAI3 MUTATED      1    2
  ORAI3 WILD-TYPE    4   89
                        clus
vv                       ORAI3 MUTATED ORAI3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(504) Variable = LAMA1 MUTATION ANALYSIS
D504V1, survival
                 sevent
clus2              0  1
  LAMA1 MUTATED    5  3
  LAMA1 WILD-TYPE 58 59
  LAMA1 MUTATED LAMA1 WILD-TYPE 
              8             117 
  LAMA1 MUTATED LAMA1 WILD-TYPE 
              3              59 
$`LAMA1 MUTATED`
TCGA-3A-A9IL TCGA-2J-AAB1 TCGA-2J-AABO TCGA-3A-A9IH TCGA-FZ-5921 TCGA-IB-7651 
       90.12         2.17        14.47        33.57         5.10        19.82 
TCGA-IB-A5SP TCGA-US-A776 
       15.85        39.98 

$`LAMA1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP TCGA-2J-AABU 
       22.22        22.72        42.31        15.91        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO 
       45.47        43.50        20.84         7.36        24.26        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ 
       50.70        32.81        15.06        36.26        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        2.01        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        12.00         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  LAMA1 MUTATED LAMA1 WILD-TYPE 
           2.17            0.23 
  LAMA1 MUTATED LAMA1 WILD-TYPE 
          90.12           75.12 
  LAMA1 MUTATED LAMA1 WILD-TYPE 
         17.835          15.190 
[1] "2.2 - 90.1 (17.8)" "0.2 - 75.1 (15.2)"
[1] "hr=" "1.7"
D504V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LAMA1 MUTATED         1        1        0         2         4         0
  LAMA1 WILD-TYPE       0        2       12        17        78         4
                 vv
clus              STAGE IV
  LAMA1 MUTATED          0
  LAMA1 WILD-TYPE        3
D504V3, multiclass
           clus
vv          LAMA1 MUTATED LAMA1 WILD-TYPE
  STAGE I               1               0
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LAMA1 MUTATED    2  0     6
  LAMA1 WILD-TYPE  3 17    96
D504V4, multiclass
       clus
vv      LAMA1 MUTATED LAMA1 WILD-TYPE
  T1                2               3
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V5, binary
                 cls
clus               0  1
  LAMA1 MUTATED    3  4
  LAMA1 WILD-TYPE 32 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA1 MUTATED      3    4
  LAMA1 WILD-TYPE   32   85
   clus
vv  LAMA1 MUTATED LAMA1 WILD-TYPE
  0             3              32
  1             4              85
[1] 2 2
[1] FALSE
D504V6, binary
                 cls
clus               0  1
  LAMA1 MUTATED    5  0
  LAMA1 WILD-TYPE 52  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA1 MUTATED      5    0
  LAMA1 WILD-TYPE   52    3
   clus
vv  LAMA1 MUTATED LAMA1 WILD-TYPE
  0             5              52
  1             0               3
[1] 2 2
[1] FALSE
D504V7, binary
                 cls
clus               0  1
  LAMA1 MUTATED    4  4
  LAMA1 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA1 MUTATED      4    4
  LAMA1 WILD-TYPE   47   71
        clus
vv       LAMA1 MUTATED LAMA1 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D504V8, binary
                 cls
clus               0  1
  LAMA1 MUTATED    6  2
  LAMA1 WILD-TYPE 82 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA1 MUTATED      6    2
  LAMA1 WILD-TYPE   82   28
     clus
vv    LAMA1 MUTATED LAMA1 WILD-TYPE
  NO              6              82
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LAMA1 MUTATED                                     5
  LAMA1 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LAMA1 MUTATED                                       2
  LAMA1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LAMA1 MUTATED                                                  1
  LAMA1 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LAMA1 MUTATED                                     0
  LAMA1 WILD-TYPE                                   1
D504V9, multiclass
                                                  clus
vv                                                 LAMA1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LAMA1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V10, continuous
D504V11, continuous
                 vv
clus              R0 R1 R2 RX
  LAMA1 MUTATED    6  1  0  0
  LAMA1 WILD-TYPE 74 34  4  2
D504V12, multiclass
    clus
vv   LAMA1 MUTATED LAMA1 WILD-TYPE
  R0             6              74
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LAMA1 MUTATED       0                         0     7
  LAMA1 WILD-TYPE     6                         5   107
D504V14, multiclass
                           clus
vv                          LAMA1 MUTATED LAMA1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V15, binary
                 cls
clus               0  1
  LAMA1 MUTATED    0  4
  LAMA1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA1 MUTATED      0    4
  LAMA1 WILD-TYPE    5   87
                        clus
vv                       LAMA1 MUTATED LAMA1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(505) Variable = AFAP1L2 MUTATION ANALYSIS
D505V1, survival
                   sevent
clus2                0  1
  AFAP1L2 MUTATED    2  2
  AFAP1L2 WILD-TYPE 61 60
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                4               121 
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                2                60 
$`AFAP1L2 MUTATED`
TCGA-LB-A7SX TCGA-3A-A9IS TCGA-HV-A7OP TCGA-IB-7651 
       12.92        32.81        32.15        19.82 

$`AFAP1L2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
            12.92              0.23 
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
            32.81             90.12 
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
           25.985            15.190 
[1] "12.9 - 32.8 (26.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D505V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AFAP1L2 MUTATED         0        0        1         0         3         0
  AFAP1L2 WILD-TYPE       1        3       11        19        79         4
                   vv
clus                STAGE IV
  AFAP1L2 MUTATED          0
  AFAP1L2 WILD-TYPE        3
D505V3, multiclass
           clus
vv          AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  AFAP1L2 MUTATED    0  1     3
  AFAP1L2 WILD-TYPE  5 16    99
D505V4, multiclass
       clus
vv      AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V5, binary
                   cls
clus                 0  1
  AFAP1L2 MUTATED    1  3
  AFAP1L2 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AFAP1L2 MUTATED      1    3
  AFAP1L2 WILD-TYPE   34   86
   clus
vv  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D505V6, binary
                   cls
clus                 0  1
  AFAP1L2 MUTATED    2  0
  AFAP1L2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AFAP1L2 MUTATED      2    0
  AFAP1L2 WILD-TYPE   55    3
   clus
vv  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D505V7, binary
                   cls
clus                 0  1
  AFAP1L2 MUTATED    2  2
  AFAP1L2 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AFAP1L2 MUTATED      2    2
  AFAP1L2 WILD-TYPE   49   73
        clus
vv       AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D505V8, binary
                   cls
clus                 0  1
  AFAP1L2 MUTATED    3  1
  AFAP1L2 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AFAP1L2 MUTATED      3    1
  AFAP1L2 WILD-TYPE   85   29
     clus
vv    AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AFAP1L2 MUTATED                                     2
  AFAP1L2 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AFAP1L2 MUTATED                                       2
  AFAP1L2 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AFAP1L2 MUTATED                                                  0
  AFAP1L2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  AFAP1L2 MUTATED                                     0
  AFAP1L2 WILD-TYPE                                   1
D505V9, multiclass
                                                  clus
vv                                                 AFAP1L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 AFAP1L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V10, continuous
[1] "Remove cluster labels:" "AFAP1L2 MUTATED"       
clus
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-YY-A8LH 
"AFAP1L2 WILD-TYPE" 
D505V11, continuous
[1] "Remove cluster labels:" "AFAP1L2 MUTATED"       
clus
  AFAP1L2 MUTATED AFAP1L2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE        TCGA-2J-AABF 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" "AFAP1L2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  AFAP1L2 MUTATED    3  1  0  0
  AFAP1L2 WILD-TYPE 77 34  4  2
D505V12, multiclass
    clus
vv   AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AFAP1L2 MUTATED       1                         1     2
  AFAP1L2 WILD-TYPE     5                         4   112
D505V14, multiclass
                           clus
vv                          AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   2               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V15, binary
                   cls
clus                 0  1
  AFAP1L2 MUTATED    0  3
  AFAP1L2 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AFAP1L2 MUTATED      0    3
  AFAP1L2 WILD-TYPE    5   88
                        clus
vv                       AFAP1L2 MUTATED AFAP1L2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(506) Variable = ATXN2L MUTATION ANALYSIS
D506V1, survival
                  sevent
clus2               0  1
  ATXN2L MUTATED    3  1
  ATXN2L WILD-TYPE 60 61
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               4              121 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               1               61 
$`ATXN2L MUTATED`
TCGA-3A-A9J0 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-A5SP 
       24.43        32.15        19.82        15.85 

$`ATXN2L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        10.13        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ATXN2L MUTATED ATXN2L WILD-TYPE 
           15.85             0.23 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
           32.15            90.12 
  ATXN2L MUTATED ATXN2L WILD-TYPE 
          22.125           15.120 
[1] "15.8 - 32.1 (22.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3"  
D506V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATXN2L MUTATED         0        0        0         1         3         0
  ATXN2L WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  ATXN2L MUTATED          0
  ATXN2L WILD-TYPE        3
D506V3, multiclass
           clus
vv          ATXN2L MUTATED ATXN2L WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ATXN2L MUTATED    0  0     4
  ATXN2L WILD-TYPE  5 17    98
D506V4, multiclass
       clus
vv      ATXN2L MUTATED ATXN2L WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V5, binary
                  cls
clus                0  1
  ATXN2L MUTATED    1  3
  ATXN2L WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      1    3
  ATXN2L WILD-TYPE   34   86
   clus
vv  ATXN2L MUTATED ATXN2L WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D506V6, binary
                  cls
clus                0  1
  ATXN2L MUTATED    3  0
  ATXN2L WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      3    0
  ATXN2L WILD-TYPE   54    3
   clus
vv  ATXN2L MUTATED ATXN2L WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D506V7, binary
                  cls
clus                0  1
  ATXN2L MUTATED    1  3
  ATXN2L WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      1    3
  ATXN2L WILD-TYPE   50   72
        clus
vv       ATXN2L MUTATED ATXN2L WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D506V8, binary
                  cls
clus                0  1
  ATXN2L MUTATED    3  1
  ATXN2L WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      3    1
  ATXN2L WILD-TYPE   85   29
     clus
vv    ATXN2L MUTATED ATXN2L WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATXN2L MUTATED                                     3
  ATXN2L WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATXN2L MUTATED                                       1
  ATXN2L WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATXN2L MUTATED                                                  0
  ATXN2L WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATXN2L MUTATED                                     0
  ATXN2L WILD-TYPE                                   1
D506V9, multiclass
                                                  clus
vv                                                 ATXN2L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ATXN2L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V10, continuous
[1] "Remove cluster labels:" "ATXN2L MUTATED"        
clus
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
D506V11, continuous
[1] "Remove cluster labels:" "ATXN2L MUTATED"        
clus
  ATXN2L MUTATED ATXN2L WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" "ATXN2L WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATXN2L MUTATED    3  1  0  0
  ATXN2L WILD-TYPE 77 34  4  2
D506V12, multiclass
    clus
vv   ATXN2L MUTATED ATXN2L WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATXN2L MUTATED       1                         0     3
  ATXN2L WILD-TYPE     5                         5   111
D506V14, multiclass
                           clus
vv                          ATXN2L MUTATED ATXN2L WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V15, binary
                  cls
clus                0  1
  ATXN2L MUTATED    0  2
  ATXN2L WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN2L MUTATED      0    2
  ATXN2L WILD-TYPE    5   89
                        clus
vv                       ATXN2L MUTATED ATXN2L WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(507) Variable = BECN1 MUTATION ANALYSIS
D507V1, survival
                 sevent
clus2              0  1
  BECN1 MUTATED    1  2
  BECN1 WILD-TYPE 62 60
  BECN1 MUTATED BECN1 WILD-TYPE 
              3             122 
  BECN1 MUTATED BECN1 WILD-TYPE 
              2              60 
$`BECN1 MUTATED`
TCGA-2L-AAQA TCGA-2L-AAQJ TCGA-US-A776 
        4.70        12.95        39.98 

$`BECN1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  BECN1 MUTATED BECN1 WILD-TYPE 
           4.70            0.23 
  BECN1 MUTATED BECN1 WILD-TYPE 
          39.98           90.12 
  BECN1 MUTATED BECN1 WILD-TYPE 
          12.95           15.27 
[1] "4.7 - 40.0 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D507V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BECN1 MUTATED         0        0        0         1         1         1
  BECN1 WILD-TYPE       1        3       12        18        81         3
                 vv
clus              STAGE IV
  BECN1 MUTATED          0
  BECN1 WILD-TYPE        3
D507V3, multiclass
           clus
vv          BECN1 MUTATED BECN1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  BECN1 MUTATED    0  0     3
  BECN1 WILD-TYPE  5 17    99
D507V4, multiclass
       clus
vv      BECN1 MUTATED BECN1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V5, binary
                 cls
clus               0  1
  BECN1 MUTATED    2  1
  BECN1 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BECN1 MUTATED      2    1
  BECN1 WILD-TYPE   33   88
   clus
vv  BECN1 MUTATED BECN1 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D507V6, binary
                 cls
clus               0  1
  BECN1 MUTATED    0  0
  BECN1 WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BECN1 MUTATED      0    0
  BECN1 WILD-TYPE   57    3
D507V7, binary
                 cls
clus               0  1
  BECN1 MUTATED    1  2
  BECN1 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BECN1 MUTATED      1    2
  BECN1 WILD-TYPE   50   73
        clus
vv       BECN1 MUTATED BECN1 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D507V8, binary
                 cls
clus               0  1
  BECN1 MUTATED    3  0
  BECN1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BECN1 MUTATED      3    0
  BECN1 WILD-TYPE   85   30
     clus
vv    BECN1 MUTATED BECN1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BECN1 MUTATED                                     2
  BECN1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BECN1 MUTATED                                       0
  BECN1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BECN1 MUTATED                                                  1
  BECN1 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  BECN1 MUTATED                                     0
  BECN1 WILD-TYPE                                   1
D507V9, multiclass
                                                  clus
vv                                                 BECN1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 BECN1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V10, continuous
[1] "Remove cluster labels:" "BECN1 MUTATED"         
clus
  BECN1 MUTATED BECN1 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"BECN1 WILD-TYPE" "BECN1 WILD-TYPE" 
D507V11, continuous
                 vv
clus              R0 R1 R2 RX
  BECN1 MUTATED    1  2  0  0
  BECN1 WILD-TYPE 79 33  4  2
D507V12, multiclass
    clus
vv   BECN1 MUTATED BECN1 WILD-TYPE
  R0             1              79
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BECN1 MUTATED       0                         0     3
  BECN1 WILD-TYPE     6                         5   111
D507V14, multiclass
                           clus
vv                          BECN1 MUTATED BECN1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V15, binary
                 cls
clus               0  1
  BECN1 MUTATED    0  1
  BECN1 WILD-TYPE  5 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BECN1 MUTATED      0    1
  BECN1 WILD-TYPE    5   90
                        clus
vv                       BECN1 MUTATED BECN1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             1              90
[1] 2 2
[1] FALSE

Clustering(508) Variable = MAP3K7 MUTATION ANALYSIS
D508V1, survival
                  sevent
clus2               0  1
  MAP3K7 MUTATED    2  2
  MAP3K7 WILD-TYPE 61 60
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               4              121 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               2               60 
$`MAP3K7 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-US-A77J TCGA-Z5-AAPL 
       19.82        15.19        18.67        15.35 

$`MAP3K7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
        9.40         0.30        39.98        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
           15.19             0.23 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
           19.82            90.12 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
           17.01            15.12 
[1] "15.2 - 19.8 (17.0)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1"  
D508V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAP3K7 MUTATED         0        0        0         1         2         1
  MAP3K7 WILD-TYPE       1        3       12        18        80         3
                  vv
clus               STAGE IV
  MAP3K7 MUTATED          0
  MAP3K7 WILD-TYPE        3
D508V3, multiclass
           clus
vv          MAP3K7 MUTATED MAP3K7 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MAP3K7 MUTATED    0  0     4
  MAP3K7 WILD-TYPE  5 17    98
D508V4, multiclass
       clus
vv      MAP3K7 MUTATED MAP3K7 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V5, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    1  3
  MAP3K7 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      1    3
  MAP3K7 WILD-TYPE   34   86
   clus
vv  MAP3K7 MUTATED MAP3K7 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D508V6, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    3  0
  MAP3K7 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      3    0
  MAP3K7 WILD-TYPE   54    3
   clus
vv  MAP3K7 MUTATED MAP3K7 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D508V7, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    4  0
  MAP3K7 WILD-TYPE 47 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      4    0
  MAP3K7 WILD-TYPE   47   75
        clus
vv       MAP3K7 MUTATED MAP3K7 WILD-TYPE
  FEMALE              4               47
  MALE                0               75
[1] 2 2
[1] FALSE
D508V8, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    3  0
  MAP3K7 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      3    0
  MAP3K7 WILD-TYPE   85   30
     clus
vv    MAP3K7 MUTATED MAP3K7 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAP3K7 MUTATED                                     4
  MAP3K7 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAP3K7 MUTATED                                       0
  MAP3K7 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAP3K7 MUTATED                                                  0
  MAP3K7 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAP3K7 MUTATED                                     0
  MAP3K7 WILD-TYPE                                   1
D508V9, multiclass
                                                  clus
vv                                                 MAP3K7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MAP3K7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V10, continuous
[1] "Remove cluster labels:" "MAP3K7 MUTATED"        
clus
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-A6UF       TCGA-IB-A6UG 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-YY-A8LH 
"MAP3K7 WILD-TYPE" 
D508V11, continuous
[1] "Remove cluster labels:" "MAP3K7 MUTATED"        
clus
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  MAP3K7 MUTATED    3  1  0  0
  MAP3K7 WILD-TYPE 77 34  4  2
D508V12, multiclass
    clus
vv   MAP3K7 MUTATED MAP3K7 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K7 MUTATED       0                         0     4
  MAP3K7 WILD-TYPE     6                         5   110
D508V14, multiclass
                           clus
vv                          MAP3K7 MUTATED MAP3K7 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V15, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    0  4
  MAP3K7 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      0    4
  MAP3K7 WILD-TYPE    5   87
                        clus
vv                       MAP3K7 MUTATED MAP3K7 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(509) Variable = HVCN1 MUTATION ANALYSIS
D509V1, survival
                 sevent
clus2              0  1
  HVCN1 MUTATED    2  2
  HVCN1 WILD-TYPE 61 60
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              4             121 
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              2              60 
$`HVCN1 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AABE TCGA-3A-A9IB TCGA-RB-AA9M 
        9.63        22.22         7.36         9.40 

$`HVCN1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HVCN1 MUTATED HVCN1 WILD-TYPE 
           7.36            0.23 
  HVCN1 MUTATED HVCN1 WILD-TYPE 
          22.22           90.12 
  HVCN1 MUTATED HVCN1 WILD-TYPE 
          9.515          15.320 
[1] "7.4 - 22.2 (9.5)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D509V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HVCN1 MUTATED         0        0        0         2         2         0
  HVCN1 WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  HVCN1 MUTATED          0
  HVCN1 WILD-TYPE        3
D509V3, multiclass
           clus
vv          HVCN1 MUTATED HVCN1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HVCN1 MUTATED    1  0     3
  HVCN1 WILD-TYPE  4 17    99
D509V4, multiclass
       clus
vv      HVCN1 MUTATED HVCN1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V5, binary
                 cls
clus               0  1
  HVCN1 MUTATED    2  2
  HVCN1 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HVCN1 MUTATED      2    2
  HVCN1 WILD-TYPE   33   87
   clus
vv  HVCN1 MUTATED HVCN1 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D509V6, binary
                 cls
clus               0  1
  HVCN1 MUTATED    2  0
  HVCN1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HVCN1 MUTATED      2    0
  HVCN1 WILD-TYPE   55    3
   clus
vv  HVCN1 MUTATED HVCN1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D509V7, binary
                 cls
clus               0  1
  HVCN1 MUTATED    1  3
  HVCN1 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HVCN1 MUTATED      1    3
  HVCN1 WILD-TYPE   50   72
        clus
vv       HVCN1 MUTATED HVCN1 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D509V8, binary
                 cls
clus               0  1
  HVCN1 MUTATED    2  2
  HVCN1 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HVCN1 MUTATED      2    2
  HVCN1 WILD-TYPE   86   28
     clus
vv    HVCN1 MUTATED HVCN1 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HVCN1 MUTATED                                     4
  HVCN1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HVCN1 MUTATED                                       0
  HVCN1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HVCN1 MUTATED                                                  0
  HVCN1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HVCN1 MUTATED                                     0
  HVCN1 WILD-TYPE                                   1
D509V9, multiclass
                                                  clus
vv                                                 HVCN1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HVCN1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V10, continuous
[1] "Remove cluster labels:" "HVCN1 MUTATED"         
clus
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IX      TCGA-F2-A8YN 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-YY-A8LH 
"HVCN1 WILD-TYPE" 
D509V11, continuous
[1] "Remove cluster labels:" "HVCN1 MUTATED"         
clus
  HVCN1 MUTATED HVCN1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABF 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IR      TCGA-3A-A9IX      TCGA-FB-A5VM 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" "HVCN1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HVCN1 MUTATED    4  0  0  0
  HVCN1 WILD-TYPE 76 35  4  2
D509V12, multiclass
    clus
vv   HVCN1 MUTATED HVCN1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HVCN1 MUTATED       0                         0     4
  HVCN1 WILD-TYPE     6                         5   110
D509V14, multiclass
                           clus
vv                          HVCN1 MUTATED HVCN1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V15, binary
                 cls
clus               0  1
  HVCN1 MUTATED    0  2
  HVCN1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HVCN1 MUTATED      0    2
  HVCN1 WILD-TYPE    5   89
                        clus
vv                       HVCN1 MUTATED HVCN1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(510) Variable = AKAP11 MUTATION ANALYSIS
D510V1, survival
                  sevent
clus2               0  1
  AKAP11 MUTATED    4  1
  AKAP11 WILD-TYPE 59 61
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               5              120 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               1               61 
$`AKAP11 MUTATED`
TCGA-2J-AABR TCGA-S4-A8RO TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-AAUP 
       14.40        17.26        32.15        19.82        14.17 

$`AKAP11 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        12.92        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
           14.17             0.23 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           32.15            90.12 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
          17.260           15.205 
[1] "14.2 - 32.1 (17.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.9"
D510V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AKAP11 MUTATED         0        0        0         1         4         0
  AKAP11 WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  AKAP11 MUTATED          0
  AKAP11 WILD-TYPE        3
D510V3, multiclass
           clus
vv          AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  AKAP11 MUTATED    0  0     5
  AKAP11 WILD-TYPE  5 17    97
D510V4, multiclass
       clus
vv      AKAP11 MUTATED AKAP11 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V5, binary
                  cls
clus                0  1
  AKAP11 MUTATED    1  4
  AKAP11 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      1    4
  AKAP11 WILD-TYPE   34   85
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D510V6, binary
                  cls
clus                0  1
  AKAP11 MUTATED    4  0
  AKAP11 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      4    0
  AKAP11 WILD-TYPE   53    3
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D510V7, binary
                  cls
clus                0  1
  AKAP11 MUTATED    3  2
  AKAP11 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      3    2
  AKAP11 WILD-TYPE   48   73
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D510V8, binary
                  cls
clus                0  1
  AKAP11 MUTATED    3  2
  AKAP11 WILD-TYPE 85 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      3    2
  AKAP11 WILD-TYPE   85   28
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO               3               85
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AKAP11 MUTATED                                     4
  AKAP11 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AKAP11 MUTATED                                       1
  AKAP11 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AKAP11 MUTATED                                                  0
  AKAP11 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  AKAP11 MUTATED                                     0
  AKAP11 WILD-TYPE                                   1
D510V9, multiclass
                                                  clus
vv                                                 AKAP11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 AKAP11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V10, continuous
[1] "Remove cluster labels:" "AKAP11 MUTATED"        
clus
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
D510V11, continuous
[1] "Remove cluster labels:" "AKAP11 MUTATED"        
clus
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" "AKAP11 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  AKAP11 MUTATED    3  2  0  0
  AKAP11 WILD-TYPE 77 33  4  2
D510V12, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0              3               77
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKAP11 MUTATED       1                         0     4
  AKAP11 WILD-TYPE     5                         5   110
D510V14, multiclass
                           clus
vv                          AKAP11 MUTATED AKAP11 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V15, binary
                  cls
clus                0  1
  AKAP11 MUTATED    0  3
  AKAP11 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED      0    3
  AKAP11 WILD-TYPE    5   88
                        clus
vv                       AKAP11 MUTATED AKAP11 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(511) Variable = ENPP7 MUTATION ANALYSIS
D511V1, survival
                 sevent
clus2              0  1
  ENPP7 MUTATED    0  6
  ENPP7 WILD-TYPE 63 56
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              6             119 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              6              56 
$`ENPP7 MUTATED`
TCGA-US-A77E TCGA-2J-AAB1 TCGA-3E-AAAZ TCGA-FZ-5922 TCGA-IB-7651 TCGA-IB-AAUO 
       14.14         2.17        71.74        36.20        19.82         7.86 

$`ENPP7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
       24.36         2.01         5.10        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        4.73        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  ENPP7 MUTATED ENPP7 WILD-TYPE 
           2.17            0.23 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          71.74           90.12 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          16.98           15.22 
[1] "2.2 - 71.7 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D511V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ENPP7 MUTATED         0        0        0         2         4         0
  ENPP7 WILD-TYPE       1        3       12        17        78         4
                 vv
clus              STAGE IV
  ENPP7 MUTATED          0
  ENPP7 WILD-TYPE        3
D511V3, multiclass
           clus
vv          ENPP7 MUTATED ENPP7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ENPP7 MUTATED    0  0     6
  ENPP7 WILD-TYPE  5 17    96
D511V4, multiclass
       clus
vv      ENPP7 MUTATED ENPP7 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V5, binary
                 cls
clus               0  1
  ENPP7 MUTATED    2  4
  ENPP7 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      2    4
  ENPP7 WILD-TYPE   33   85
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D511V6, binary
                 cls
clus               0  1
  ENPP7 MUTATED    4  0
  ENPP7 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      4    0
  ENPP7 WILD-TYPE   53    3
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D511V7, binary
                 cls
clus               0  1
  ENPP7 MUTATED    2  4
  ENPP7 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      2    4
  ENPP7 WILD-TYPE   49   71
        clus
vv       ENPP7 MUTATED ENPP7 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D511V8, binary
                 cls
clus               0  1
  ENPP7 MUTATED    5  0
  ENPP7 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      5    0
  ENPP7 WILD-TYPE   83   30
     clus
vv    ENPP7 MUTATED ENPP7 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ENPP7 MUTATED                                     4
  ENPP7 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ENPP7 MUTATED                                       2
  ENPP7 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ENPP7 MUTATED                                                  0
  ENPP7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ENPP7 MUTATED                                     0
  ENPP7 WILD-TYPE                                   1
D511V9, multiclass
                                                  clus
vv                                                 ENPP7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ENPP7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V10, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AABA      TCGA-2J-AABE 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" 
D511V11, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AABE      TCGA-2J-AABF 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ENPP7 MUTATED    3  2  0  0
  ENPP7 WILD-TYPE 77 33  4  2
D511V12, multiclass
    clus
vv   ENPP7 MUTATED ENPP7 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENPP7 MUTATED       0                         0     6
  ENPP7 WILD-TYPE     6                         5   108
D511V14, multiclass
                           clus
vv                          ENPP7 MUTATED ENPP7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V15, binary
                 cls
clus               0  1
  ENPP7 MUTATED    1  4
  ENPP7 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      1    4
  ENPP7 WILD-TYPE    4   87
                        clus
vv                       ENPP7 MUTATED ENPP7 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(512) Variable = UNC5D MUTATION ANALYSIS
D512V1, survival
                 sevent
clus2              0  1
  UNC5D MUTATED    1  3
  UNC5D WILD-TYPE 62 59
  UNC5D MUTATED UNC5D WILD-TYPE 
              4             121 
  UNC5D MUTATED UNC5D WILD-TYPE 
              3              59 
$`UNC5D MUTATED`
TCGA-LB-A7SX TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-AAUN 
       12.92        19.82        15.19         4.73 

$`UNC5D WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  UNC5D MUTATED UNC5D WILD-TYPE 
           4.73            0.23 
  UNC5D MUTATED UNC5D WILD-TYPE 
          19.82           90.12 
  UNC5D MUTATED UNC5D WILD-TYPE 
         14.055          15.320 
[1] "4.7 - 19.8 (14.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.2"
D512V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UNC5D MUTATED         0        0        1         0         2         1
  UNC5D WILD-TYPE       1        3       11        19        80         3
                 vv
clus              STAGE IV
  UNC5D MUTATED          0
  UNC5D WILD-TYPE        3
D512V3, multiclass
           clus
vv          UNC5D MUTATED UNC5D WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  UNC5D MUTATED    0  1     3
  UNC5D WILD-TYPE  5 16    99
D512V4, multiclass
       clus
vv      UNC5D MUTATED UNC5D WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V5, binary
                 cls
clus               0  1
  UNC5D MUTATED    1  3
  UNC5D WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      1    3
  UNC5D WILD-TYPE   34   86
   clus
vv  UNC5D MUTATED UNC5D WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D512V6, binary
                 cls
clus               0  1
  UNC5D MUTATED    3  0
  UNC5D WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      3    0
  UNC5D WILD-TYPE   54    3
   clus
vv  UNC5D MUTATED UNC5D WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D512V7, binary
                 cls
clus               0  1
  UNC5D MUTATED    4  0
  UNC5D WILD-TYPE 47 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      4    0
  UNC5D WILD-TYPE   47   75
        clus
vv       UNC5D MUTATED UNC5D WILD-TYPE
  FEMALE             4              47
  MALE               0              75
[1] 2 2
[1] FALSE
D512V8, binary
                 cls
clus               0  1
  UNC5D MUTATED    4  0
  UNC5D WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      4    0
  UNC5D WILD-TYPE   84   30
     clus
vv    UNC5D MUTATED UNC5D WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UNC5D MUTATED                                     4
  UNC5D WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UNC5D MUTATED                                       0
  UNC5D WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UNC5D MUTATED                                                  0
  UNC5D WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  UNC5D MUTATED                                     0
  UNC5D WILD-TYPE                                   1
D512V9, multiclass
                                                  clus
vv                                                 UNC5D MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 UNC5D WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V10, continuous
D512V11, continuous
                 vv
clus              R0 R1 R2 RX
  UNC5D MUTATED    1  3  0  0
  UNC5D WILD-TYPE 79 32  4  2
D512V12, multiclass
    clus
vv   UNC5D MUTATED UNC5D WILD-TYPE
  R0             1              79
  R1             3              32
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC5D MUTATED       0                         1     3
  UNC5D WILD-TYPE     6                         4   111
D512V14, multiclass
                           clus
vv                          UNC5D MUTATED UNC5D WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V15, binary
                 cls
clus               0  1
  UNC5D MUTATED    0  4
  UNC5D WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      0    4
  UNC5D WILD-TYPE    5   87
                        clus
vv                       UNC5D MUTATED UNC5D WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(513) Variable = TTF1 MUTATION ANALYSIS
D513V1, survival
                sevent
clus2             0  1
  TTF1 MUTATED    3  1
  TTF1 WILD-TYPE 60 61
  TTF1 MUTATED TTF1 WILD-TYPE 
             4            121 
  TTF1 MUTATED TTF1 WILD-TYPE 
             1             61 
$`TTF1 MUTATED`
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-IB-7651 TCGA-IB-7652 
        8.28        30.25        19.82        36.69 

$`TTF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8X 
       36.20        20.35        17.79        22.06        32.15        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TTF1 MUTATED TTF1 WILD-TYPE 
          8.28           0.23 
  TTF1 MUTATED TTF1 WILD-TYPE 
         36.69          90.12 
  TTF1 MUTATED TTF1 WILD-TYPE 
        25.035         15.190 
[1] "8.3 - 36.7 (25.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.8"
D513V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TTF1 MUTATED         0        0        0         1         3         0
  TTF1 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  TTF1 MUTATED          0
  TTF1 WILD-TYPE        3
D513V3, multiclass
           clus
vv          TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TTF1 MUTATED    0  0     4
  TTF1 WILD-TYPE  5 17    98
D513V4, multiclass
       clus
vv      TTF1 MUTATED TTF1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V5, binary
                cls
clus              0  1
  TTF1 MUTATED    1  3
  TTF1 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      1    3
  TTF1 WILD-TYPE   34   86
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D513V6, binary
                cls
clus              0  1
  TTF1 MUTATED    2  0
  TTF1 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      2    0
  TTF1 WILD-TYPE   55    3
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D513V7, binary
                cls
clus              0  1
  TTF1 MUTATED    2  2
  TTF1 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      2    2
  TTF1 WILD-TYPE   49   73
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D513V8, binary
                cls
clus              0  1
  TTF1 MUTATED    4  0
  TTF1 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      4    0
  TTF1 WILD-TYPE   84   30
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TTF1 MUTATED                                     4
  TTF1 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TTF1 MUTATED                                       0
  TTF1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TTF1 MUTATED                                                  0
  TTF1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TTF1 MUTATED                                     0
  TTF1 WILD-TYPE                                   1
D513V9, multiclass
                                                  clus
vv                                                 TTF1 MUTATED TTF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V10, continuous
[1] "Remove cluster labels:" "TTF1 MUTATED"          
clus
  TTF1 MUTATED TTF1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-YY-A8LH 
"TTF1 WILD-TYPE" 
D513V11, continuous
[1] "Remove cluster labels:" "TTF1 MUTATED"          
clus
  TTF1 MUTATED TTF1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" "TTF1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TTF1 MUTATED    1  1  2  0
  TTF1 WILD-TYPE 79 34  2  2
D513V12, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0            1             79
  R1            1             34
  R2            2              2
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TTF1 MUTATED       3                         0     1
  TTF1 WILD-TYPE     3                         5   113
D513V14, multiclass
                           clus
vv                          TTF1 MUTATED TTF1 WILD-TYPE
  ASIAN                                3              3
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                1            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V15, binary
                cls
clus              0  1
  TTF1 MUTATED    0  2
  TTF1 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      0    2
  TTF1 WILD-TYPE    5   89
                        clus
vv                       TTF1 MUTATED TTF1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(514) Variable = CD93 MUTATION ANALYSIS
D514V1, survival
                sevent
clus2             0  1
  CD93 MUTATED    4  1
  CD93 WILD-TYPE 59 61
  CD93 MUTATED CD93 WILD-TYPE 
             5            120 
  CD93 MUTATED CD93 WILD-TYPE 
             1             61 
$`CD93 MUTATED`
TCGA-2J-AABP TCGA-3A-A9IV TCGA-F2-A8YN TCGA-IB-7651 TCGA-IB-A6UF 
       15.22        36.26        17.00        19.82        21.90 

$`CD93 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
        7.20        20.88         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CD93 MUTATED CD93 WILD-TYPE 
         15.22           0.23 
  CD93 MUTATED CD93 WILD-TYPE 
         36.26          90.12 
  CD93 MUTATED CD93 WILD-TYPE 
         19.82          15.09 
[1] "15.2 - 36.3 (19.8)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3.4"
D514V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CD93 MUTATED         0        0        1         1         3         0
  CD93 WILD-TYPE       1        3       11        18        79         4
                vv
clus             STAGE IV
  CD93 MUTATED          0
  CD93 WILD-TYPE        3
D514V3, multiclass
           clus
vv          CD93 MUTATED CD93 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CD93 MUTATED    0  1     4
  CD93 WILD-TYPE  5 16    98
D514V4, multiclass
       clus
vv      CD93 MUTATED CD93 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V5, binary
                cls
clus              0  1
  CD93 MUTATED    2  3
  CD93 WILD-TYPE 33 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      2    3
  CD93 WILD-TYPE   33   86
   clus
vv  CD93 MUTATED CD93 WILD-TYPE
  0            2             33
  1            3             86
[1] 2 2
[1] FALSE
D514V6, binary
                cls
clus              0  1
  CD93 MUTATED    4  0
  CD93 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      4    0
  CD93 WILD-TYPE   53    3
   clus
vv  CD93 MUTATED CD93 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D514V7, binary
                cls
clus              0  1
  CD93 MUTATED    3  2
  CD93 WILD-TYPE 48 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      3    2
  CD93 WILD-TYPE   48   73
        clus
vv       CD93 MUTATED CD93 WILD-TYPE
  FEMALE            3             48
  MALE              2             73
[1] 2 2
[1] FALSE
D514V8, binary
                cls
clus              0  1
  CD93 MUTATED    5  0
  CD93 WILD-TYPE 83 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      5    0
  CD93 WILD-TYPE   83   30
     clus
vv    CD93 MUTATED CD93 WILD-TYPE
  NO             5             83
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD93 MUTATED                                     3
  CD93 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD93 MUTATED                                       1
  CD93 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD93 MUTATED                                                  0
  CD93 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CD93 MUTATED                                     1
  CD93 WILD-TYPE                                   0
D514V9, multiclass
                                                  clus
vv                                                 CD93 MUTATED CD93 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         1              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V10, continuous
D514V11, continuous
[1] "Remove cluster labels:" "CD93 MUTATED"          
clus
  CD93 MUTATED CD93 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CD93 WILD-TYPE" "CD93 WILD-TYPE" "CD93 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CD93 MUTATED    3  2  0  0
  CD93 WILD-TYPE 77 33  4  2
D514V12, multiclass
    clus
vv   CD93 MUTATED CD93 WILD-TYPE
  R0            3             77
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD93 MUTATED       0                         0     5
  CD93 WILD-TYPE     6                         5   109
D514V14, multiclass
                           clus
vv                          CD93 MUTATED CD93 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V15, binary
                cls
clus              0  1
  CD93 MUTATED    0  4
  CD93 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD93 MUTATED      0    4
  CD93 WILD-TYPE    5   87
                        clus
vv                       CD93 MUTATED CD93 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(515) Variable = CEACAM8 MUTATION ANALYSIS
D515V1, survival
                   sevent
clus2                0  1
  CEACAM8 MUTATED    0  3
  CEACAM8 WILD-TYPE 63 59
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
                3               122 
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
                3                59 
$`CEACAM8 MUTATED`
TCGA-2L-AAQA TCGA-FB-AAPP TCGA-FZ-5920 
        4.70        15.95         2.01 

$`CEACAM8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        12.33        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
             2.01              0.23 
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
            15.95             90.12 
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
             4.70             15.27 
[1] "2.0 - 15.9 (4.7)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "5.6"
D515V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CEACAM8 MUTATED         0        0        0         0         3         0
  CEACAM8 WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  CEACAM8 MUTATED          0
  CEACAM8 WILD-TYPE        3
D515V3, multiclass
           clus
vv          CEACAM8 MUTATED CEACAM8 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CEACAM8 MUTATED    0  0     3
  CEACAM8 WILD-TYPE  5 17    99
D515V4, multiclass
       clus
vv      CEACAM8 MUTATED CEACAM8 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V5, binary
                   cls
clus                 0  1
  CEACAM8 MUTATED    0  3
  CEACAM8 WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM8 MUTATED      0    3
  CEACAM8 WILD-TYPE   35   86
   clus
vv  CEACAM8 MUTATED CEACAM8 WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D515V6, binary
                   cls
clus                 0  1
  CEACAM8 MUTATED    1  0
  CEACAM8 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM8 MUTATED      1    0
  CEACAM8 WILD-TYPE   56    3
   clus
vv  CEACAM8 MUTATED CEACAM8 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D515V7, binary
                   cls
clus                 0  1
  CEACAM8 MUTATED    0  3
  CEACAM8 WILD-TYPE 51 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM8 MUTATED      0    3
  CEACAM8 WILD-TYPE   51   72
        clus
vv       CEACAM8 MUTATED CEACAM8 WILD-TYPE
  FEMALE               0                51
  MALE                 3                72
[1] 2 2
[1] FALSE
D515V8, binary
                   cls
clus                 0  1
  CEACAM8 MUTATED    2  1
  CEACAM8 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM8 MUTATED      2    1
  CEACAM8 WILD-TYPE   86   29
     clus
vv    CEACAM8 MUTATED CEACAM8 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEACAM8 MUTATED                                     3
  CEACAM8 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEACAM8 MUTATED                                       0
  CEACAM8 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEACAM8 MUTATED                                                  0
  CEACAM8 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CEACAM8 MUTATED                                     0
  CEACAM8 WILD-TYPE                                   1
D515V9, multiclass
                                                  clus
vv                                                 CEACAM8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CEACAM8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V10, continuous
[1] "Remove cluster labels:" "CEACAM8 MUTATED"       
clus
  CEACAM8 MUTATED CEACAM8 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"CEACAM8 WILD-TYPE" "CEACAM8 WILD-TYPE" 
D515V11, continuous
                   vv
clus                R0 R1 R2 RX
  CEACAM8 MUTATED    2  1  0  0
  CEACAM8 WILD-TYPE 78 34  4  2
D515V12, multiclass
    clus
vv   CEACAM8 MUTATED CEACAM8 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM8 MUTATED       0                         1     2
  CEACAM8 WILD-TYPE     6                         4   112
D515V14, multiclass
                           clus
vv                          CEACAM8 MUTATED CEACAM8 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   2               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V15, binary
                   cls
clus                 0  1
  CEACAM8 MUTATED    0  2
  CEACAM8 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM8 MUTATED      0    2
  CEACAM8 WILD-TYPE    5   89
                        clus
vv                       CEACAM8 MUTATED CEACAM8 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(516) Variable = PARP1 MUTATION ANALYSIS
D516V1, survival
                 sevent
clus2              0  1
  PARP1 MUTATED    2  2
  PARP1 WILD-TYPE 61 60
  PARP1 MUTATED PARP1 WILD-TYPE 
              4             121 
  PARP1 MUTATED PARP1 WILD-TYPE 
              2              60 
$`PARP1 MUTATED`
TCGA-XD-AAUL TCGA-3A-A9I9 TCGA-IB-7651 TCGA-RB-AA9M 
       16.37        20.84        19.82         9.40 

$`PARP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12        15.32         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PARP1 MUTATED PARP1 WILD-TYPE 
           9.40            0.23 
  PARP1 MUTATED PARP1 WILD-TYPE 
          20.84           90.12 
  PARP1 MUTATED PARP1 WILD-TYPE 
         18.095          15.190 
[1] "9.4 - 20.8 (18.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D516V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PARP1 MUTATED         0        0        0         2         2         0
  PARP1 WILD-TYPE       1        3       12        17        80         4
                 vv
clus              STAGE IV
  PARP1 MUTATED          0
  PARP1 WILD-TYPE        3
D516V3, multiclass
           clus
vv          PARP1 MUTATED PARP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PARP1 MUTATED    1  0     3
  PARP1 WILD-TYPE  4 17    99
D516V4, multiclass
       clus
vv      PARP1 MUTATED PARP1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V5, binary
                 cls
clus               0  1
  PARP1 MUTATED    2  2
  PARP1 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      2    2
  PARP1 WILD-TYPE   33   87
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D516V6, binary
                 cls
clus               0  1
  PARP1 MUTATED    1  0
  PARP1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      1    0
  PARP1 WILD-TYPE   56    3
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D516V7, binary
                 cls
clus               0  1
  PARP1 MUTATED    1  3
  PARP1 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      1    3
  PARP1 WILD-TYPE   50   72
        clus
vv       PARP1 MUTATED PARP1 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D516V8, binary
                 cls
clus               0  1
  PARP1 MUTATED    2  2
  PARP1 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      2    2
  PARP1 WILD-TYPE   86   28
     clus
vv    PARP1 MUTATED PARP1 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PARP1 MUTATED                                     4
  PARP1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PARP1 MUTATED                                       0
  PARP1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PARP1 MUTATED                                                  0
  PARP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PARP1 MUTATED                                     0
  PARP1 WILD-TYPE                                   1
D516V9, multiclass
                                                  clus
vv                                                 PARP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PARP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V10, continuous
D516V11, continuous
[1] "Remove cluster labels:" "PARP1 MUTATED"         
clus
  PARP1 MUTATED PARP1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PARP1 WILD-TYPE" "PARP1 WILD-TYPE" "PARP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PARP1 MUTATED    4  0  0  0
  PARP1 WILD-TYPE 76 35  4  2
D516V12, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARP1 MUTATED       0                         0     4
  PARP1 WILD-TYPE     6                         5   110
D516V14, multiclass
                           clus
vv                          PARP1 MUTATED PARP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V15, binary
                 cls
clus               0  1
  PARP1 MUTATED    0  4
  PARP1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      0    4
  PARP1 WILD-TYPE    5   87
                        clus
vv                       PARP1 MUTATED PARP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(517) Variable = CRNN MUTATION ANALYSIS
D517V1, survival
                sevent
clus2             0  1
  CRNN MUTATED    5  5
  CRNN WILD-TYPE 58 57
  CRNN MUTATED CRNN WILD-TYPE 
            10            115 
  CRNN MUTATED CRNN WILD-TYPE 
             5             57 
$`CRNN MUTATED`
TCGA-2J-AAB1 TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABU TCGA-3A-A9IX TCGA-3A-A9J0 
        2.17        42.31        15.91         9.11        34.09        24.43 
TCGA-FB-AAPQ TCGA-IB-7651 TCGA-IB-AAUU TCGA-OE-A75W 
       37.15        19.82         8.05         8.78 

$`CRNN WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV 
       19.96        22.22        22.72        14.47        15.22        21.44 
TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM 
        4.70        22.49         3.39        12.95         9.60        45.47 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO 
       43.50        20.84         7.36        24.26        33.57        63.85 
TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3E-AAAY 
       50.70        32.81        15.06        36.26        10.13        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CRNN MUTATED CRNN WILD-TYPE 
          2.17           0.23 
  CRNN MUTATED CRNN WILD-TYPE 
         42.31          90.12 
  CRNN MUTATED CRNN WILD-TYPE 
        17.865         15.190 
[1] "2.2 - 42.3 (17.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D517V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CRNN MUTATED         0        1        0         2         7         0
  CRNN WILD-TYPE       1        2       12        17        75         4
                vv
clus             STAGE IV
  CRNN MUTATED          0
  CRNN WILD-TYPE        3
D517V3, multiclass
           clus
vv          CRNN MUTATED CRNN WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            7             75
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CRNN MUTATED    1  0     9
  CRNN WILD-TYPE  4 17    93
D517V4, multiclass
       clus
vv      CRNN MUTATED CRNN WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            9             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V5, binary
                cls
clus              0  1
  CRNN MUTATED    3  7
  CRNN WILD-TYPE 32 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRNN MUTATED      3    7
  CRNN WILD-TYPE   32   82
   clus
vv  CRNN MUTATED CRNN WILD-TYPE
  0            3             32
  1            7             82
[1] 2 2
[1] FALSE
D517V6, binary
                cls
clus              0  1
  CRNN MUTATED    7  0
  CRNN WILD-TYPE 50  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRNN MUTATED      7    0
  CRNN WILD-TYPE   50    3
   clus
vv  CRNN MUTATED CRNN WILD-TYPE
  0            7             50
  1            0              3
[1] 2 2
[1] FALSE
D517V7, binary
                cls
clus              0  1
  CRNN MUTATED    1  9
  CRNN WILD-TYPE 50 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRNN MUTATED      1    9
  CRNN WILD-TYPE   50   66
        clus
vv       CRNN MUTATED CRNN WILD-TYPE
  FEMALE            1             50
  MALE              9             66
[1] 2 2
[1] FALSE
D517V8, binary
                cls
clus              0  1
  CRNN MUTATED    7  3
  CRNN WILD-TYPE 81 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRNN MUTATED      7    3
  CRNN WILD-TYPE   81   27
     clus
vv    CRNN MUTATED CRNN WILD-TYPE
  NO             7             81
  YES            3             27
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CRNN MUTATED                                     8
  CRNN WILD-TYPE                                  97
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CRNN MUTATED                                       2
  CRNN WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CRNN MUTATED                                                  0
  CRNN WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CRNN MUTATED                                     0
  CRNN WILD-TYPE                                   1
D517V9, multiclass
                                                  clus
vv                                                 CRNN MUTATED CRNN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         8             97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V10, continuous
D517V11, continuous
                vv
clus             R0 R1 R2 RX
  CRNN MUTATED    9  1  0  0
  CRNN WILD-TYPE 71 34  4  2
D517V12, multiclass
    clus
vv   CRNN MUTATED CRNN WILD-TYPE
  R0            9             71
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRNN MUTATED       0                         0    10
  CRNN WILD-TYPE     6                         5   104
D517V14, multiclass
                           clus
vv                          CRNN MUTATED CRNN WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               10            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V15, binary
                cls
clus              0  1
  CRNN MUTATED    0  6
  CRNN WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRNN MUTATED      0    6
  CRNN WILD-TYPE    5   85
                        clus
vv                       CRNN MUTATED CRNN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(518) Variable = ZNF254 MUTATION ANALYSIS
D518V1, survival
                  sevent
clus2               0  1
  ZNF254 MUTATED    2  3
  ZNF254 WILD-TYPE 61 59
  ZNF254 MUTATED ZNF254 WILD-TYPE 
               5              120 
  ZNF254 MUTATED ZNF254 WILD-TYPE 
               3               59 
$`ZNF254 MUTATED`
TCGA-XD-AAUL TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-A7LX TCGA-IB-AAUQ 
       16.37         7.50        19.82         8.22         6.02 

$`ZNF254 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         1.35        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         4.73         7.86        14.17        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ZNF254 MUTATED ZNF254 WILD-TYPE 
            6.02             0.23 
  ZNF254 MUTATED ZNF254 WILD-TYPE 
           19.82            90.12 
  ZNF254 MUTATED ZNF254 WILD-TYPE 
            8.22            15.27 
[1] "6.0 - 19.8 (8.2)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D518V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF254 MUTATED         0        0        0         1         4         0
  ZNF254 WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  ZNF254 MUTATED          0
  ZNF254 WILD-TYPE        3
D518V3, multiclass
           clus
vv          ZNF254 MUTATED ZNF254 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ZNF254 MUTATED    0  1     4
  ZNF254 WILD-TYPE  5 16    98
D518V4, multiclass
       clus
vv      ZNF254 MUTATED ZNF254 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V5, binary
                  cls
clus                0  1
  ZNF254 MUTATED    1  4
  ZNF254 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF254 MUTATED      1    4
  ZNF254 WILD-TYPE   34   85
   clus
vv  ZNF254 MUTATED ZNF254 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D518V6, binary
                  cls
clus                0  1
  ZNF254 MUTATED    2  0
  ZNF254 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF254 MUTATED      2    0
  ZNF254 WILD-TYPE   55    3
   clus
vv  ZNF254 MUTATED ZNF254 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D518V7, binary
                  cls
clus                0  1
  ZNF254 MUTATED    2  3
  ZNF254 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF254 MUTATED      2    3
  ZNF254 WILD-TYPE   49   72
        clus
vv       ZNF254 MUTATED ZNF254 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D518V8, binary
                  cls
clus                0  1
  ZNF254 MUTATED    4  1
  ZNF254 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF254 MUTATED      4    1
  ZNF254 WILD-TYPE   84   29
     clus
vv    ZNF254 MUTATED ZNF254 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF254 MUTATED                                     5
  ZNF254 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF254 MUTATED                                       0
  ZNF254 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF254 MUTATED                                                  0
  ZNF254 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF254 MUTATED                                     0
  ZNF254 WILD-TYPE                                   1
D518V9, multiclass
                                                  clus
vv                                                 ZNF254 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF254 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V10, continuous
D518V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF254 MUTATED    4  1  0  0
  ZNF254 WILD-TYPE 76 34  4  2
D518V12, multiclass
    clus
vv   ZNF254 MUTATED ZNF254 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF254 MUTATED       0                         0     5
  ZNF254 WILD-TYPE     6                         5   109
D518V14, multiclass
                           clus
vv                          ZNF254 MUTATED ZNF254 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V15, binary
                  cls
clus                0  1
  ZNF254 MUTATED    0  5
  ZNF254 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF254 MUTATED      0    5
  ZNF254 WILD-TYPE    5   86
                        clus
vv                       ZNF254 MUTATED ZNF254 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(519) Variable = ADAM30 MUTATION ANALYSIS
D519V1, survival
                  sevent
clus2               0  1
  ADAM30 MUTATED    1  2
  ADAM30 WILD-TYPE 62 60
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               3              122 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               2               60 
$`ADAM30 MUTATED`
TCGA-F2-7273 TCGA-FB-AAPQ TCGA-HV-A7OL 
       19.46        37.15         8.28 

$`ADAM30 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            8.28             0.23 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           37.15            90.12 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          19.460           15.205 
[1] "8.3 - 37.1 (19.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D519V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ADAM30 MUTATED         0        0        0         1         2         0
  ADAM30 WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  ADAM30 MUTATED          0
  ADAM30 WILD-TYPE        3
D519V3, multiclass
           clus
vv          ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ADAM30 MUTATED    0  0     3
  ADAM30 WILD-TYPE  5 17    99
D519V4, multiclass
       clus
vv      ADAM30 MUTATED ADAM30 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V5, binary
                  cls
clus                0  1
  ADAM30 MUTATED    1  2
  ADAM30 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      1    2
  ADAM30 WILD-TYPE   34   87
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D519V6, binary
                  cls
clus                0  1
  ADAM30 MUTATED    1  0
  ADAM30 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      1    0
  ADAM30 WILD-TYPE   56    3
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D519V7, binary
                  cls
clus                0  1
  ADAM30 MUTATED    0  3
  ADAM30 WILD-TYPE 51 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      0    3
  ADAM30 WILD-TYPE   51   72
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              0               51
  MALE                3               72
[1] 2 2
[1] FALSE
D519V8, binary
                  cls
clus                0  1
  ADAM30 MUTATED    2  1
  ADAM30 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      2    1
  ADAM30 WILD-TYPE   86   29
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ADAM30 MUTATED                                     3
  ADAM30 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ADAM30 MUTATED                                       0
  ADAM30 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ADAM30 MUTATED                                                  0
  ADAM30 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ADAM30 MUTATED                                     0
  ADAM30 WILD-TYPE                                   1
D519V9, multiclass
                                                  clus
vv                                                 ADAM30 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ADAM30 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V10, continuous
[1] "Remove cluster labels:" "ADAM30 MUTATED"        
clus
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
D519V11, continuous
[1] "Remove cluster labels:" "ADAM30 MUTATED"        
clus
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ADAM30 MUTATED    1  1  1  0
  ADAM30 WILD-TYPE 79 34  3  2
D519V12, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0              1               79
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V13, continuous
[1] "Remove cluster labels:" "ADAM30 MUTATED"        
clus
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               2              122 
      TCGA-2J-AABR       TCGA-2J-AABT       TCGA-3A-A9I5       TCGA-3A-A9IJ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9IL       TCGA-F2-A44G       TCGA-FB-AAQ6       TCGA-FZ-5924 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-S4-A8RO       TCGA-US-A77E       TCGA-XD-AAUL       TCGA-2J-AAB1 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AAB4       TCGA-2J-AAB6       TCGA-2J-AAB8       TCGA-2J-AAB9 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABH 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AABK       TCGA-2J-AABO       TCGA-2J-AABP       TCGA-2J-AABU 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-2L-AAQI 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-2L-AAQJ       TCGA-2L-AAQL       TCGA-2L-AAQM       TCGA-3A-A9I7 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IC       TCGA-3A-A9IH 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9IR       TCGA-3A-A9IS       TCGA-3A-A9IU       TCGA-3A-A9IV 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-3A-A9IZ       TCGA-3A-A9J0       TCGA-3E-AAAY 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-3E-AAAZ       TCGA-F2-A7TX       TCGA-F2-A8YN       TCGA-FB-A5VM 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-FB-A78T       TCGA-FB-AAPP       TCGA-FB-AAPS       TCGA-FB-AAPU 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-FB-AAPZ       TCGA-FB-AAQ0       TCGA-FB-AAQ1       TCGA-FB-AAQ2 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-FB-AAQ3       TCGA-FZ-5919       TCGA-FZ-5920       TCGA-FZ-5921 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-FZ-5922       TCGA-FZ-5923       TCGA-FZ-5926       TCGA-H8-A6C1 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-HV-A7OP       TCGA-HV-AA8V       TCGA-HV-AA8X       TCGA-HZ-7918 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-HZ-7925       TCGA-HZ-8637       TCGA-HZ-A49I       TCGA-HZ-A77O 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-HZ-A77P       TCGA-HZ-A8P1       TCGA-HZ-A9TJ       TCGA-IB-7651 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-7652       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SO 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-A5SP       TCGA-IB-A5SQ       TCGA-IB-A5ST       TCGA-IB-A6UF 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7LX       TCGA-IB-A7M4       TCGA-IB-AAUM 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-AAUN       TCGA-IB-AAUO       TCGA-IB-AAUP       TCGA-IB-AAUQ 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-AAUR       TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-IB-AAUW       TCGA-LB-A8F3       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-Q3-A5QY       TCGA-Q3-AA2A       TCGA-RB-A7B8       TCGA-RB-AA9M 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-RL-AAAS       TCGA-US-A776       TCGA-US-A779       TCGA-US-A77G 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-US-A77J       TCGA-XD-AAUG       TCGA-XD-AAUH       TCGA-XD-AAUI 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-XN-A8T3       TCGA-XN-A8T5       TCGA-YB-A89D       TCGA-YH-A8SY 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
      TCGA-YY-A8LH       TCGA-Z5-AAPL 
"ADAM30 WILD-TYPE" "ADAM30 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED       1                         1     1
  ADAM30 WILD-TYPE     5                         4   113
D519V14, multiclass
                           clus
vv                          ADAM30 MUTATED ADAM30 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  1              113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V15, binary
                  cls
clus                0  1
  ADAM30 MUTATED    0  2
  ADAM30 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      0    2
  ADAM30 WILD-TYPE    5   89
                        clus
vv                       ADAM30 MUTATED ADAM30 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(520) Variable = DRD5 MUTATION ANALYSIS
D520V1, survival
                sevent
clus2             0  1
  DRD5 MUTATED    3  1
  DRD5 WILD-TYPE 60 61
  DRD5 MUTATED DRD5 WILD-TYPE 
             4            121 
  DRD5 MUTATED DRD5 WILD-TYPE 
             1             61 
$`DRD5 MUTATED`
TCGA-2J-AABO TCGA-FB-AAQ2 TCGA-H8-A6C1 TCGA-US-A776 
       14.47         5.03        22.06        39.98 

$`DRD5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  DRD5 MUTATED DRD5 WILD-TYPE 
          5.03           0.23 
  DRD5 MUTATED DRD5 WILD-TYPE 
         39.98          90.12 
  DRD5 MUTATED DRD5 WILD-TYPE 
        18.265         15.220 
[1] "5.0 - 40.0 (18.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.3"
D520V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DRD5 MUTATED         0        0        0         2         2         0
  DRD5 WILD-TYPE       1        3       12        17        80         4
                vv
clus             STAGE IV
  DRD5 MUTATED          0
  DRD5 WILD-TYPE        3
D520V3, multiclass
           clus
vv          DRD5 MUTATED DRD5 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  DRD5 MUTATED    0  0     4
  DRD5 WILD-TYPE  5 17    98
D520V4, multiclass
       clus
vv      DRD5 MUTATED DRD5 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V5, binary
                cls
clus              0  1
  DRD5 MUTATED    2  2
  DRD5 WILD-TYPE 33 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD5 MUTATED      2    2
  DRD5 WILD-TYPE   33   87
   clus
vv  DRD5 MUTATED DRD5 WILD-TYPE
  0            2             33
  1            2             87
[1] 2 2
[1] FALSE
D520V6, binary
                cls
clus              0  1
  DRD5 MUTATED    1  0
  DRD5 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD5 MUTATED      1    0
  DRD5 WILD-TYPE   56    3
   clus
vv  DRD5 MUTATED DRD5 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D520V7, binary
                cls
clus              0  1
  DRD5 MUTATED    1  3
  DRD5 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD5 MUTATED      1    3
  DRD5 WILD-TYPE   50   72
        clus
vv       DRD5 MUTATED DRD5 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D520V8, binary
                cls
clus              0  1
  DRD5 MUTATED    3  1
  DRD5 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD5 MUTATED      3    1
  DRD5 WILD-TYPE   85   29
     clus
vv    DRD5 MUTATED DRD5 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DRD5 MUTATED                                     2
  DRD5 WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DRD5 MUTATED                                       1
  DRD5 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DRD5 MUTATED                                                  1
  DRD5 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  DRD5 MUTATED                                     0
  DRD5 WILD-TYPE                                   1
D520V9, multiclass
                                                  clus
vv                                                 DRD5 MUTATED DRD5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V10, continuous
[1] "Remove cluster labels:" "DRD5 MUTATED"          
clus
  DRD5 MUTATED DRD5 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABV     TCGA-2L-AAQA 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-YY-A8LH 
"DRD5 WILD-TYPE" 
D520V11, continuous
[1] "Remove cluster labels:" "DRD5 MUTATED"          
clus
  DRD5 MUTATED DRD5 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"DRD5 WILD-TYPE" "DRD5 WILD-TYPE" "DRD5 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  DRD5 MUTATED    3  1  0  0
  DRD5 WILD-TYPE 77 34  4  2
D520V12, multiclass
    clus
vv   DRD5 MUTATED DRD5 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DRD5 MUTATED       0                         0     4
  DRD5 WILD-TYPE     6                         5   110
D520V14, multiclass
                           clus
vv                          DRD5 MUTATED DRD5 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V15, binary
                cls
clus              0  1
  DRD5 MUTATED    0  3
  DRD5 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD5 MUTATED      0    3
  DRD5 WILD-TYPE    5   88
                        clus
vv                       DRD5 MUTATED DRD5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(521) Variable = MKI67IP MUTATION ANALYSIS
D521V1, survival
                   sevent
clus2                0  1
  MKI67IP MUTATED    2  2
  MKI67IP WILD-TYPE 61 60
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                4               121 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
                2                60 
$`MKI67IP MUTATED`
TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7M4 
        1.08        19.82         1.35        15.88 

$`MKI67IP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MKI67IP MUTATED MKI67IP WILD-TYPE 
             1.08              0.23 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
            19.82             90.12 
  MKI67IP MUTATED MKI67IP WILD-TYPE 
            8.615            15.220 
[1] "1.1 - 19.8 (8.6)"  "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D521V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MKI67IP MUTATED         0        0        0         0         4         0
  MKI67IP WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  MKI67IP MUTATED          0
  MKI67IP WILD-TYPE        3
D521V3, multiclass
           clus
vv          MKI67IP MUTATED MKI67IP WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  MKI67IP MUTATED    0  0     4
  MKI67IP WILD-TYPE  5 17    98
D521V4, multiclass
       clus
vv      MKI67IP MUTATED MKI67IP WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V5, binary
                   cls
clus                 0  1
  MKI67IP MUTATED    0  4
  MKI67IP WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      0    4
  MKI67IP WILD-TYPE   35   85
   clus
vv  MKI67IP MUTATED MKI67IP WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D521V6, binary
                   cls
clus                 0  1
  MKI67IP MUTATED    2  0
  MKI67IP WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      2    0
  MKI67IP WILD-TYPE   55    3
   clus
vv  MKI67IP MUTATED MKI67IP WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D521V7, binary
                   cls
clus                 0  1
  MKI67IP MUTATED    2  2
  MKI67IP WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      2    2
  MKI67IP WILD-TYPE   49   73
        clus
vv       MKI67IP MUTATED MKI67IP WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D521V8, binary
                   cls
clus                 0  1
  MKI67IP MUTATED    3  0
  MKI67IP WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      3    0
  MKI67IP WILD-TYPE   85   30
     clus
vv    MKI67IP MUTATED MKI67IP WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MKI67IP MUTATED                                     3
  MKI67IP WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MKI67IP MUTATED                                       1
  MKI67IP WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MKI67IP MUTATED                                                  0
  MKI67IP WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  MKI67IP MUTATED                                     0
  MKI67IP WILD-TYPE                                   1
D521V9, multiclass
                                                  clus
vv                                                 MKI67IP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 MKI67IP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V10, continuous
D521V11, continuous
                   vv
clus                R0 R1 R2 RX
  MKI67IP MUTATED    3  1  0  0
  MKI67IP WILD-TYPE 77 34  4  2
D521V12, multiclass
    clus
vv   MKI67IP MUTATED MKI67IP WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MKI67IP MUTATED       0                         0     4
  MKI67IP WILD-TYPE     6                         5   110
D521V14, multiclass
                           clus
vv                          MKI67IP MUTATED MKI67IP WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V15, binary
                   cls
clus                 0  1
  MKI67IP MUTATED    0  4
  MKI67IP WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MKI67IP MUTATED      0    4
  MKI67IP WILD-TYPE    5   87
                        clus
vv                       MKI67IP MUTATED MKI67IP WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(522) Variable = SYNPO2L MUTATION ANALYSIS
D522V1, survival
                   sevent
clus2                0  1
  SYNPO2L MUTATED    2  4
  SYNPO2L WILD-TYPE 61 58
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
                6               119 
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
                4                58 
$`SYNPO2L MUTATED`
TCGA-IB-A5SS TCGA-LB-A7SX TCGA-3A-A9I9 TCGA-FB-AAPS TCGA-HZ-A77P TCGA-IB-7651 
       15.12        12.92        20.84         7.50        10.85        19.82 

$`SYNPO2L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        8.02        15.78         1.08        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
        9.60        45.47        43.50         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU 
       17.00        16.37        12.33        15.95        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       17.00        10.13         5.26         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
             7.50              0.23 
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
            20.84             90.12 
  SYNPO2L MUTATED SYNPO2L WILD-TYPE 
            14.02             15.32 
[1] "7.5 - 20.8 (14.0)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.6"
D522V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SYNPO2L MUTATED         0        0        0         1         5         0
  SYNPO2L WILD-TYPE       1        3       12        18        77         4
                   vv
clus                STAGE IV
  SYNPO2L MUTATED          0
  SYNPO2L WILD-TYPE        3
D522V3, multiclass
           clus
vv          SYNPO2L MUTATED SYNPO2L WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SYNPO2L MUTATED    0  1     5
  SYNPO2L WILD-TYPE  5 16    97
D522V4, multiclass
       clus
vv      SYNPO2L MUTATED SYNPO2L WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V5, binary
                   cls
clus                 0  1
  SYNPO2L MUTATED    1  5
  SYNPO2L WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNPO2L MUTATED      1    5
  SYNPO2L WILD-TYPE   34   84
   clus
vv  SYNPO2L MUTATED SYNPO2L WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D522V6, binary
                   cls
clus                 0  1
  SYNPO2L MUTATED    2  0
  SYNPO2L WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNPO2L MUTATED      2    0
  SYNPO2L WILD-TYPE   55    3
   clus
vv  SYNPO2L MUTATED SYNPO2L WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D522V7, binary
                   cls
clus                 0  1
  SYNPO2L MUTATED    4  2
  SYNPO2L WILD-TYPE 47 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNPO2L MUTATED      4    2
  SYNPO2L WILD-TYPE   47   73
        clus
vv       SYNPO2L MUTATED SYNPO2L WILD-TYPE
  FEMALE               4                47
  MALE                 2                73
[1] 2 2
[1] FALSE
D522V8, binary
                   cls
clus                 0  1
  SYNPO2L MUTATED    4  2
  SYNPO2L WILD-TYPE 84 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNPO2L MUTATED      4    2
  SYNPO2L WILD-TYPE   84   28
     clus
vv    SYNPO2L MUTATED SYNPO2L WILD-TYPE
  NO                4                84
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYNPO2L MUTATED                                     5
  SYNPO2L WILD-TYPE                                 100
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYNPO2L MUTATED                                       1
  SYNPO2L WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYNPO2L MUTATED                                                  0
  SYNPO2L WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SYNPO2L MUTATED                                     0
  SYNPO2L WILD-TYPE                                   1
D522V9, multiclass
                                                  clus
vv                                                 SYNPO2L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SYNPO2L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V10, continuous
D522V11, continuous
                   vv
clus                R0 R1 R2 RX
  SYNPO2L MUTATED    5  1  0  0
  SYNPO2L WILD-TYPE 75 34  4  2
D522V12, multiclass
    clus
vv   SYNPO2L MUTATED SYNPO2L WILD-TYPE
  R0               5                75
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNPO2L MUTATED       0                         1     5
  SYNPO2L WILD-TYPE     6                         4   109
D522V14, multiclass
                           clus
vv                          SYNPO2L MUTATED SYNPO2L WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V15, binary
                   cls
clus                 0  1
  SYNPO2L MUTATED    0  6
  SYNPO2L WILD-TYPE  5 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNPO2L MUTATED      0    6
  SYNPO2L WILD-TYPE    5   85
                        clus
vv                       SYNPO2L MUTATED SYNPO2L WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                85
[1] 2 2
[1] FALSE

Clustering(523) Variable = PROX1 MUTATION ANALYSIS
D523V1, survival
                 sevent
clus2              0  1
  PROX1 MUTATED    1  3
  PROX1 WILD-TYPE 62 59
  PROX1 MUTATED PROX1 WILD-TYPE 
              4             121 
  PROX1 MUTATED PROX1 WILD-TYPE 
              3              59 
$`PROX1 MUTATED`
TCGA-LB-A7SX TCGA-IB-7651 TCGA-IB-AAUP TCGA-RB-A7B8 
       12.92        19.82        14.17        15.32 

$`PROX1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73         7.86         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PROX1 MUTATED PROX1 WILD-TYPE 
          12.92            0.23 
  PROX1 MUTATED PROX1 WILD-TYPE 
          19.82           90.12 
  PROX1 MUTATED PROX1 WILD-TYPE 
         14.745          15.220 
[1] "12.9 - 19.8 (14.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.8"
D523V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PROX1 MUTATED         0        0        0         0         4         0
  PROX1 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  PROX1 MUTATED          0
  PROX1 WILD-TYPE        3
D523V3, multiclass
           clus
vv          PROX1 MUTATED PROX1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PROX1 MUTATED    0  0     4
  PROX1 WILD-TYPE  5 17    98
D523V4, multiclass
       clus
vv      PROX1 MUTATED PROX1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V5, binary
                 cls
clus               0  1
  PROX1 MUTATED    0  4
  PROX1 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      0    4
  PROX1 WILD-TYPE   35   85
   clus
vv  PROX1 MUTATED PROX1 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D523V6, binary
                 cls
clus               0  1
  PROX1 MUTATED    2  0
  PROX1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      2    0
  PROX1 WILD-TYPE   55    3
   clus
vv  PROX1 MUTATED PROX1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D523V7, binary
                 cls
clus               0  1
  PROX1 MUTATED    3  1
  PROX1 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      3    1
  PROX1 WILD-TYPE   48   74
        clus
vv       PROX1 MUTATED PROX1 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D523V8, binary
                 cls
clus               0  1
  PROX1 MUTATED    4  0
  PROX1 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      4    0
  PROX1 WILD-TYPE   84   30
     clus
vv    PROX1 MUTATED PROX1 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PROX1 MUTATED                                     3
  PROX1 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PROX1 MUTATED                                       1
  PROX1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PROX1 MUTATED                                                  0
  PROX1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PROX1 MUTATED                                     0
  PROX1 WILD-TYPE                                   1
D523V9, multiclass
                                                  clus
vv                                                 PROX1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PROX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V10, continuous
[1] "Remove cluster labels:" "PROX1 MUTATED"         
clus
  PROX1 MUTATED PROX1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-YY-A8LH 
"PROX1 WILD-TYPE" 
D523V11, continuous
[1] "Remove cluster labels:" "PROX1 MUTATED"         
clus
  PROX1 MUTATED PROX1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PROX1 MUTATED    2  2  0  0
  PROX1 WILD-TYPE 78 33  4  2
D523V12, multiclass
    clus
vv   PROX1 MUTATED PROX1 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PROX1 MUTATED       0                         1     3
  PROX1 WILD-TYPE     6                         4   111
D523V14, multiclass
                           clus
vv                          PROX1 MUTATED PROX1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V15, binary
                 cls
clus               0  1
  PROX1 MUTATED    0  4
  PROX1 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      0    4
  PROX1 WILD-TYPE    5   87
                        clus
vv                       PROX1 MUTATED PROX1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(524) Variable = KLK15 MUTATION ANALYSIS
D524V1, survival
                 sevent
clus2              0  1
  KLK15 MUTATED    3  3
  KLK15 WILD-TYPE 60 59
  KLK15 MUTATED KLK15 WILD-TYPE 
              6             119 
  KLK15 MUTATED KLK15 WILD-TYPE 
              3              59 
$`KLK15 MUTATED`
TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-2J-AAB9 TCGA-3A-A9J0 TCGA-IB-7651 TCGA-IB-A6UG 
       58.98        60.95        20.61        24.43        19.82         1.35 

$`KLK15 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        10.49        90.12         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        19.96        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88        21.90         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  KLK15 MUTATED KLK15 WILD-TYPE 
           1.35            0.23 
  KLK15 MUTATED KLK15 WILD-TYPE 
          60.95           90.12 
  KLK15 MUTATED KLK15 WILD-TYPE 
          22.52           15.12 
[1] "1.4 - 61.0 (22.5)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.5"
D524V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KLK15 MUTATED         0        0        1         0         4         0
  KLK15 WILD-TYPE       1        3       11        19        78         4
                 vv
clus              STAGE IV
  KLK15 MUTATED          0
  KLK15 WILD-TYPE        3
D524V3, multiclass
           clus
vv          KLK15 MUTATED KLK15 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KLK15 MUTATED    0  1     4
  KLK15 WILD-TYPE  5 16    98
D524V4, multiclass
       clus
vv      KLK15 MUTATED KLK15 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V5, binary
                 cls
clus               0  1
  KLK15 MUTATED    2  4
  KLK15 WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      2    4
  KLK15 WILD-TYPE   33   85
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D524V6, binary
                 cls
clus               0  1
  KLK15 MUTATED    3  0
  KLK15 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      3    0
  KLK15 WILD-TYPE   54    3
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D524V7, binary
                 cls
clus               0  1
  KLK15 MUTATED    2  4
  KLK15 WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      2    4
  KLK15 WILD-TYPE   49   71
        clus
vv       KLK15 MUTATED KLK15 WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D524V8, binary
                 cls
clus               0  1
  KLK15 MUTATED    4  2
  KLK15 WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      4    2
  KLK15 WILD-TYPE   84   28
     clus
vv    KLK15 MUTATED KLK15 WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK15 MUTATED                                     5
  KLK15 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK15 MUTATED                                       1
  KLK15 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK15 MUTATED                                                  0
  KLK15 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KLK15 MUTATED                                     0
  KLK15 WILD-TYPE                                   1
D524V9, multiclass
                                                  clus
vv                                                 KLK15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KLK15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V10, continuous
D524V11, continuous
                 vv
clus              R0 R1 R2 RX
  KLK15 MUTATED    5  1  0  0
  KLK15 WILD-TYPE 75 34  4  2
D524V12, multiclass
    clus
vv   KLK15 MUTATED KLK15 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK15 MUTATED       0                         0     6
  KLK15 WILD-TYPE     6                         5   108
D524V14, multiclass
                           clus
vv                          KLK15 MUTATED KLK15 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V15, binary
                 cls
clus               0  1
  KLK15 MUTATED    0  5
  KLK15 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      0    5
  KLK15 WILD-TYPE    5   86
                        clus
vv                       KLK15 MUTATED KLK15 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(525) Variable = C14ORF115 MUTATION ANALYSIS
D525V1, survival
                     sevent
clus2                  0  1
  C14ORF115 MUTATED    1  1
  C14ORF115 WILD-TYPE 62 61
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  2                 123 
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  1                  61 
$`C14ORF115 MUTATED`
TCGA-IB-7651 TCGA-YB-A89D 
       19.82        11.51 

$`C14ORF115 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
              11.51                0.23 
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
              19.82               90.12 
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
             15.665              15.220 
[1] "11.5 - 19.8 (15.7)" "0.2 - 90.1 (15.2)" 
[1] "Remove cluster labels:" "C14ORF115 MUTATED"     
D525V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C14ORF115 MUTATED         0        0        0         0         3         0
  C14ORF115 WILD-TYPE       1        3       12        19        79         4
                     vv
clus                  STAGE IV
  C14ORF115 MUTATED          0
  C14ORF115 WILD-TYPE        3
D525V3, multiclass
           clus
vv          C14ORF115 MUTATED C14ORF115 WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  0                   3
  STAGE IB                  0                  12
  STAGE IIA                 0                  19
  STAGE IIB                 3                  79
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3+T4
  C14ORF115 MUTATED    0  0     3
  C14ORF115 WILD-TYPE  5 17    99
D525V4, multiclass
       clus
vv      C14ORF115 MUTATED C14ORF115 WILD-TYPE
  T1                    0                   5
  T2                    0                  17
  T3+T4                 3                  99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V5, binary
                     cls
clus                   0  1
  C14ORF115 MUTATED    0  3
  C14ORF115 WILD-TYPE 35 86
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF115 MUTATED      0    3
  C14ORF115 WILD-TYPE   35   86
   clus
vv  C14ORF115 MUTATED C14ORF115 WILD-TYPE
  0                 0                  35
  1                 3                  86
[1] 2 2
[1] FALSE
D525V6, binary
                     cls
clus                   0  1
  C14ORF115 MUTATED    1  0
  C14ORF115 WILD-TYPE 56  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF115 MUTATED      1    0
  C14ORF115 WILD-TYPE   56    3
   clus
vv  C14ORF115 MUTATED C14ORF115 WILD-TYPE
  0                 1                  56
  1                 0                   3
[1] 2 2
[1] FALSE
D525V7, binary
                     cls
clus                   0  1
  C14ORF115 MUTATED    1  2
  C14ORF115 WILD-TYPE 50 73
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF115 MUTATED      1    2
  C14ORF115 WILD-TYPE   50   73
        clus
vv       C14ORF115 MUTATED C14ORF115 WILD-TYPE
  FEMALE                 1                  50
  MALE                   2                  73
[1] 2 2
[1] FALSE
D525V8, binary
                     cls
clus                   0  1
  C14ORF115 MUTATED    1  1
  C14ORF115 WILD-TYPE 87 29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF115 MUTATED      1    1
  C14ORF115 WILD-TYPE   87   29
     clus
vv    C14ORF115 MUTATED C14ORF115 WILD-TYPE
  NO                  1                  87
  YES                 1                  29
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C14ORF115 MUTATED                                     3
  C14ORF115 WILD-TYPE                                 102
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C14ORF115 MUTATED                                       0
  C14ORF115 WILD-TYPE                                    18
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C14ORF115 MUTATED                                                  0
  C14ORF115 WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  C14ORF115 MUTATED                                     0
  C14ORF115 WILD-TYPE                                   1
D525V9, multiclass
                                                  clus
vv                                                 C14ORF115 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 C14ORF115 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V10, continuous
[1] "Remove cluster labels:" "C14ORF115 MUTATED"     
clus
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  2                  37 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-IB-A5SS 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-LB-A7SX          TCGA-XD-AAUL          TCGA-2J-AAB1 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-2J-AABA          TCGA-2J-AABE          TCGA-2J-AABF 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-2J-AABO          TCGA-2J-AABV          TCGA-2L-AAQA 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-2L-AAQE          TCGA-3A-A9I9          TCGA-3A-A9IB 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-F2-A8YN          TCGA-FB-A5VM 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-FB-A78T          TCGA-FB-AAPQ          TCGA-FB-AAPS 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-H8-A6C1          TCGA-HV-AA8V          TCGA-HZ-A8P1 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-7885          TCGA-IB-8126          TCGA-IB-A6UF 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-A6UG          TCGA-IB-A7M4          TCGA-IB-AAUQ 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-AAUS          TCGA-IB-AAUU          TCGA-IB-AAUV 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XN-A8T5 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-YY-A8LH 
"C14ORF115 WILD-TYPE" 
D525V11, continuous
[1] "Remove cluster labels:" "C14ORF115 MUTATED"     
clus
  C14ORF115 MUTATED C14ORF115 WILD-TYPE 
                  2                  31 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-IB-A5SS 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-LB-A7SX          TCGA-XD-AAUL          TCGA-2J-AAB1 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-2J-AABE          TCGA-2J-AABF          TCGA-2J-AABO 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IR          TCGA-3A-A9IX 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-FB-A5VM          TCGA-FB-A78T          TCGA-FB-AAPQ 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-H8-A6C1          TCGA-HZ-A8P1 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-7885          TCGA-IB-8126          TCGA-IB-A6UF 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-A6UG          TCGA-IB-A7M4          TCGA-IB-AAUQ 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-IB-AAUS          TCGA-IB-AAUV          TCGA-LB-A9Q5 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-OE-A75W          TCGA-XD-AAUI          TCGA-XN-A8T5 
"C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" "C14ORF115 WILD-TYPE" 
         TCGA-YY-A8LH 
"C14ORF115 WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  C14ORF115 MUTATED    3  0  0  0
  C14ORF115 WILD-TYPE 77 35  4  2
D525V12, multiclass
    clus
vv   C14ORF115 MUTATED C14ORF115 WILD-TYPE
  R0                 3                  77
  R1                 0                  35
  R2                 0                   4
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF115 MUTATED       0                         0     3
  C14ORF115 WILD-TYPE     6                         5   111
D525V14, multiclass
                           clus
vv                          C14ORF115 MUTATED C14ORF115 WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     3                 111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V15, binary
                     cls
clus                   0  1
  C14ORF115 MUTATED    0  3
  C14ORF115 WILD-TYPE  5 88
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF115 MUTATED      0    3
  C14ORF115 WILD-TYPE    5   88
                        clus
vv                       C14ORF115 MUTATED C14ORF115 WILD-TYPE
  HISPANIC OR LATINO                     0                   5
  NOT HISPANIC OR LATINO                 3                  88
[1] 2 2
[1] FALSE

Clustering(526) Variable = SNIP1 MUTATION ANALYSIS
D526V1, survival
                 sevent
clus2              0  1
  SNIP1 MUTATED    2  1
  SNIP1 WILD-TYPE 61 61
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              3             122 
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              1              61 
$`SNIP1 MUTATED`
TCGA-3A-A9IR TCGA-F2-A8YN TCGA-IB-7651 
       50.70        17.00        19.82 

$`SNIP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SNIP1 MUTATED SNIP1 WILD-TYPE 
          17.00            0.23 
  SNIP1 MUTATED SNIP1 WILD-TYPE 
          50.70           90.12 
  SNIP1 MUTATED SNIP1 WILD-TYPE 
         19.820          15.155 
[1] "17.0 - 50.7 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.2"
D526V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SNIP1 MUTATED         0        0        1         1         1         0
  SNIP1 WILD-TYPE       1        3       11        18        81         4
                 vv
clus              STAGE IV
  SNIP1 MUTATED          0
  SNIP1 WILD-TYPE        3
D526V3, multiclass
           clus
vv          SNIP1 MUTATED SNIP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SNIP1 MUTATED     0   1     2
  SNIP1 WILD-TYPE   5  16   100
D526V4, multiclass
       clus
vv      SNIP1 MUTATED SNIP1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V5, binary
                 cls
clus               0  1
  SNIP1 MUTATED    2  1
  SNIP1 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNIP1 MUTATED      2    1
  SNIP1 WILD-TYPE   33   88
   clus
vv  SNIP1 MUTATED SNIP1 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D526V6, binary
                 cls
clus               0  1
  SNIP1 MUTATED    2  0
  SNIP1 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNIP1 MUTATED      2    0
  SNIP1 WILD-TYPE   55    3
   clus
vv  SNIP1 MUTATED SNIP1 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D526V7, binary
                 cls
clus               0  1
  SNIP1 MUTATED    2  1
  SNIP1 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNIP1 MUTATED      2    1
  SNIP1 WILD-TYPE   49   74
        clus
vv       SNIP1 MUTATED SNIP1 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D526V8, binary
                 cls
clus               0  1
  SNIP1 MUTATED    3  0
  SNIP1 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNIP1 MUTATED      3    0
  SNIP1 WILD-TYPE   85   30
     clus
vv    SNIP1 MUTATED SNIP1 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SNIP1 MUTATED                                     2
  SNIP1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SNIP1 MUTATED                                       1
  SNIP1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SNIP1 MUTATED                                                  0
  SNIP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SNIP1 MUTATED                                     0
  SNIP1 WILD-TYPE                                   1
D526V9, multiclass
                                                  clus
vv                                                 SNIP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SNIP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V10, continuous
[1] "Remove cluster labels:" "SNIP1 MUTATED"         
clus
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-YY-A8LH 
"SNIP1 WILD-TYPE" 
D526V11, continuous
[1] "Remove cluster labels:" "SNIP1 MUTATED"         
clus
  SNIP1 MUTATED SNIP1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IX 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" "SNIP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SNIP1 MUTATED    2  1  0  0
  SNIP1 WILD-TYPE 78 34  4  2
D526V12, multiclass
    clus
vv   SNIP1 MUTATED SNIP1 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNIP1 MUTATED       0                         0     3
  SNIP1 WILD-TYPE     6                         5   111
D526V14, multiclass
                           clus
vv                          SNIP1 MUTATED SNIP1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V15, binary
                 cls
clus               0  1
  SNIP1 MUTATED    0  3
  SNIP1 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNIP1 MUTATED      0    3
  SNIP1 WILD-TYPE    5   88
                        clus
vv                       SNIP1 MUTATED SNIP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(527) Variable = MAP7D3 MUTATION ANALYSIS
D527V1, survival
                  sevent
clus2               0  1
  MAP7D3 MUTATED    3  1
  MAP7D3 WILD-TYPE 60 61
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               4              121 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               1               61 
$`MAP7D3 MUTATED`
TCGA-3A-A9IL TCGA-2J-AABO TCGA-IB-7651 TCGA-IB-A6UF 
       90.12        14.47        19.82        21.90 

$`MAP7D3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABP 
       19.96        22.22        22.72        42.31        15.91        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           14.47             0.23 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           90.12            75.12 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           20.86            15.19 
[1] "14.5 - 90.1 (20.9)" "0.2 - 75.1 (15.2)" 
[1] "hr=" "3.3"
D527V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MAP7D3 MUTATED         1        0        0         0         3         0
  MAP7D3 WILD-TYPE       0        3       12        19        79         4
                  vv
clus               STAGE IV
  MAP7D3 MUTATED          0
  MAP7D3 WILD-TYPE        3
D527V3, multiclass
           clus
vv          MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  MAP7D3 MUTATED    1  0     3
  MAP7D3 WILD-TYPE  4 17    99
D527V4, multiclass
       clus
vv      MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V5, binary
                  cls
clus                0  1
  MAP7D3 MUTATED    0  3
  MAP7D3 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      0    3
  MAP7D3 WILD-TYPE   35   86
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D527V6, binary
                  cls
clus                0  1
  MAP7D3 MUTATED    3  0
  MAP7D3 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      3    0
  MAP7D3 WILD-TYPE   54    3
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D527V7, binary
                  cls
clus                0  1
  MAP7D3 MUTATED    2  2
  MAP7D3 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      2    2
  MAP7D3 WILD-TYPE   49   73
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D527V8, binary
                  cls
clus                0  1
  MAP7D3 MUTATED    3  1
  MAP7D3 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      3    1
  MAP7D3 WILD-TYPE   85   29
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAP7D3 MUTATED                                     3
  MAP7D3 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAP7D3 MUTATED                                       1
  MAP7D3 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAP7D3 MUTATED                                                  0
  MAP7D3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  MAP7D3 MUTATED                                     0
  MAP7D3 WILD-TYPE                                   1
D527V9, multiclass
                                                  clus
vv                                                 MAP7D3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 MAP7D3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V10, continuous
D527V11, continuous
                  vv
clus               R0 R1 R2 RX
  MAP7D3 MUTATED    3  1  0  0
  MAP7D3 WILD-TYPE 77 34  4  2
D527V12, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP7D3 MUTATED       0                         0     4
  MAP7D3 WILD-TYPE     6                         5   110
D527V14, multiclass
                           clus
vv                          MAP7D3 MUTATED MAP7D3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V15, binary
                  cls
clus                0  1
  MAP7D3 MUTATED    0  3
  MAP7D3 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED      0    3
  MAP7D3 WILD-TYPE    5   88
                        clus
vv                       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(528) Variable = RBM16 MUTATION ANALYSIS
D528V1, survival
                 sevent
clus2              0  1
  RBM16 MUTATED    0  4
  RBM16 WILD-TYPE 63 58
  RBM16 MUTATED RBM16 WILD-TYPE 
              4             121 
  RBM16 MUTATED RBM16 WILD-TYPE 
              4              58 
$`RBM16 MUTATED`
TCGA-FB-AAQ3 TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-AAUW 
        1.02        17.49        19.82         7.56 

$`RBM16 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         5.03        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RBM16 MUTATED RBM16 WILD-TYPE 
           1.02            0.23 
  RBM16 MUTATED RBM16 WILD-TYPE 
          19.82           90.12 
  RBM16 MUTATED RBM16 WILD-TYPE 
         12.525          15.220 
[1] "1.0 - 19.8 (12.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "3.2"
D528V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RBM16 MUTATED         0        0        0         0         4         0
  RBM16 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  RBM16 MUTATED          0
  RBM16 WILD-TYPE        3
D528V3, multiclass
           clus
vv          RBM16 MUTATED RBM16 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  RBM16 MUTATED    0  1     3
  RBM16 WILD-TYPE  5 16    99
D528V4, multiclass
       clus
vv      RBM16 MUTATED RBM16 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V5, binary
                 cls
clus               0  1
  RBM16 MUTATED    0  4
  RBM16 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      0    4
  RBM16 WILD-TYPE   35   85
   clus
vv  RBM16 MUTATED RBM16 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D528V6, binary
                 cls
clus               0  1
  RBM16 MUTATED    2  0
  RBM16 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      2    0
  RBM16 WILD-TYPE   55    3
   clus
vv  RBM16 MUTATED RBM16 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D528V7, binary
                 cls
clus               0  1
  RBM16 MUTATED    4  0
  RBM16 WILD-TYPE 47 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      4    0
  RBM16 WILD-TYPE   47   75
        clus
vv       RBM16 MUTATED RBM16 WILD-TYPE
  FEMALE             4              47
  MALE               0              75
[1] 2 2
[1] FALSE
D528V8, binary
                 cls
clus               0  1
  RBM16 MUTATED    4  0
  RBM16 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      4    0
  RBM16 WILD-TYPE   84   30
     clus
vv    RBM16 MUTATED RBM16 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM16 MUTATED                                     4
  RBM16 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM16 MUTATED                                       0
  RBM16 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM16 MUTATED                                                  0
  RBM16 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RBM16 MUTATED                                     0
  RBM16 WILD-TYPE                                   1
D528V9, multiclass
                                                  clus
vv                                                 RBM16 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 RBM16 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V10, continuous
[1] "Remove cluster labels:" "RBM16 MUTATED"         
clus
  RBM16 MUTATED RBM16 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
D528V11, continuous
[1] "Remove cluster labels:" "RBM16 MUTATED"         
clus
  RBM16 MUTATED RBM16 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" "RBM16 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RBM16 MUTATED    3  0  1  0
  RBM16 WILD-TYPE 77 35  3  2
D528V12, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM16 MUTATED       1                         0     3
  RBM16 WILD-TYPE     5                         5   111
D528V14, multiclass
                           clus
vv                          RBM16 MUTATED RBM16 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V15, binary
                 cls
clus               0  1
  RBM16 MUTATED    0  3
  RBM16 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      0    3
  RBM16 WILD-TYPE    5   88
                        clus
vv                       RBM16 MUTATED RBM16 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(529) Variable = PHACTR2 MUTATION ANALYSIS
D529V1, survival
                   sevent
clus2                0  1
  PHACTR2 MUTATED    2  1
  PHACTR2 WILD-TYPE 61 61
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                3               122 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                1                61 
$`PHACTR2 MUTATED`
TCGA-3A-A9IV TCGA-IB-7651 TCGA-XN-A8T5 
       36.26        19.82        23.67 

$`PHACTR2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            19.82              0.23 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
            36.26             90.12 
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
           23.670            15.155 
[1] "19.8 - 36.3 (23.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.5"
D529V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHACTR2 MUTATED         0        0        2         0         1         0
  PHACTR2 WILD-TYPE       1        3       10        19        81         4
                   vv
clus                STAGE IV
  PHACTR2 MUTATED          0
  PHACTR2 WILD-TYPE        3
D529V3, multiclass
           clus
vv          PHACTR2 MUTATED PHACTR2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               0                19
  STAGE IIB               1                81
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  PHACTR2 MUTATED     0   2     1
  PHACTR2 WILD-TYPE   5  15   101
D529V4, multiclass
       clus
vv      PHACTR2 MUTATED PHACTR2 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               1               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V5, binary
                   cls
clus                 0  1
  PHACTR2 MUTATED    2  1
  PHACTR2 WILD-TYPE 33 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      2    1
  PHACTR2 WILD-TYPE   33   88
   clus
vv  PHACTR2 MUTATED PHACTR2 WILD-TYPE
  0               2                33
  1               1                88
[1] 2 2
[1] FALSE
D529V6, binary
                   cls
clus                 0  1
  PHACTR2 MUTATED    2  0
  PHACTR2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      2    0
  PHACTR2 WILD-TYPE   55    3
   clus
vv  PHACTR2 MUTATED PHACTR2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D529V7, binary
                   cls
clus                 0  1
  PHACTR2 MUTATED    3  0
  PHACTR2 WILD-TYPE 48 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      3    0
  PHACTR2 WILD-TYPE   48   75
        clus
vv       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  FEMALE               3                48
  MALE                 0                75
[1] 2 2
[1] FALSE
D529V8, binary
                   cls
clus                 0  1
  PHACTR2 MUTATED    2  1
  PHACTR2 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      2    1
  PHACTR2 WILD-TYPE   86   29
     clus
vv    PHACTR2 MUTATED PHACTR2 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHACTR2 MUTATED                                     1
  PHACTR2 WILD-TYPE                                 104
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHACTR2 MUTATED                                       2
  PHACTR2 WILD-TYPE                                    16
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHACTR2 MUTATED                                                  0
  PHACTR2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHACTR2 MUTATED                                     0
  PHACTR2 WILD-TYPE                                   1
D529V9, multiclass
                                                  clus
vv                                                 PHACTR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PHACTR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V10, continuous
[1] "Remove cluster labels:" "PHACTR2 MUTATED"       
clus
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-YY-A8LH 
"PHACTR2 WILD-TYPE" 
D529V11, continuous
[1] "Remove cluster labels:" "PHACTR2 MUTATED"       
clus
  PHACTR2 MUTATED PHACTR2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-YY-A8LH 
"PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" "PHACTR2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  PHACTR2 MUTATED    2  1  0  0
  PHACTR2 WILD-TYPE 78 34  4  2
D529V12, multiclass
    clus
vv   PHACTR2 MUTATED PHACTR2 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHACTR2 MUTATED       0                         0     3
  PHACTR2 WILD-TYPE     6                         5   111
D529V14, multiclass
                           clus
vv                          PHACTR2 MUTATED PHACTR2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V15, binary
                   cls
clus                 0  1
  PHACTR2 MUTATED    1  2
  PHACTR2 WILD-TYPE  4 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR2 MUTATED      1    2
  PHACTR2 WILD-TYPE    4   89
                        clus
vv                       PHACTR2 MUTATED PHACTR2 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(530) Variable = TLR1 MUTATION ANALYSIS
D530V1, survival
                sevent
clus2             0  1
  TLR1 MUTATED    2  2
  TLR1 WILD-TYPE 61 60
  TLR1 MUTATED TLR1 WILD-TYPE 
             4            121 
  TLR1 MUTATED TLR1 WILD-TYPE 
             2             60 
$`TLR1 MUTATED`
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-IB-7651 TCGA-US-A77G 
       45.47        43.50        19.82         0.39 

$`TLR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39        12.95         9.60        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TLR1 MUTATED TLR1 WILD-TYPE 
          0.39           0.23 
  TLR1 MUTATED TLR1 WILD-TYPE 
         45.47          90.12 
  TLR1 MUTATED TLR1 WILD-TYPE 
         31.66          15.19 
[1] "0.4 - 45.5 (31.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D530V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TLR1 MUTATED         0        0        0         0         4         0
  TLR1 WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  TLR1 MUTATED          0
  TLR1 WILD-TYPE        3
D530V3, multiclass
           clus
vv          TLR1 MUTATED TLR1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TLR1 MUTATED    0  0     4
  TLR1 WILD-TYPE  5 17    98
D530V4, multiclass
       clus
vv      TLR1 MUTATED TLR1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V5, binary
                cls
clus              0  1
  TLR1 MUTATED    0  4
  TLR1 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR1 MUTATED      0    4
  TLR1 WILD-TYPE   35   85
   clus
vv  TLR1 MUTATED TLR1 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D530V6, binary
                cls
clus              0  1
  TLR1 MUTATED    1  0
  TLR1 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR1 MUTATED      1    0
  TLR1 WILD-TYPE   56    3
   clus
vv  TLR1 MUTATED TLR1 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D530V7, binary
                cls
clus              0  1
  TLR1 MUTATED    1  3
  TLR1 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR1 MUTATED      1    3
  TLR1 WILD-TYPE   50   72
        clus
vv       TLR1 MUTATED TLR1 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D530V8, binary
                cls
clus              0  1
  TLR1 MUTATED    3  1
  TLR1 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR1 MUTATED      3    1
  TLR1 WILD-TYPE   85   29
     clus
vv    TLR1 MUTATED TLR1 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TLR1 MUTATED                                     3
  TLR1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TLR1 MUTATED                                       1
  TLR1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TLR1 MUTATED                                                  0
  TLR1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TLR1 MUTATED                                     0
  TLR1 WILD-TYPE                                   1
D530V9, multiclass
                                                  clus
vv                                                 TLR1 MUTATED TLR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V10, continuous
[1] "Remove cluster labels:" "TLR1 MUTATED"          
clus
  TLR1 MUTATED TLR1 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
D530V11, continuous
[1] "Remove cluster labels:" "TLR1 MUTATED"          
clus
  TLR1 MUTATED TLR1 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" "TLR1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TLR1 MUTATED    3  1  0  0
  TLR1 WILD-TYPE 77 34  4  2
D530V12, multiclass
    clus
vv   TLR1 MUTATED TLR1 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TLR1 MUTATED       0                         1     3
  TLR1 WILD-TYPE     6                         4   111
D530V14, multiclass
                           clus
vv                          TLR1 MUTATED TLR1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V15, binary
                cls
clus              0  1
  TLR1 MUTATED    0  3
  TLR1 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR1 MUTATED      0    3
  TLR1 WILD-TYPE    5   88
                        clus
vv                       TLR1 MUTATED TLR1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(531) Variable = OR6C74 MUTATION ANALYSIS
D531V1, survival
                  sevent
clus2               0  1
  OR6C74 MUTATED    2  1
  OR6C74 WILD-TYPE 61 61
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               3              122 
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               1               61 
$`OR6C74 MUTATED`
TCGA-IB-7651 TCGA-Q3-AA2A TCGA-XN-A8T3 
       19.82         3.12        31.27 

$`OR6C74 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 
        7.56        12.46        10.29         8.78        13.68        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  OR6C74 MUTATED OR6C74 WILD-TYPE 
            3.12             0.23 
  OR6C74 MUTATED OR6C74 WILD-TYPE 
           31.27            90.12 
  OR6C74 MUTATED OR6C74 WILD-TYPE 
          19.820           15.205 
[1] "3.1 - 31.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D531V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  OR6C74 MUTATED         0        0        2         0         1         0
  OR6C74 WILD-TYPE       1        3       10        19        81         4
                  vv
clus               STAGE IV
  OR6C74 MUTATED          0
  OR6C74 WILD-TYPE        3
D531V3, multiclass
           clus
vv          OR6C74 MUTATED OR6C74 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  OR6C74 MUTATED     0   1     2
  OR6C74 WILD-TYPE   5  16   100
D531V4, multiclass
       clus
vv      OR6C74 MUTATED OR6C74 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V5, binary
                  cls
clus                0  1
  OR6C74 MUTATED    1  2
  OR6C74 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C74 MUTATED      1    2
  OR6C74 WILD-TYPE   34   87
   clus
vv  OR6C74 MUTATED OR6C74 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D531V6, binary
                  cls
clus                0  1
  OR6C74 MUTATED    2  0
  OR6C74 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C74 MUTATED      2    0
  OR6C74 WILD-TYPE   55    3
   clus
vv  OR6C74 MUTATED OR6C74 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D531V7, binary
                  cls
clus                0  1
  OR6C74 MUTATED    2  1
  OR6C74 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C74 MUTATED      2    1
  OR6C74 WILD-TYPE   49   74
        clus
vv       OR6C74 MUTATED OR6C74 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D531V8, binary
                  cls
clus                0  1
  OR6C74 MUTATED    2  1
  OR6C74 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C74 MUTATED      2    1
  OR6C74 WILD-TYPE   86   29
     clus
vv    OR6C74 MUTATED OR6C74 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR6C74 MUTATED                                     3
  OR6C74 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR6C74 MUTATED                                       0
  OR6C74 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR6C74 MUTATED                                                  0
  OR6C74 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  OR6C74 MUTATED                                     0
  OR6C74 WILD-TYPE                                   1
D531V9, multiclass
                                                  clus
vv                                                 OR6C74 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 OR6C74 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V10, continuous
[1] "Remove cluster labels:" "OR6C74 MUTATED"        
clus
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
D531V11, continuous
[1] "Remove cluster labels:" "OR6C74 MUTATED"        
clus
  OR6C74 MUTATED OR6C74 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" "OR6C74 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OR6C74 MUTATED    1  1  0  1
  OR6C74 WILD-TYPE 79 34  4  1
D531V12, multiclass
    clus
vv   OR6C74 MUTATED OR6C74 WILD-TYPE
  R0              1               79
  R1              1               34
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR6C74 MUTATED       0                         0     3
  OR6C74 WILD-TYPE     6                         5   111
D531V14, multiclass
                           clus
vv                          OR6C74 MUTATED OR6C74 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V15, binary
                  cls
clus                0  1
  OR6C74 MUTATED    1  2
  OR6C74 WILD-TYPE  4 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C74 MUTATED      1    2
  OR6C74 WILD-TYPE    4   89
                        clus
vv                       OR6C74 MUTATED OR6C74 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(532) Variable = ROBO3 MUTATION ANALYSIS
D532V1, survival
                 sevent
clus2              0  1
  ROBO3 MUTATED    3  4
  ROBO3 WILD-TYPE 60 58
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              7             118 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              4              58 
$`ROBO3 MUTATED`
TCGA-2L-AAQA TCGA-3E-AAAY TCGA-FB-AAPP TCGA-FB-AAPS TCGA-HV-AA8X TCGA-IB-7651 
        4.70        75.12        15.95         7.50        17.49        19.82 
TCGA-RL-AAAS 
        0.30 

$`ROBO3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        10.13        24.43        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPU 
        3.12        17.00        16.37        12.33        37.15        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        30.25        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        3.12        15.32         9.40        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ROBO3 MUTATED ROBO3 WILD-TYPE 
           0.30            0.23 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
          75.12           90.12 
  ROBO3 MUTATED ROBO3 WILD-TYPE 
         15.950          15.205 
[1] "0.3 - 75.1 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D532V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ROBO3 MUTATED         0        0        1         0         6         0
  ROBO3 WILD-TYPE       1        3       11        19        76         4
                 vv
clus              STAGE IV
  ROBO3 MUTATED          0
  ROBO3 WILD-TYPE        3
D532V3, multiclass
           clus
vv          ROBO3 MUTATED ROBO3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ROBO3 MUTATED    0  3     4
  ROBO3 WILD-TYPE  5 14    98
D532V4, multiclass
       clus
vv      ROBO3 MUTATED ROBO3 WILD-TYPE
  T1                0               5
  T2                3              14
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V5, binary
                 cls
clus               0  1
  ROBO3 MUTATED    1  6
  ROBO3 WILD-TYPE 34 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      1    6
  ROBO3 WILD-TYPE   34   83
   clus
vv  ROBO3 MUTATED ROBO3 WILD-TYPE
  0             1              34
  1             6              83
[1] 2 2
[1] FALSE
D532V6, binary
                 cls
clus               0  1
  ROBO3 MUTATED    2  0
  ROBO3 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      2    0
  ROBO3 WILD-TYPE   55    3
   clus
vv  ROBO3 MUTATED ROBO3 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D532V7, binary
                 cls
clus               0  1
  ROBO3 MUTATED    4  3
  ROBO3 WILD-TYPE 47 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      4    3
  ROBO3 WILD-TYPE   47   72
        clus
vv       ROBO3 MUTATED ROBO3 WILD-TYPE
  FEMALE             4              47
  MALE               3              72
[1] 2 2
[1] FALSE
D532V8, binary
                 cls
clus               0  1
  ROBO3 MUTATED    5  2
  ROBO3 WILD-TYPE 83 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      5    2
  ROBO3 WILD-TYPE   83   28
     clus
vv    ROBO3 MUTATED ROBO3 WILD-TYPE
  NO              5              83
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ROBO3 MUTATED                                     7
  ROBO3 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ROBO3 MUTATED                                       0
  ROBO3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ROBO3 MUTATED                                                  0
  ROBO3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ROBO3 MUTATED                                     0
  ROBO3 WILD-TYPE                                   1
D532V9, multiclass
                                                  clus
vv                                                 ROBO3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ROBO3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V10, continuous
D532V11, continuous
[1] "Remove cluster labels:" "ROBO3 MUTATED"         
clus
  ROBO3 MUTATED ROBO3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" "ROBO3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ROBO3 MUTATED    4  1  1  0
  ROBO3 WILD-TYPE 76 34  3  2
D532V12, multiclass
    clus
vv   ROBO3 MUTATED ROBO3 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ROBO3 MUTATED       1                         0     6
  ROBO3 WILD-TYPE     5                         5   108
D532V14, multiclass
                           clus
vv                          ROBO3 MUTATED ROBO3 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V15, binary
                 cls
clus               0  1
  ROBO3 MUTATED    0  5
  ROBO3 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ROBO3 MUTATED      0    5
  ROBO3 WILD-TYPE    5   86
                        clus
vv                       ROBO3 MUTATED ROBO3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(533) Variable = SLC45A4 MUTATION ANALYSIS
D533V1, survival
                   sevent
clus2                0  1
  SLC45A4 MUTATED    2  4
  SLC45A4 WILD-TYPE 61 58
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                6               119 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                4                58 
$`SLC45A4 MUTATED`
TCGA-3A-A9IZ TCGA-FZ-5923 TCGA-HZ-7918 TCGA-IB-7651 TCGA-OE-A75W TCGA-RB-AA9M 
       10.13        20.35        31.86        19.82         8.78         9.40 

$`SLC45A4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12        15.32         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
             8.78              0.23 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
            31.86             90.12 
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
           14.975            15.220 
[1] "8.8 - 31.9 (15.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D533V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC45A4 MUTATED         0        0        0         1         4         0
  SLC45A4 WILD-TYPE       1        3       12        18        78         4
                   vv
clus                STAGE IV
  SLC45A4 MUTATED          1
  SLC45A4 WILD-TYPE        2
D533V3, multiclass
           clus
vv          SLC45A4 MUTATED SLC45A4 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                1                 2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLC45A4 MUTATED    1  0     5
  SLC45A4 WILD-TYPE  4 17    97
D533V4, multiclass
       clus
vv      SLC45A4 MUTATED SLC45A4 WILD-TYPE
  T1                  1                 4
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V5, binary
                   cls
clus                 0  1
  SLC45A4 MUTATED    1  5
  SLC45A4 WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      1    5
  SLC45A4 WILD-TYPE   34   84
   clus
vv  SLC45A4 MUTATED SLC45A4 WILD-TYPE
  0               1                34
  1               5                84
[1] 2 2
[1] FALSE
D533V6, binary
                   cls
clus                 0  1
  SLC45A4 MUTATED    3  1
  SLC45A4 WILD-TYPE 54  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      3    1
  SLC45A4 WILD-TYPE   54    2
   clus
vv  SLC45A4 MUTATED SLC45A4 WILD-TYPE
  0               3                54
  1               1                 2
[1] 2 2
[1] FALSE
D533V7, binary
                   cls
clus                 0  1
  SLC45A4 MUTATED    1  5
  SLC45A4 WILD-TYPE 50 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      1    5
  SLC45A4 WILD-TYPE   50   70
        clus
vv       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  FEMALE               1                50
  MALE                 5                70
[1] 2 2
[1] FALSE
D533V8, binary
                   cls
clus                 0  1
  SLC45A4 MUTATED    3  3
  SLC45A4 WILD-TYPE 85 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      3    3
  SLC45A4 WILD-TYPE   85   27
     clus
vv    SLC45A4 MUTATED SLC45A4 WILD-TYPE
  NO                3                85
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC45A4 MUTATED                                     6
  SLC45A4 WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC45A4 MUTATED                                       0
  SLC45A4 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC45A4 MUTATED                                                  0
  SLC45A4 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC45A4 MUTATED                                     0
  SLC45A4 WILD-TYPE                                   1
D533V9, multiclass
                                                  clus
vv                                                 SLC45A4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLC45A4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V10, continuous
[1] "Remove cluster labels:" "SLC45A4 MUTATED"       
clus
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-XN-A8T5 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-YY-A8LH 
"SLC45A4 WILD-TYPE" 
D533V11, continuous
[1] "Remove cluster labels:" "SLC45A4 MUTATED"       
clus
  SLC45A4 MUTATED SLC45A4 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" "SLC45A4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SLC45A4 MUTATED    5  1  0  0
  SLC45A4 WILD-TYPE 75 34  4  2
D533V12, multiclass
    clus
vv   SLC45A4 MUTATED SLC45A4 WILD-TYPE
  R0               5                75
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC45A4 MUTATED       0                         0     6
  SLC45A4 WILD-TYPE     6                         5   108
D533V14, multiclass
                           clus
vv                          SLC45A4 MUTATED SLC45A4 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V15, binary
                   cls
clus                 0  1
  SLC45A4 MUTATED    1  5
  SLC45A4 WILD-TYPE  4 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A4 MUTATED      1    5
  SLC45A4 WILD-TYPE    4   86
                        clus
vv                       SLC45A4 MUTATED SLC45A4 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(534) Variable = COQ9 MUTATION ANALYSIS
D534V1, survival
                sevent
clus2             0  1
  COQ9 MUTATED    1  2
  COQ9 WILD-TYPE 62 60
  COQ9 MUTATED COQ9 WILD-TYPE 
             3            122 
  COQ9 MUTATED COQ9 WILD-TYPE 
             2             60 
$`COQ9 MUTATED`
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-IB-7651 
       15.06        34.09        19.82 

$`COQ9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  COQ9 MUTATED COQ9 WILD-TYPE 
         15.06           0.23 
  COQ9 MUTATED COQ9 WILD-TYPE 
         34.09          90.12 
  COQ9 MUTATED COQ9 WILD-TYPE 
        19.820         15.205 
[1] "15.1 - 34.1 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1"  
D534V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  COQ9 MUTATED         0        1        0         0         2         0
  COQ9 WILD-TYPE       1        2       12        19        80         4
                vv
clus             STAGE IV
  COQ9 MUTATED          0
  COQ9 WILD-TYPE        3
D534V3, multiclass
           clus
vv          COQ9 MUTATED COQ9 WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  COQ9 MUTATED     1   0     2
  COQ9 WILD-TYPE   4  17   100
D534V4, multiclass
       clus
vv      COQ9 MUTATED COQ9 WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V5, binary
                cls
clus              0  1
  COQ9 MUTATED    1  2
  COQ9 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ9 MUTATED      1    2
  COQ9 WILD-TYPE   34   87
   clus
vv  COQ9 MUTATED COQ9 WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D534V6, binary
                cls
clus              0  1
  COQ9 MUTATED    1  0
  COQ9 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ9 MUTATED      1    0
  COQ9 WILD-TYPE   56    3
   clus
vv  COQ9 MUTATED COQ9 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D534V7, binary
                cls
clus              0  1
  COQ9 MUTATED    1  2
  COQ9 WILD-TYPE 50 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ9 MUTATED      1    2
  COQ9 WILD-TYPE   50   73
        clus
vv       COQ9 MUTATED COQ9 WILD-TYPE
  FEMALE            1             50
  MALE              2             73
[1] 2 2
[1] FALSE
D534V8, binary
                cls
clus              0  1
  COQ9 MUTATED    2  1
  COQ9 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ9 MUTATED      2    1
  COQ9 WILD-TYPE   86   29
     clus
vv    COQ9 MUTATED COQ9 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COQ9 MUTATED                                     3
  COQ9 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COQ9 MUTATED                                       0
  COQ9 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COQ9 MUTATED                                                  0
  COQ9 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  COQ9 MUTATED                                     0
  COQ9 WILD-TYPE                                   1
D534V9, multiclass
                                                  clus
vv                                                 COQ9 MUTATED COQ9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V10, continuous
[1] "Remove cluster labels:" "COQ9 MUTATED"          
clus
  COQ9 MUTATED COQ9 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-YY-A8LH 
"COQ9 WILD-TYPE" 
D534V11, continuous
[1] "Remove cluster labels:" "COQ9 MUTATED"          
clus
  COQ9 MUTATED COQ9 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"COQ9 WILD-TYPE" "COQ9 WILD-TYPE" "COQ9 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  COQ9 MUTATED    3  0  0  0
  COQ9 WILD-TYPE 77 35  4  2
D534V12, multiclass
    clus
vv   COQ9 MUTATED COQ9 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COQ9 MUTATED       0                         0     3
  COQ9 WILD-TYPE     6                         5   111
D534V14, multiclass
                           clus
vv                          COQ9 MUTATED COQ9 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V15, binary
                cls
clus              0  1
  COQ9 MUTATED    0  3
  COQ9 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  COQ9 MUTATED      0    3
  COQ9 WILD-TYPE    5   88
                        clus
vv                       COQ9 MUTATED COQ9 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(535) Variable = CLCN3 MUTATION ANALYSIS
D535V1, survival
                 sevent
clus2              0  1
  CLCN3 MUTATED    2  1
  CLCN3 WILD-TYPE 61 61
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              3             122 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              1              61 
$`CLCN3 MUTATED`
TCGA-HZ-A77O TCGA-IB-A6UF TCGA-US-A776 
        5.26        21.90        39.98 

$`CLCN3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG 
       15.19        12.00        15.85         7.20        20.88         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CLCN3 MUTATED CLCN3 WILD-TYPE 
           5.26            0.23 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
          39.98           90.12 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
         21.900          15.205 
[1] "5.3 - 40.0 (21.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D535V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CLCN3 MUTATED         0        0        0         1         2         0
  CLCN3 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  CLCN3 MUTATED          0
  CLCN3 WILD-TYPE        3
D535V3, multiclass
           clus
vv          CLCN3 MUTATED CLCN3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  CLCN3 MUTATED     0   1     2
  CLCN3 WILD-TYPE   5  16   100
D535V4, multiclass
       clus
vv      CLCN3 MUTATED CLCN3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V5, binary
                 cls
clus               0  1
  CLCN3 MUTATED    1  2
  CLCN3 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      1    2
  CLCN3 WILD-TYPE   34   87
   clus
vv  CLCN3 MUTATED CLCN3 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D535V6, binary
                 cls
clus               0  1
  CLCN3 MUTATED    1  0
  CLCN3 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      1    0
  CLCN3 WILD-TYPE   56    3
   clus
vv  CLCN3 MUTATED CLCN3 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D535V7, binary
                 cls
clus               0  1
  CLCN3 MUTATED    1  2
  CLCN3 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      1    2
  CLCN3 WILD-TYPE   50   73
        clus
vv       CLCN3 MUTATED CLCN3 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D535V8, binary
                 cls
clus               0  1
  CLCN3 MUTATED    3  0
  CLCN3 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      3    0
  CLCN3 WILD-TYPE   85   30
     clus
vv    CLCN3 MUTATED CLCN3 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CLCN3 MUTATED                                     2
  CLCN3 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CLCN3 MUTATED                                       0
  CLCN3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CLCN3 MUTATED                                                  1
  CLCN3 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CLCN3 MUTATED                                     0
  CLCN3 WILD-TYPE                                   1
D535V9, multiclass
                                                  clus
vv                                                 CLCN3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CLCN3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V10, continuous
[1] "Remove cluster labels:" "CLCN3 MUTATED"         
clus
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
D535V11, continuous
[1] "Remove cluster labels:" "CLCN3 MUTATED"         
clus
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" "CLCN3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CLCN3 MUTATED    2  1  0  0
  CLCN3 WILD-TYPE 78 34  4  2
D535V12, multiclass
    clus
vv   CLCN3 MUTATED CLCN3 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCN3 MUTATED       0                         0     3
  CLCN3 WILD-TYPE     6                         5   111
D535V14, multiclass
                           clus
vv                          CLCN3 MUTATED CLCN3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V15, binary
                 cls
clus               0  1
  CLCN3 MUTATED    0  3
  CLCN3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      0    3
  CLCN3 WILD-TYPE    5   88
                        clus
vv                       CLCN3 MUTATED CLCN3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(536) Variable = SFRS11 MUTATION ANALYSIS
D536V1, survival
                  sevent
clus2               0  1
  SFRS11 MUTATED    2  1
  SFRS11 WILD-TYPE 61 61
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               3              122 
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               1               61 
$`SFRS11 MUTATED`
TCGA-HV-AA8V TCGA-IB-7651 TCGA-XD-AAUH 
       30.25        19.82        12.99 

$`SFRS11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SFRS11 MUTATED SFRS11 WILD-TYPE 
           12.99             0.23 
  SFRS11 MUTATED SFRS11 WILD-TYPE 
           30.25            90.12 
  SFRS11 MUTATED SFRS11 WILD-TYPE 
          19.820           15.205 
[1] "13.0 - 30.2 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.9"
D536V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SFRS11 MUTATED         0        0        0         0         3         0
  SFRS11 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  SFRS11 MUTATED          0
  SFRS11 WILD-TYPE        3
D536V3, multiclass
           clus
vv          SFRS11 MUTATED SFRS11 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SFRS11 MUTATED    0  0     3
  SFRS11 WILD-TYPE  5 17    99
D536V4, multiclass
       clus
vv      SFRS11 MUTATED SFRS11 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V5, binary
                  cls
clus                0  1
  SFRS11 MUTATED    0  3
  SFRS11 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS11 MUTATED      0    3
  SFRS11 WILD-TYPE   35   86
   clus
vv  SFRS11 MUTATED SFRS11 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D536V6, binary
                  cls
clus                0  1
  SFRS11 MUTATED    2  0
  SFRS11 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS11 MUTATED      2    0
  SFRS11 WILD-TYPE   55    3
   clus
vv  SFRS11 MUTATED SFRS11 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D536V7, binary
                  cls
clus                0  1
  SFRS11 MUTATED    2  1
  SFRS11 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS11 MUTATED      2    1
  SFRS11 WILD-TYPE   49   74
        clus
vv       SFRS11 MUTATED SFRS11 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D536V8, binary
                  cls
clus                0  1
  SFRS11 MUTATED    2  1
  SFRS11 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS11 MUTATED      2    1
  SFRS11 WILD-TYPE   86   29
     clus
vv    SFRS11 MUTATED SFRS11 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SFRS11 MUTATED                                     3
  SFRS11 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SFRS11 MUTATED                                       0
  SFRS11 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SFRS11 MUTATED                                                  0
  SFRS11 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SFRS11 MUTATED                                     0
  SFRS11 WILD-TYPE                                   1
D536V9, multiclass
                                                  clus
vv                                                 SFRS11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SFRS11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V10, continuous
[1] "Remove cluster labels:" "SFRS11 MUTATED"        
clus
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-YY-A8LH 
"SFRS11 WILD-TYPE" 
D536V11, continuous
[1] "Remove cluster labels:" "SFRS11 MUTATED"        
clus
  SFRS11 MUTATED SFRS11 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" "SFRS11 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SFRS11 MUTATED    1  0  2  0
  SFRS11 WILD-TYPE 79 35  2  2
D536V12, multiclass
    clus
vv   SFRS11 MUTATED SFRS11 WILD-TYPE
  R0              1               79
  R1              0               35
  R2              2                2
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SFRS11 MUTATED       1                         0     2
  SFRS11 WILD-TYPE     5                         5   112
D536V14, multiclass
                           clus
vv                          SFRS11 MUTATED SFRS11 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V15, binary
                  cls
clus                0  1
  SFRS11 MUTATED    0  2
  SFRS11 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS11 MUTATED      0    2
  SFRS11 WILD-TYPE    5   89
                        clus
vv                       SFRS11 MUTATED SFRS11 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(537) Variable = SIGLEC14 MUTATION ANALYSIS
D537V1, survival
                    sevent
clus2                 0  1
  SIGLEC14 MUTATED    0  3
  SIGLEC14 WILD-TYPE 63 59
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                122 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                 59 
$`SIGLEC14 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-IB-7651 
        2.17         9.63        19.82 

$`SIGLEC14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14        16.37        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              2.17               0.23 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             19.82              90.12 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              9.63              15.27 
[1] "2.2 - 19.8 (9.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "3.5"
D537V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SIGLEC14 MUTATED         0        0        0         1         2         0
  SIGLEC14 WILD-TYPE       1        3       12        18        80         4
                    vv
clus                 STAGE IV
  SIGLEC14 MUTATED          0
  SIGLEC14 WILD-TYPE        3
D537V3, multiclass
           clus
vv          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                2                 80
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  SIGLEC14 MUTATED    0  0     3
  SIGLEC14 WILD-TYPE  5 17    99
D537V4, multiclass
       clus
vv      SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V5, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    1  2
  SIGLEC14 WILD-TYPE 34 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      1    2
  SIGLEC14 WILD-TYPE   34   87
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                1                 34
  1                2                 87
[1] 2 2
[1] FALSE
D537V6, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    3  0
  SIGLEC14 WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      3    0
  SIGLEC14 WILD-TYPE   54    3
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D537V7, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    1  2
  SIGLEC14 WILD-TYPE 50 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      1    2
  SIGLEC14 WILD-TYPE   50   73
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                1                 50
  MALE                  2                 73
[1] 2 2
[1] FALSE
D537V8, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    3  0
  SIGLEC14 WILD-TYPE 85 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      3    0
  SIGLEC14 WILD-TYPE   85   30
     clus
vv    SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  NO                 3                 85
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIGLEC14 MUTATED                                     2
  SIGLEC14 WILD-TYPE                                 103
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIGLEC14 MUTATED                                       1
  SIGLEC14 WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIGLEC14 MUTATED                                                  0
  SIGLEC14 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  SIGLEC14 MUTATED                                     0
  SIGLEC14 WILD-TYPE                                   1
D537V9, multiclass
                                                  clus
vv                                                 SIGLEC14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 SIGLEC14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V10, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" 
D537V11, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  SIGLEC14 MUTATED    3  0  0  0
  SIGLEC14 WILD-TYPE 77 35  4  2
D537V12, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                3                 77
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC14 MUTATED       0                         0     3
  SIGLEC14 WILD-TYPE     6                         5   111
D537V14, multiclass
                           clus
vv                          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V15, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    0  1
  SIGLEC14 WILD-TYPE  5 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      0    1
  SIGLEC14 WILD-TYPE    5   90
                        clus
vv                       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                1                 90
[1] 2 2
[1] FALSE

Clustering(538) Variable = PRKCD MUTATION ANALYSIS
D538V1, survival
                 sevent
clus2              0  1
  PRKCD MUTATED    3  2
  PRKCD WILD-TYPE 60 60
  PRKCD MUTATED PRKCD WILD-TYPE 
              5             120 
  PRKCD MUTATED PRKCD WILD-TYPE 
              2              60 
$`PRKCD MUTATED`
TCGA-IB-7651 TCGA-IB-A5SQ TCGA-IB-AAUR TCGA-XD-AAUG TCGA-YB-A89D 
       19.82         7.20        11.11        13.81        11.51 

$`PRKCD WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00        15.85        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        18.67        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  PRKCD MUTATED PRKCD WILD-TYPE 
           7.20            0.23 
  PRKCD MUTATED PRKCD WILD-TYPE 
          19.82           90.12 
  PRKCD MUTATED PRKCD WILD-TYPE 
         11.510          15.335 
[1] "7.2 - 19.8 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D538V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRKCD MUTATED         0        0        1         0         3         0
  PRKCD WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  PRKCD MUTATED          1
  PRKCD WILD-TYPE        2
D538V3, multiclass
           clus
vv          PRKCD MUTATED PRKCD WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PRKCD MUTATED    0  1     4
  PRKCD WILD-TYPE  5 16    98
D538V4, multiclass
       clus
vv      PRKCD MUTATED PRKCD WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V5, binary
                 cls
clus               0  1
  PRKCD MUTATED    1  4
  PRKCD WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      1    4
  PRKCD WILD-TYPE   34   85
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D538V6, binary
                 cls
clus               0  1
  PRKCD MUTATED    3  1
  PRKCD WILD-TYPE 54  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      3    1
  PRKCD WILD-TYPE   54    2
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0             3              54
  1             1               2
[1] 2 2
[1] FALSE
D538V7, binary
                 cls
clus               0  1
  PRKCD MUTATED    3  2
  PRKCD WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      3    2
  PRKCD WILD-TYPE   48   73
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D538V8, binary
                 cls
clus               0  1
  PRKCD MUTATED    4  1
  PRKCD WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      4    1
  PRKCD WILD-TYPE   84   29
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRKCD MUTATED                                     5
  PRKCD WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRKCD MUTATED                                       0
  PRKCD WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRKCD MUTATED                                                  0
  PRKCD WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRKCD MUTATED                                     0
  PRKCD WILD-TYPE                                   1
D538V9, multiclass
                                                  clus
vv                                                 PRKCD MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRKCD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V10, continuous
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
D538V11, continuous
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRKCD MUTATED    4  1  0  0
  PRKCD WILD-TYPE 76 34  4  2
D538V12, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKCD MUTATED       0                         0     5
  PRKCD WILD-TYPE     6                         5   109
D538V14, multiclass
                           clus
vv                          PRKCD MUTATED PRKCD WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V15, binary
                 cls
clus               0  1
  PRKCD MUTATED    0  5
  PRKCD WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      0    5
  PRKCD WILD-TYPE    5   86
                        clus
vv                       PRKCD MUTATED PRKCD WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(539) Variable = ATP2B2 MUTATION ANALYSIS
D539V1, survival
                  sevent
clus2               0  1
  ATP2B2 MUTATED    3  2
  ATP2B2 WILD-TYPE 60 60
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               5              120 
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               2               60 
$`ATP2B2 MUTATED`
TCGA-LB-A7SX TCGA-2J-AAB8 TCGA-HZ-A77P TCGA-IB-7651 TCGA-YH-A8SY 
       12.92         2.63        10.85        19.82        12.76 

$`ATP2B2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         9.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
            2.63             0.23 
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
           19.82            90.12 
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
          12.760           15.335 
[1] "2.6 - 19.8 (12.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D539V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP2B2 MUTATED         0        0        0         0         4         1
  ATP2B2 WILD-TYPE       1        3       12        19        78         3
                  vv
clus               STAGE IV
  ATP2B2 MUTATED          0
  ATP2B2 WILD-TYPE        3
D539V3, multiclass
           clus
vv          ATP2B2 MUTATED ATP2B2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ATP2B2 MUTATED    0  0     5
  ATP2B2 WILD-TYPE  5 17    97
D539V4, multiclass
       clus
vv      ATP2B2 MUTATED ATP2B2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V5, binary
                  cls
clus                0  1
  ATP2B2 MUTATED    0  5
  ATP2B2 WILD-TYPE 35 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B2 MUTATED      0    5
  ATP2B2 WILD-TYPE   35   84
   clus
vv  ATP2B2 MUTATED ATP2B2 WILD-TYPE
  0              0               35
  1              5               84
[1] 2 2
[1] FALSE
D539V6, binary
                  cls
clus                0  1
  ATP2B2 MUTATED    2  0
  ATP2B2 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B2 MUTATED      2    0
  ATP2B2 WILD-TYPE   55    3
   clus
vv  ATP2B2 MUTATED ATP2B2 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D539V7, binary
                  cls
clus                0  1
  ATP2B2 MUTATED    3  2
  ATP2B2 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B2 MUTATED      3    2
  ATP2B2 WILD-TYPE   48   73
        clus
vv       ATP2B2 MUTATED ATP2B2 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D539V8, binary
                  cls
clus                0  1
  ATP2B2 MUTATED    3  1
  ATP2B2 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B2 MUTATED      3    1
  ATP2B2 WILD-TYPE   85   29
     clus
vv    ATP2B2 MUTATED ATP2B2 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2B2 MUTATED                                     3
  ATP2B2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2B2 MUTATED                                       1
  ATP2B2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2B2 MUTATED                                                  0
  ATP2B2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP2B2 MUTATED                                     0
  ATP2B2 WILD-TYPE                                   1
D539V9, multiclass
                                                  clus
vv                                                 ATP2B2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ATP2B2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V10, continuous
[1] "Remove cluster labels:" "ATP2B2 MUTATED"        
clus
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-YY-A8LH 
"ATP2B2 WILD-TYPE" 
D539V11, continuous
[1] "Remove cluster labels:" "ATP2B2 MUTATED"        
clus
  ATP2B2 MUTATED ATP2B2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" "ATP2B2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATP2B2 MUTATED    2  2  0  0
  ATP2B2 WILD-TYPE 78 33  4  2
D539V12, multiclass
    clus
vv   ATP2B2 MUTATED ATP2B2 WILD-TYPE
  R0              2               78
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2B2 MUTATED       0                         1     4
  ATP2B2 WILD-TYPE     6                         4   110
D539V14, multiclass
                           clus
vv                          ATP2B2 MUTATED ATP2B2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V15, binary
                  cls
clus                0  1
  ATP2B2 MUTATED    0  4
  ATP2B2 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B2 MUTATED      0    4
  ATP2B2 WILD-TYPE    5   87
                        clus
vv                       ATP2B2 MUTATED ATP2B2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(540) Variable = RASAL1 MUTATION ANALYSIS
D540V1, survival
                  sevent
clus2               0  1
  RASAL1 MUTATED    2  1
  RASAL1 WILD-TYPE 61 61
  RASAL1 MUTATED RASAL1 WILD-TYPE 
               3              122 
  RASAL1 MUTATED RASAL1 WILD-TYPE 
               1               61 
$`RASAL1 MUTATED`
TCGA-3A-A9IJ TCGA-IB-7651 TCGA-IB-8126 
       60.95        19.82        15.19 

$`RASAL1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RASAL1 MUTATED RASAL1 WILD-TYPE 
           15.19             0.23 
  RASAL1 MUTATED RASAL1 WILD-TYPE 
           60.95            90.12 
  RASAL1 MUTATED RASAL1 WILD-TYPE 
           19.82            15.17 
[1] "15.2 - 61.0 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.1"
D540V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RASAL1 MUTATED         0        0        1         0         1         1
  RASAL1 WILD-TYPE       1        3       11        19        81         3
                  vv
clus               STAGE IV
  RASAL1 MUTATED          0
  RASAL1 WILD-TYPE        3
D540V3, multiclass
           clus
vv          RASAL1 MUTATED RASAL1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              1               81
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  RASAL1 MUTATED     0   1     2
  RASAL1 WILD-TYPE   5  16   100
D540V4, multiclass
       clus
vv      RASAL1 MUTATED RASAL1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V5, binary
                  cls
clus                0  1
  RASAL1 MUTATED    1  2
  RASAL1 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL1 MUTATED      1    2
  RASAL1 WILD-TYPE   34   87
   clus
vv  RASAL1 MUTATED RASAL1 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D540V6, binary
                  cls
clus                0  1
  RASAL1 MUTATED    2  0
  RASAL1 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL1 MUTATED      2    0
  RASAL1 WILD-TYPE   55    3
   clus
vv  RASAL1 MUTATED RASAL1 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D540V7, binary
                  cls
clus                0  1
  RASAL1 MUTATED    2  1
  RASAL1 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL1 MUTATED      2    1
  RASAL1 WILD-TYPE   49   74
        clus
vv       RASAL1 MUTATED RASAL1 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D540V8, binary
                  cls
clus                0  1
  RASAL1 MUTATED    3  0
  RASAL1 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL1 MUTATED      3    0
  RASAL1 WILD-TYPE   85   30
     clus
vv    RASAL1 MUTATED RASAL1 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RASAL1 MUTATED                                     2
  RASAL1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RASAL1 MUTATED                                       1
  RASAL1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RASAL1 MUTATED                                                  0
  RASAL1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  RASAL1 MUTATED                                     0
  RASAL1 WILD-TYPE                                   1
D540V9, multiclass
                                                  clus
vv                                                 RASAL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 RASAL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V10, continuous
D540V11, continuous
                  vv
clus               R0 R1 R2 RX
  RASAL1 MUTATED    2  1  0  0
  RASAL1 WILD-TYPE 78 34  4  2
D540V12, multiclass
    clus
vv   RASAL1 MUTATED RASAL1 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RASAL1 MUTATED       0                         0     3
  RASAL1 WILD-TYPE     6                         5   111
D540V14, multiclass
                           clus
vv                          RASAL1 MUTATED RASAL1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V15, binary
                  cls
clus                0  1
  RASAL1 MUTATED    0  3
  RASAL1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL1 MUTATED      0    3
  RASAL1 WILD-TYPE    5   88
                        clus
vv                       RASAL1 MUTATED RASAL1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(541) Variable = NPIP MUTATION ANALYSIS
D541V1, survival
                sevent
clus2             0  1
  NPIP MUTATED    2  1
  NPIP WILD-TYPE 61 61
  NPIP MUTATED NPIP WILD-TYPE 
             3            122 
  NPIP MUTATED NPIP WILD-TYPE 
             1             61 
$`NPIP MUTATED`
TCGA-FB-AAPP TCGA-HV-A7OL TCGA-XN-A8T3 
       15.95         8.28        31.27 

$`NPIP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NPIP MUTATED NPIP WILD-TYPE 
          8.28           0.23 
  NPIP MUTATED NPIP WILD-TYPE 
         31.27          90.12 
  NPIP MUTATED NPIP WILD-TYPE 
        15.950         15.205 
[1] "8.3 - 31.3 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.6"
D541V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NPIP MUTATED         0        0        1         1         1         0
  NPIP WILD-TYPE       1        3       11        18        81         4
                vv
clus             STAGE IV
  NPIP MUTATED          0
  NPIP WILD-TYPE        3
D541V3, multiclass
           clus
vv          NPIP MUTATED NPIP WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            1             18
  STAGE IIB            1             81
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  NPIP MUTATED     0   1     2
  NPIP WILD-TYPE   5  16   100
D541V4, multiclass
       clus
vv      NPIP MUTATED NPIP WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V5, binary
                cls
clus              0  1
  NPIP MUTATED    2  1
  NPIP WILD-TYPE 33 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPIP MUTATED      2    1
  NPIP WILD-TYPE   33   88
   clus
vv  NPIP MUTATED NPIP WILD-TYPE
  0            2             33
  1            1             88
[1] 2 2
[1] FALSE
D541V6, binary
                cls
clus              0  1
  NPIP MUTATED    1  0
  NPIP WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPIP MUTATED      1    0
  NPIP WILD-TYPE   56    3
   clus
vv  NPIP MUTATED NPIP WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D541V7, binary
                cls
clus              0  1
  NPIP MUTATED    0  3
  NPIP WILD-TYPE 51 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPIP MUTATED      0    3
  NPIP WILD-TYPE   51   72
        clus
vv       NPIP MUTATED NPIP WILD-TYPE
  FEMALE            0             51
  MALE              3             72
[1] 2 2
[1] FALSE
D541V8, binary
                cls
clus              0  1
  NPIP MUTATED    1  2
  NPIP WILD-TYPE 87 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPIP MUTATED      1    2
  NPIP WILD-TYPE   87   28
     clus
vv    NPIP MUTATED NPIP WILD-TYPE
  NO             1             87
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NPIP MUTATED                                     3
  NPIP WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NPIP MUTATED                                       0
  NPIP WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NPIP MUTATED                                                  0
  NPIP WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  NPIP MUTATED                                     0
  NPIP WILD-TYPE                                   1
D541V9, multiclass
                                                  clus
vv                                                 NPIP MUTATED NPIP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V10, continuous
D541V11, continuous
                vv
clus             R0 R1 R2 RX
  NPIP MUTATED    1  1  1  0
  NPIP WILD-TYPE 79 34  3  2
D541V12, multiclass
    clus
vv   NPIP MUTATED NPIP WILD-TYPE
  R0            1             79
  R1            1             34
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V13, continuous
[1] "Remove cluster labels:" "NPIP MUTATED"          
clus
  NPIP MUTATED NPIP WILD-TYPE 
             2            122 
    TCGA-2J-AABR     TCGA-2J-AABT     TCGA-3A-A9I5     TCGA-3A-A9IJ 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-3A-A9IL     TCGA-F2-A44G     TCGA-FB-AAQ6     TCGA-FZ-5924 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-S4-A8RO     TCGA-US-A77E     TCGA-XD-AAUL     TCGA-2J-AAB1 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8     TCGA-2J-AAB9 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABH 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABP     TCGA-2J-AABU 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-2L-AAQI 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-2L-AAQJ     TCGA-2L-AAQL     TCGA-2L-AAQM     TCGA-3A-A9I7 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IC     TCGA-3A-A9IH 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-3A-A9IR     TCGA-3A-A9IS     TCGA-3A-A9IU     TCGA-3A-A9IV 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-3A-A9IZ     TCGA-3A-A9J0     TCGA-3E-AAAY 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-3E-AAAZ     TCGA-F2-7273     TCGA-F2-A7TX     TCGA-F2-A8YN 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-FB-AAPU     TCGA-FB-AAPZ     TCGA-FB-AAQ0     TCGA-FB-AAQ1 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-FB-AAQ2     TCGA-FB-AAQ3     TCGA-FZ-5919     TCGA-FZ-5920 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-FZ-5921     TCGA-FZ-5922     TCGA-FZ-5923     TCGA-FZ-5926 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-A7OP     TCGA-HV-AA8V     TCGA-HV-AA8X 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-HZ-7918     TCGA-HZ-7925     TCGA-HZ-8637     TCGA-HZ-A49I 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-HZ-A77O     TCGA-HZ-A77P     TCGA-HZ-A8P1     TCGA-HZ-A9TJ 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7652     TCGA-IB-7885     TCGA-IB-8126 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-A5SO     TCGA-IB-A5SP     TCGA-IB-A5SQ     TCGA-IB-A5ST 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7LX     TCGA-IB-A7M4 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-AAUM     TCGA-IB-AAUN     TCGA-IB-AAUO     TCGA-IB-AAUP 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUR     TCGA-IB-AAUS     TCGA-IB-AAUU 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-IB-AAUW     TCGA-LB-A8F3     TCGA-LB-A9Q5 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-OE-A75W     TCGA-Q3-A5QY     TCGA-Q3-AA2A     TCGA-RB-A7B8 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-RB-AA9M     TCGA-RL-AAAS     TCGA-US-A776     TCGA-US-A779 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-US-A77G     TCGA-US-A77J     TCGA-XD-AAUG     TCGA-XD-AAUH 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YB-A89D     TCGA-YH-A8SY 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" "NPIP WILD-TYPE" 
    TCGA-YY-A8LH     TCGA-Z5-AAPL 
"NPIP WILD-TYPE" "NPIP WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPIP MUTATED       1                         0     2
  NPIP WILD-TYPE     5                         5   112
D541V14, multiclass
                           clus
vv                          NPIP MUTATED NPIP WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V15, binary
                cls
clus              0  1
  NPIP MUTATED    1  1
  NPIP WILD-TYPE  4 90
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPIP MUTATED      1    1
  NPIP WILD-TYPE    4   90
                        clus
vv                       NPIP MUTATED NPIP WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            1             90
[1] 2 2
[1] FALSE

Clustering(542) Variable = DISP1 MUTATION ANALYSIS
D542V1, survival
                 sevent
clus2              0  1
  DISP1 MUTATED    6  2
  DISP1 WILD-TYPE 57 60
  DISP1 MUTATED DISP1 WILD-TYPE 
              8             117 
  DISP1 MUTATED DISP1 WILD-TYPE 
              2              60 
$`DISP1 MUTATED`
TCGA-2J-AAB8 TCGA-2J-AABE TCGA-2L-AAQI TCGA-3A-A9IV TCGA-3A-A9J0 TCGA-HV-A7OP 
        2.63        22.22         3.39        36.26        24.43        32.15 
TCGA-IB-7651 TCGA-YB-A89D 
       19.82        11.51 

$`DISP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        34.09        10.13 
TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM 
       75.12        71.74        19.46         3.12        17.00        16.37 
TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ 
       12.33        15.95        37.15         7.50        12.53        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 
       15.55         4.04         5.03         1.02        24.36         2.01 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  DISP1 MUTATED DISP1 WILD-TYPE 
           2.63            0.23 
  DISP1 MUTATED DISP1 WILD-TYPE 
          36.26           90.12 
  DISP1 MUTATED DISP1 WILD-TYPE 
          21.02           15.19 
[1] "2.6 - 36.3 (21.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.4"
D542V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DISP1 MUTATED         0        0        1         1         7         0
  DISP1 WILD-TYPE       1        3       11        18        75         4
                 vv
clus              STAGE IV
  DISP1 MUTATED          0
  DISP1 WILD-TYPE        3
D542V3, multiclass
           clus
vv          DISP1 MUTATED DISP1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             7              75
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DISP1 MUTATED    0  1     8
  DISP1 WILD-TYPE  5 16    94
D542V4, multiclass
       clus
vv      DISP1 MUTATED DISP1 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             8              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V5, binary
                 cls
clus               0  1
  DISP1 MUTATED    2  7
  DISP1 WILD-TYPE 33 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP1 MUTATED      2    7
  DISP1 WILD-TYPE   33   82
   clus
vv  DISP1 MUTATED DISP1 WILD-TYPE
  0             2              33
  1             7              82
[1] 2 2
[1] FALSE
D542V6, binary
                 cls
clus               0  1
  DISP1 MUTATED    4  0
  DISP1 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP1 MUTATED      4    0
  DISP1 WILD-TYPE   53    3
   clus
vv  DISP1 MUTATED DISP1 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D542V7, binary
                 cls
clus               0  1
  DISP1 MUTATED    2  7
  DISP1 WILD-TYPE 49 68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP1 MUTATED      2    7
  DISP1 WILD-TYPE   49   68
        clus
vv       DISP1 MUTATED DISP1 WILD-TYPE
  FEMALE             2              49
  MALE               7              68
[1] 2 2
[1] FALSE
D542V8, binary
                 cls
clus               0  1
  DISP1 MUTATED    4  3
  DISP1 WILD-TYPE 84 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP1 MUTATED      4    3
  DISP1 WILD-TYPE   84   27
     clus
vv    DISP1 MUTATED DISP1 WILD-TYPE
  NO              4              84
  YES             3              27
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DISP1 MUTATED                                     7
  DISP1 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DISP1 MUTATED                                       2
  DISP1 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DISP1 MUTATED                                                  0
  DISP1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DISP1 MUTATED                                     0
  DISP1 WILD-TYPE                                   1
D542V9, multiclass
                                                  clus
vv                                                 DISP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DISP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V10, continuous
D542V11, continuous
                 vv
clus              R0 R1 R2 RX
  DISP1 MUTATED    7  2  0  0
  DISP1 WILD-TYPE 73 33  4  2
D542V12, multiclass
    clus
vv   DISP1 MUTATED DISP1 WILD-TYPE
  R0             7              73
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DISP1 MUTATED       1                         0     8
  DISP1 WILD-TYPE     5                         5   106
D542V14, multiclass
                           clus
vv                          DISP1 MUTATED DISP1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V15, binary
                 cls
clus               0  1
  DISP1 MUTATED    0  5
  DISP1 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DISP1 MUTATED      0    5
  DISP1 WILD-TYPE    5   86
                        clus
vv                       DISP1 MUTATED DISP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(543) Variable = CD14 MUTATION ANALYSIS
D543V1, survival
                sevent
clus2             0  1
  CD14 MUTATED    0  3
  CD14 WILD-TYPE 63 59
  CD14 MUTATED CD14 WILD-TYPE 
             3            122 
  CD14 MUTATED CD14 WILD-TYPE 
             3             59 
$`CD14 MUTATED`
TCGA-FZ-5923 TCGA-HV-AA8X TCGA-IB-7651 
       20.35        17.49        19.82 

$`CD14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CD14 MUTATED CD14 WILD-TYPE 
         17.49           0.23 
  CD14 MUTATED CD14 WILD-TYPE 
         20.35          90.12 
  CD14 MUTATED CD14 WILD-TYPE 
        19.820         15.155 
[1] "17.5 - 20.4 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.6"
D543V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CD14 MUTATED         0        0        0         0         2         0
  CD14 WILD-TYPE       1        3       12        19        80         4
                vv
clus             STAGE IV
  CD14 MUTATED          1
  CD14 WILD-TYPE        2
D543V3, multiclass
           clus
vv          CD14 MUTATED CD14 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  CD14 MUTATED     0   1     2
  CD14 WILD-TYPE   5  16   100
D543V4, multiclass
       clus
vv      CD14 MUTATED CD14 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V5, binary
                cls
clus              0  1
  CD14 MUTATED    0  3
  CD14 WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD14 MUTATED      0    3
  CD14 WILD-TYPE   35   86
   clus
vv  CD14 MUTATED CD14 WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D543V6, binary
                cls
clus              0  1
  CD14 MUTATED    1  1
  CD14 WILD-TYPE 56  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD14 MUTATED      1    1
  CD14 WILD-TYPE   56    2
   clus
vv  CD14 MUTATED CD14 WILD-TYPE
  0            1             56
  1            1              2
[1] 2 2
[1] FALSE
D543V7, binary
                cls
clus              0  1
  CD14 MUTATED    2  1
  CD14 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD14 MUTATED      2    1
  CD14 WILD-TYPE   49   74
        clus
vv       CD14 MUTATED CD14 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D543V8, binary
                cls
clus              0  1
  CD14 MUTATED    3  0
  CD14 WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD14 MUTATED      3    0
  CD14 WILD-TYPE   85   30
     clus
vv    CD14 MUTATED CD14 WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD14 MUTATED                                     3
  CD14 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD14 MUTATED                                       0
  CD14 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD14 MUTATED                                                  0
  CD14 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CD14 MUTATED                                     0
  CD14 WILD-TYPE                                   1
D543V9, multiclass
                                                  clus
vv                                                 CD14 MUTATED CD14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V10, continuous
[1] "Remove cluster labels:" "CD14 MUTATED"          
clus
  CD14 MUTATED CD14 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" 
D543V11, continuous
[1] "Remove cluster labels:" "CD14 MUTATED"          
clus
  CD14 MUTATED CD14 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" "CD14 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CD14 MUTATED    2  0  1  0
  CD14 WILD-TYPE 78 35  3  2
D543V12, multiclass
    clus
vv   CD14 MUTATED CD14 WILD-TYPE
  R0            2             78
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD14 MUTATED       1                         0     2
  CD14 WILD-TYPE     5                         5   112
D543V14, multiclass
                           clus
vv                          CD14 MUTATED CD14 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V15, binary
                cls
clus              0  1
  CD14 MUTATED    0  2
  CD14 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD14 MUTATED      0    2
  CD14 WILD-TYPE    5   89
                        clus
vv                       CD14 MUTATED CD14 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(544) Variable = TATDN2 MUTATION ANALYSIS
D544V1, survival
                  sevent
clus2               0  1
  TATDN2 MUTATED    3  1
  TATDN2 WILD-TYPE 60 61
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               4              121 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               1               61 
$`TATDN2 MUTATED`
TCGA-2J-AABE TCGA-3A-A9I7 TCGA-IB-7651 TCGA-IB-A6UF 
       22.22        43.50        19.82        21.90 

$`TATDN2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        45.47        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TATDN2 MUTATED TATDN2 WILD-TYPE 
           19.82             0.23 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
           43.50            90.12 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
           22.06            15.12 
[1] "19.8 - 43.5 (22.1)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3.4"
D544V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TATDN2 MUTATED         0        0        0         1         3         0
  TATDN2 WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  TATDN2 MUTATED          0
  TATDN2 WILD-TYPE        3
D544V3, multiclass
           clus
vv          TATDN2 MUTATED TATDN2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TATDN2 MUTATED    0  0     4
  TATDN2 WILD-TYPE  5 17    98
D544V4, multiclass
       clus
vv      TATDN2 MUTATED TATDN2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V5, binary
                  cls
clus                0  1
  TATDN2 MUTATED    1  3
  TATDN2 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      1    3
  TATDN2 WILD-TYPE   34   86
   clus
vv  TATDN2 MUTATED TATDN2 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D544V6, binary
                  cls
clus                0  1
  TATDN2 MUTATED    3  0
  TATDN2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      3    0
  TATDN2 WILD-TYPE   54    3
   clus
vv  TATDN2 MUTATED TATDN2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D544V7, binary
                  cls
clus                0  1
  TATDN2 MUTATED    1  3
  TATDN2 WILD-TYPE 50 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      1    3
  TATDN2 WILD-TYPE   50   72
        clus
vv       TATDN2 MUTATED TATDN2 WILD-TYPE
  FEMALE              1               50
  MALE                3               72
[1] 2 2
[1] FALSE
D544V8, binary
                  cls
clus                0  1
  TATDN2 MUTATED    2  2
  TATDN2 WILD-TYPE 86 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      2    2
  TATDN2 WILD-TYPE   86   28
     clus
vv    TATDN2 MUTATED TATDN2 WILD-TYPE
  NO               2               86
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TATDN2 MUTATED                                     4
  TATDN2 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TATDN2 MUTATED                                       0
  TATDN2 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TATDN2 MUTATED                                                  0
  TATDN2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TATDN2 MUTATED                                     0
  TATDN2 WILD-TYPE                                   1
D544V9, multiclass
                                                  clus
vv                                                 TATDN2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TATDN2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V10, continuous
D544V11, continuous
                  vv
clus               R0 R1 R2 RX
  TATDN2 MUTATED    3  1  0  0
  TATDN2 WILD-TYPE 77 34  4  2
D544V12, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TATDN2 MUTATED       0                         1     3
  TATDN2 WILD-TYPE     6                         4   111
D544V14, multiclass
                           clus
vv                          TATDN2 MUTATED TATDN2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V15, binary
                  cls
clus                0  1
  TATDN2 MUTATED    0  3
  TATDN2 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      0    3
  TATDN2 WILD-TYPE    5   88
                        clus
vv                       TATDN2 MUTATED TATDN2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(545) Variable = ARID1A MUTATION ANALYSIS
D545V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    3  6
  ARID1A WILD-TYPE 60 56
  ARID1A MUTATED ARID1A WILD-TYPE 
               9              116 
  ARID1A MUTATED ARID1A WILD-TYPE 
               6               56 
$`ARID1A MUTATED`
TCGA-2J-AABA TCGA-F2-A7TX TCGA-FZ-5922 TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-IB-A5SQ 
       19.96         3.12        36.20         0.23        19.82         7.20 
TCGA-IB-AAUR TCGA-RB-A7B8 TCGA-YY-A8LH 
       11.11        15.32        66.28 

$`ARID1A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
       20.19        17.00        10.13         5.26        10.85        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST 
       36.69        41.33        15.19        12.00        15.85        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
        7.86        14.17         6.02         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.23             0.26 
  ARID1A MUTATED ARID1A WILD-TYPE 
           66.28            90.12 
  ARID1A MUTATED ARID1A WILD-TYPE 
          15.320           15.205 
[1] "0.2 - 66.3 (15.3)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.5"
D545V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ARID1A MUTATED         0        0        2         1         6         0
  ARID1A WILD-TYPE       1        3       10        18        76         4
                  vv
clus               STAGE IV
  ARID1A MUTATED          0
  ARID1A WILD-TYPE        3
D545V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              1               18
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ARID1A MUTATED    0  2     7
  ARID1A WILD-TYPE  5 15    95
D545V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  6
  ARID1A WILD-TYPE 32 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    6
  ARID1A WILD-TYPE   32   83
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              3               32
  1              6               83
[1] 2 2
[1] FALSE
D545V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    6  0
  ARID1A WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    0
  ARID1A WILD-TYPE   51    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              6               51
  1              0                3
[1] 2 2
[1] FALSE
D545V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    4  5
  ARID1A WILD-TYPE 47 70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    5
  ARID1A WILD-TYPE   47   70
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              4               47
  MALE                5               70
[1] 2 2
[1] FALSE
D545V8, binary
                  cls
clus                0  1
  ARID1A MUTATED    7  1
  ARID1A WILD-TYPE 81 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      7    1
  ARID1A WILD-TYPE   81   29
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               7               81
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARID1A MUTATED                                     8
  ARID1A WILD-TYPE                                  97
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARID1A MUTATED                                       1
  ARID1A WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARID1A MUTATED                                                  0
  ARID1A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ARID1A MUTATED                                     0
  ARID1A WILD-TYPE                                   1
D545V9, multiclass
                                                  clus
vv                                                 ARID1A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ARID1A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            97
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V10, continuous
D545V11, continuous
                  vv
clus               R0 R1 R2 RX
  ARID1A MUTATED    6  3  0  0
  ARID1A WILD-TYPE 74 32  4  2
D545V12, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              6               74
  R1              3               32
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0     9
  ARID1A WILD-TYPE     6                         5   105
D545V14, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V15, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  7
  ARID1A WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    7
  ARID1A WILD-TYPE    5   84
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               84
[1] 2 2
[1] FALSE

Clustering(546) Variable = ZC3H11A MUTATION ANALYSIS
D546V1, survival
                   sevent
clus2                0  1
  ZC3H11A MUTATED    1  4
  ZC3H11A WILD-TYPE 62 58
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                5               120 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                4                58 
$`ZC3H11A MUTATED`
TCGA-3E-AAAZ TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-AAUW TCGA-XN-A8T5 
       71.74        20.19        19.82         7.56        23.67 

$`ZC3H11A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         8.05        13.28        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        11.51        12.76        66.28        15.35 

  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
             7.56              0.23 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            71.74             90.12 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
           20.190            15.155 
[1] "7.6 - 71.7 (20.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D546V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZC3H11A MUTATED         0        0        1         1         3         0
  ZC3H11A WILD-TYPE       1        3       11        18        79         4
                   vv
clus                STAGE IV
  ZC3H11A MUTATED          0
  ZC3H11A WILD-TYPE        3
D546V3, multiclass
           clus
vv          ZC3H11A MUTATED ZC3H11A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ZC3H11A MUTATED    0  1     4
  ZC3H11A WILD-TYPE  5 16    98
D546V4, multiclass
       clus
vv      ZC3H11A MUTATED ZC3H11A WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V5, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    2  3
  ZC3H11A WILD-TYPE 33 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      2    3
  ZC3H11A WILD-TYPE   33   86
   clus
vv  ZC3H11A MUTATED ZC3H11A WILD-TYPE
  0               2                33
  1               3                86
[1] 2 2
[1] FALSE
D546V6, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    3  0
  ZC3H11A WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      3    0
  ZC3H11A WILD-TYPE   54    3
   clus
vv  ZC3H11A MUTATED ZC3H11A WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D546V7, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    3  2
  ZC3H11A WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      3    2
  ZC3H11A WILD-TYPE   48   73
        clus
vv       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  FEMALE               3                48
  MALE                 2                73
[1] 2 2
[1] FALSE
D546V8, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    3  1
  ZC3H11A WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      3    1
  ZC3H11A WILD-TYPE   85   29
     clus
vv    ZC3H11A MUTATED ZC3H11A WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZC3H11A MUTATED                                     4
  ZC3H11A WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZC3H11A MUTATED                                       1
  ZC3H11A WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZC3H11A MUTATED                                                  0
  ZC3H11A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZC3H11A MUTATED                                     0
  ZC3H11A WILD-TYPE                                   1
D546V9, multiclass
                                                  clus
vv                                                 ZC3H11A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ZC3H11A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V10, continuous
[1] "Remove cluster labels:" "ZC3H11A MUTATED"       
clus
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-YY-A8LH 
"ZC3H11A WILD-TYPE" 
D546V11, continuous
[1] "Remove cluster labels:" "ZC3H11A MUTATED"       
clus
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-YY-A8LH 
"ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" "ZC3H11A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ZC3H11A MUTATED    3  1  0  0
  ZC3H11A WILD-TYPE 77 34  4  2
D546V12, multiclass
    clus
vv   ZC3H11A MUTATED ZC3H11A WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZC3H11A MUTATED       0                         0     5
  ZC3H11A WILD-TYPE     6                         5   109
D546V14, multiclass
                           clus
vv                          ZC3H11A MUTATED ZC3H11A WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V15, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    2  3
  ZC3H11A WILD-TYPE  3 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      2    3
  ZC3H11A WILD-TYPE    3   88
                        clus
vv                       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(547) Variable = ANKRD49 MUTATION ANALYSIS
D547V1, survival
                   sevent
clus2                0  1
  ANKRD49 MUTATED    1  2
  ANKRD49 WILD-TYPE 62 60
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               122 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                2                60 
$`ANKRD49 MUTATED`
TCGA-2J-AABH TCGA-2L-AAQJ TCGA-IB-7651 
       42.31        12.95        19.82 

$`ANKRD49 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
            12.95              0.23 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
            42.31             90.12 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
           19.820            15.205 
[1] "12.9 - 42.3 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1"  
D547V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ANKRD49 MUTATED         0        0        0         1         1         1
  ANKRD49 WILD-TYPE       1        3       12        18        81         3
                   vv
clus                STAGE IV
  ANKRD49 MUTATED          0
  ANKRD49 WILD-TYPE        3
D547V3, multiclass
           clus
vv          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               1                81
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ANKRD49 MUTATED    0  0     3
  ANKRD49 WILD-TYPE  5 17    99
D547V4, multiclass
       clus
vv      ANKRD49 MUTATED ANKRD49 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V5, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  1
  ANKRD49 WILD-TYPE 33 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    1
  ANKRD49 WILD-TYPE   33   88
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               2                33
  1               1                88
[1] 2 2
[1] FALSE
D547V6, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  0
  ANKRD49 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    0
  ANKRD49 WILD-TYPE   55    3
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D547V7, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  1
  ANKRD49 WILD-TYPE 49 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    1
  ANKRD49 WILD-TYPE   49   74
        clus
vv       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  FEMALE               2                49
  MALE                 1                74
[1] 2 2
[1] FALSE
D547V8, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    3  0
  ANKRD49 WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      3    0
  ANKRD49 WILD-TYPE   85   30
     clus
vv    ANKRD49 MUTATED ANKRD49 WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD49 MUTATED                                     2
  ANKRD49 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD49 MUTATED                                       1
  ANKRD49 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD49 MUTATED                                                  0
  ANKRD49 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ANKRD49 MUTATED                                     0
  ANKRD49 WILD-TYPE                                   1
D547V9, multiclass
                                                  clus
vv                                                 ANKRD49 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 ANKRD49 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V10, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
D547V11, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ANKRD49 MUTATED    2  1  0  0
  ANKRD49 WILD-TYPE 78 34  4  2
D547V12, multiclass
    clus
vv   ANKRD49 MUTATED ANKRD49 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD49 MUTATED       0                         0     3
  ANKRD49 WILD-TYPE     6                         5   111
D547V14, multiclass
                           clus
vv                          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V15, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    0  1
  ANKRD49 WILD-TYPE  5 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      0    1
  ANKRD49 WILD-TYPE    5   90
                        clus
vv                       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               1                90
[1] 2 2
[1] FALSE

Clustering(548) Variable = NDUFV2 MUTATION ANALYSIS
D548V1, survival
                  sevent
clus2               0  1
  NDUFV2 MUTATED    3  0
  NDUFV2 WILD-TYPE 60 62
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              122 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               0               62 
$`NDUFV2 MUTATED`
TCGA-S4-A8RO TCGA-F2-A8YN TCGA-YY-A8LH 
       17.26        17.00        66.28 

$`NDUFV2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           17.00             0.23 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           66.28            90.12 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
          17.260           15.155 
[1] "17.0 - 66.3 (17.3)" "0.2 - 90.1 (15.2)" 
[1] "hr="     "2.6e+07"
D548V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NDUFV2 MUTATED         0        0        0         1         2         0
  NDUFV2 WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  NDUFV2 MUTATED          0
  NDUFV2 WILD-TYPE        3
D548V3, multiclass
           clus
vv          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  NDUFV2 MUTATED    0  0     3
  NDUFV2 WILD-TYPE  5 17    99
D548V4, multiclass
       clus
vv      NDUFV2 MUTATED NDUFV2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V5, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  2
  NDUFV2 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE   34   87
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D548V6, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  0
  NDUFV2 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    0
  NDUFV2 WILD-TYPE   56    3
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D548V7, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    2  1
  NDUFV2 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    1
  NDUFV2 WILD-TYPE   49   74
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D548V8, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  2
  NDUFV2 WILD-TYPE 87 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE   87   28
     clus
vv    NDUFV2 MUTATED NDUFV2 WILD-TYPE
  NO               1               87
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NDUFV2 MUTATED                                     3
  NDUFV2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NDUFV2 MUTATED                                       0
  NDUFV2 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NDUFV2 MUTATED                                                  0
  NDUFV2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  NDUFV2 MUTATED                                     0
  NDUFV2 WILD-TYPE                                   1
D548V9, multiclass
                                                  clus
vv                                                 NDUFV2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 NDUFV2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V10, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-XN-A8T5 
"NDUFV2 WILD-TYPE" 
D548V11, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NDUFV2 MUTATED    1  2  0  0
  NDUFV2 WILD-TYPE 79 33  4  2
D548V12, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  R0              1               79
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NDUFV2 MUTATED       0                         0     3
  NDUFV2 WILD-TYPE     6                         5   111
D548V14, multiclass
                           clus
vv                          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V15, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    0  3
  NDUFV2 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      0    3
  NDUFV2 WILD-TYPE    5   88
                        clus
vv                       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(549) Variable = PPP1R12C MUTATION ANALYSIS
D549V1, survival
                    sevent
clus2                 0  1
  PPP1R12C MUTATED    2  2
  PPP1R12C WILD-TYPE 61 60
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 4                121 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 2                 60 
$`PPP1R12C MUTATED`
TCGA-2J-AAB8 TCGA-HZ-8637 TCGA-HZ-A9TJ TCGA-IB-7651 
        2.63        17.00        19.82        19.82 

$`PPP1R12C WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        20.19        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
              2.63               0.23 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             19.82              90.12 
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
             18.41              15.19 
[1] "2.6 - 19.8 (18.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D549V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPP1R12C MUTATED         0        0        0         0         3         0
  PPP1R12C WILD-TYPE       1        3       12        19        79         4
                    vv
clus                 STAGE IV
  PPP1R12C MUTATED          1
  PPP1R12C WILD-TYPE        2
D549V3, multiclass
           clus
vv          PPP1R12C MUTATED PPP1R12C WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 1                  2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  PPP1R12C MUTATED    0  0     4
  PPP1R12C WILD-TYPE  5 17    98
D549V4, multiclass
       clus
vv      PPP1R12C MUTATED PPP1R12C WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V5, binary
                    cls
clus                  0  1
  PPP1R12C MUTATED    1  3
  PPP1R12C WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      1    3
  PPP1R12C WILD-TYPE   34   86
   clus
vv  PPP1R12C MUTATED PPP1R12C WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D549V6, binary
                    cls
clus                  0  1
  PPP1R12C MUTATED    2  1
  PPP1R12C WILD-TYPE 55  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      2    1
  PPP1R12C WILD-TYPE   55    2
   clus
vv  PPP1R12C MUTATED PPP1R12C WILD-TYPE
  0                2                 55
  1                1                  2
[1] 2 2
[1] FALSE
D549V7, binary
                    cls
clus                  0  1
  PPP1R12C MUTATED    2  2
  PPP1R12C WILD-TYPE 49 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      2    2
  PPP1R12C WILD-TYPE   49   73
        clus
vv       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  FEMALE                2                 49
  MALE                  2                 73
[1] 2 2
[1] FALSE
D549V8, binary
                    cls
clus                  0  1
  PPP1R12C MUTATED    2  1
  PPP1R12C WILD-TYPE 86 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      2    1
  PPP1R12C WILD-TYPE   86   29
     clus
vv    PPP1R12C MUTATED PPP1R12C WILD-TYPE
  NO                 2                 86
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPP1R12C MUTATED                                     3
  PPP1R12C WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPP1R12C MUTATED                                       1
  PPP1R12C WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPP1R12C MUTATED                                                  0
  PPP1R12C WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPP1R12C MUTATED                                     0
  PPP1R12C WILD-TYPE                                   1
D549V9, multiclass
                                                  clus
vv                                                 PPP1R12C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 PPP1R12C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V10, continuous
[1] "Remove cluster labels:" "PPP1R12C MUTATED"      
clus
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
D549V11, continuous
[1] "Remove cluster labels:" "PPP1R12C MUTATED"      
clus
  PPP1R12C MUTATED PPP1R12C WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"PPP1R12C WILD-TYPE" "PPP1R12C WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  PPP1R12C MUTATED    3  1  0  0
  PPP1R12C WILD-TYPE 77 34  4  2
D549V12, multiclass
    clus
vv   PPP1R12C MUTATED PPP1R12C WILD-TYPE
  R0                3                 77
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12C MUTATED       0                         0     4
  PPP1R12C WILD-TYPE     6                         5   110
D549V14, multiclass
                           clus
vv                          PPP1R12C MUTATED PPP1R12C WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V15, binary
                    cls
clus                  0  1
  PPP1R12C MUTATED    1  2
  PPP1R12C WILD-TYPE  4 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12C MUTATED      1    2
  PPP1R12C WILD-TYPE    4   89
                        clus
vv                       PPP1R12C MUTATED PPP1R12C WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(550) Variable = CCDC74A MUTATION ANALYSIS
D550V1, survival
                   sevent
clus2                0  1
  CCDC74A MUTATED    1  3
  CCDC74A WILD-TYPE 62 59
  CCDC74A MUTATED CCDC74A WILD-TYPE 
                4               121 
  CCDC74A MUTATED CCDC74A WILD-TYPE 
                3                59 
$`CCDC74A MUTATED`
TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-AAUU TCGA-LB-A9Q5 
       17.00        19.82         8.05        10.29 

$`CCDC74A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        17.49        31.86        20.19        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40        13.28         7.56        12.46 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CCDC74A MUTATED CCDC74A WILD-TYPE 
             8.05              0.23 
  CCDC74A MUTATED CCDC74A WILD-TYPE 
            19.82             90.12 
  CCDC74A MUTATED CCDC74A WILD-TYPE 
           13.645            15.220 
[1] "8.1 - 19.8 (13.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D550V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC74A MUTATED         0        0        0         0         4         0
  CCDC74A WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  CCDC74A MUTATED          0
  CCDC74A WILD-TYPE        3
D550V3, multiclass
           clus
vv          CCDC74A MUTATED CCDC74A WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC74A MUTATED    0  0     4
  CCDC74A WILD-TYPE  5 17    98
D550V4, multiclass
       clus
vv      CCDC74A MUTATED CCDC74A WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V5, binary
                   cls
clus                 0  1
  CCDC74A MUTATED    0  4
  CCDC74A WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC74A MUTATED      0    4
  CCDC74A WILD-TYPE   35   85
   clus
vv  CCDC74A MUTATED CCDC74A WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D550V6, binary
                   cls
clus                 0  1
  CCDC74A MUTATED    2  0
  CCDC74A WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC74A MUTATED      2    0
  CCDC74A WILD-TYPE   55    3
   clus
vv  CCDC74A MUTATED CCDC74A WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D550V7, binary
                   cls
clus                 0  1
  CCDC74A MUTATED    3  1
  CCDC74A WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC74A MUTATED      3    1
  CCDC74A WILD-TYPE   48   74
        clus
vv       CCDC74A MUTATED CCDC74A WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D550V8, binary
                   cls
clus                 0  1
  CCDC74A MUTATED    2  2
  CCDC74A WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC74A MUTATED      2    2
  CCDC74A WILD-TYPE   86   28
     clus
vv    CCDC74A MUTATED CCDC74A WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC74A MUTATED                                     4
  CCDC74A WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC74A MUTATED                                       0
  CCDC74A WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC74A MUTATED                                                  0
  CCDC74A WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC74A MUTATED                                     0
  CCDC74A WILD-TYPE                                   1
D550V9, multiclass
                                                  clus
vv                                                 CCDC74A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC74A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V10, continuous
D550V11, continuous
[1] "Remove cluster labels:" "CCDC74A MUTATED"       
clus
  CCDC74A MUTATED CCDC74A WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-OE-A75W 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" "CCDC74A WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC74A MUTATED    4  0  0  0
  CCDC74A WILD-TYPE 76 35  4  2
D550V12, multiclass
    clus
vv   CCDC74A MUTATED CCDC74A WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC74A MUTATED       0                         0     4
  CCDC74A WILD-TYPE     6                         5   110
D550V14, multiclass
                           clus
vv                          CCDC74A MUTATED CCDC74A WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V15, binary
                   cls
clus                 0  1
  CCDC74A MUTATED    1  3
  CCDC74A WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC74A MUTATED      1    3
  CCDC74A WILD-TYPE    4   88
                        clus
vv                       CCDC74A MUTATED CCDC74A WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(551) Variable = C3ORF15 MUTATION ANALYSIS
D551V1, survival
                   sevent
clus2                0  1
  C3ORF15 MUTATED    1  3
  C3ORF15 WILD-TYPE 62 59
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                4               121 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                3                59 
$`C3ORF15 MUTATED`
TCGA-3A-A9I5 TCGA-LB-A7SX TCGA-IB-7651 TCGA-LB-A9Q5 
       58.98        12.92        19.82        10.29 

$`C3ORF15 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
            10.29              0.23 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
            58.98             90.12 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
            16.37             15.22 
[1] "10.3 - 59.0 (16.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.3"
D551V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C3ORF15 MUTATED         0        0        0         0         3         0
  C3ORF15 WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  C3ORF15 MUTATED          0
  C3ORF15 WILD-TYPE        3
D551V3, multiclass
           clus
vv          C3ORF15 MUTATED C3ORF15 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  C3ORF15 MUTATED    0  0     3
  C3ORF15 WILD-TYPE  5 17    99
D551V4, multiclass
       clus
vv      C3ORF15 MUTATED C3ORF15 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V5, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    1  3
  C3ORF15 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      1    3
  C3ORF15 WILD-TYPE   34   86
   clus
vv  C3ORF15 MUTATED C3ORF15 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D551V6, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    1  0
  C3ORF15 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      1    0
  C3ORF15 WILD-TYPE   56    3
   clus
vv  C3ORF15 MUTATED C3ORF15 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D551V7, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    3  1
  C3ORF15 WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      3    1
  C3ORF15 WILD-TYPE   48   74
        clus
vv       C3ORF15 MUTATED C3ORF15 WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D551V8, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    2  2
  C3ORF15 WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      2    2
  C3ORF15 WILD-TYPE   86   28
     clus
vv    C3ORF15 MUTATED C3ORF15 WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C3ORF15 MUTATED                                     4
  C3ORF15 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C3ORF15 MUTATED                                       0
  C3ORF15 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C3ORF15 MUTATED                                                  0
  C3ORF15 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  C3ORF15 MUTATED                                     0
  C3ORF15 WILD-TYPE                                   1
D551V9, multiclass
                                                  clus
vv                                                 C3ORF15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 C3ORF15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V10, continuous
D551V11, continuous
                   vv
clus                R0 R1 R2 RX
  C3ORF15 MUTATED    3  1  0  0
  C3ORF15 WILD-TYPE 77 34  4  2
D551V12, multiclass
    clus
vv   C3ORF15 MUTATED C3ORF15 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF15 MUTATED       0                         1     3
  C3ORF15 WILD-TYPE     6                         4   111
D551V14, multiclass
                           clus
vv                          C3ORF15 MUTATED C3ORF15 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V15, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    0  4
  C3ORF15 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      0    4
  C3ORF15 WILD-TYPE    5   87
                        clus
vv                       C3ORF15 MUTATED C3ORF15 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(552) Variable = DCX MUTATION ANALYSIS
D552V1, survival
               sevent
clus2            0  1
  DCX MUTATED    2  1
  DCX WILD-TYPE 61 61
  DCX MUTATED DCX WILD-TYPE 
            3           122 
  DCX MUTATED DCX WILD-TYPE 
            1            61 
$`DCX MUTATED`
TCGA-S4-A8RO TCGA-HZ-A77O TCGA-HZ-A77P 
       17.26         5.26        10.85 

$`DCX WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A8P1 
       17.49        31.86        20.19        17.00        10.13         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DCX MUTATED DCX WILD-TYPE 
         5.26          0.23 
  DCX MUTATED DCX WILD-TYPE 
        17.26         90.12 
  DCX MUTATED DCX WILD-TYPE 
        10.85         15.27 
[1] "5.3 - 17.3 (10.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D552V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DCX MUTATED         0        0        0         0         3         0
  DCX WILD-TYPE       1        3       12        19        79         4
               vv
clus            STAGE IV
  DCX MUTATED          0
  DCX WILD-TYPE        3
D552V3, multiclass
           clus
vv          DCX MUTATED DCX WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           0            19
  STAGE IIB           3            79
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2 T3+T4
  DCX MUTATED     0   1     2
  DCX WILD-TYPE   5  16   100
D552V4, multiclass
       clus
vv      DCX MUTATED DCX WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           2           100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V5, binary
               cls
clus             0  1
  DCX MUTATED    0  3
  DCX WILD-TYPE 35 86
[1] "tbl2"
               cls
clus            [,1] [,2]
  DCX MUTATED      0    3
  DCX WILD-TYPE   35   86
   clus
vv  DCX MUTATED DCX WILD-TYPE
  0           0            35
  1           3            86
[1] 2 2
[1] FALSE
D552V6, binary
               cls
clus             0  1
  DCX MUTATED    0  0
  DCX WILD-TYPE 57  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  DCX MUTATED      0    0
  DCX WILD-TYPE   57    3
D552V7, binary
               cls
clus             0  1
  DCX MUTATED    2  1
  DCX WILD-TYPE 49 74
[1] "tbl2"
               cls
clus            [,1] [,2]
  DCX MUTATED      2    1
  DCX WILD-TYPE   49   74
        clus
vv       DCX MUTATED DCX WILD-TYPE
  FEMALE           2            49
  MALE             1            74
[1] 2 2
[1] FALSE
D552V8, binary
               cls
clus             0  1
  DCX MUTATED    2  1
  DCX WILD-TYPE 86 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  DCX MUTATED      2    1
  DCX WILD-TYPE   86   29
     clus
vv    DCX MUTATED DCX WILD-TYPE
  NO            2            86
  YES           1            29
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DCX MUTATED                                     2
  DCX WILD-TYPE                                 103
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DCX MUTATED                                       1
  DCX WILD-TYPE                                    17
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DCX MUTATED                                                  0
  DCX WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  DCX MUTATED                                     0
  DCX WILD-TYPE                                   1
D552V9, multiclass
                                                  clus
vv                                                 DCX MUTATED DCX WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        2           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      1            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V10, continuous
D552V11, continuous
               vv
clus            R0 R1 R2 RX
  DCX MUTATED    2  1  0  0
  DCX WILD-TYPE 78 34  4  2
D552V12, multiclass
    clus
vv   DCX MUTATED DCX WILD-TYPE
  R0           2            78
  R1           1            34
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DCX MUTATED       0                         0     3
  DCX WILD-TYPE     6                         5   111
D552V14, multiclass
                           clus
vv                          DCX MUTATED DCX WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V15, binary
               cls
clus             0  1
  DCX MUTATED    0  3
  DCX WILD-TYPE  5 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  DCX MUTATED      0    3
  DCX WILD-TYPE    5   88
                        clus
vv                       DCX MUTATED DCX WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3            88
[1] 2 2
[1] FALSE

Clustering(553) Variable = HMGCR MUTATION ANALYSIS
D553V1, survival
                 sevent
clus2              0  1
  HMGCR MUTATED    3  3
  HMGCR WILD-TYPE 60 59
  HMGCR MUTATED HMGCR WILD-TYPE 
              6             119 
  HMGCR MUTATED HMGCR WILD-TYPE 
              3              59 
$`HMGCR MUTATED`
TCGA-2J-AABO TCGA-3A-A9IC TCGA-3A-A9IV TCGA-IB-7651 TCGA-OE-A75W TCGA-XN-A8T3 
       14.47        24.26        36.26        19.82         8.78        31.27 

$`HMGCR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  HMGCR MUTATED HMGCR WILD-TYPE 
           8.78            0.23 
  HMGCR MUTATED HMGCR WILD-TYPE 
          36.26           90.12 
  HMGCR MUTATED HMGCR WILD-TYPE 
          22.04           15.19 
[1] "8.8 - 36.3 (22.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D553V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HMGCR MUTATED         0        0        2         1         3         0
  HMGCR WILD-TYPE       1        3       10        18        79         4
                 vv
clus              STAGE IV
  HMGCR MUTATED          0
  HMGCR WILD-TYPE        3
D553V3, multiclass
           clus
vv          HMGCR MUTATED HMGCR WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             1              18
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  HMGCR MUTATED    0  2     4
  HMGCR WILD-TYPE  5 15    98
D553V4, multiclass
       clus
vv      HMGCR MUTATED HMGCR WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V5, binary
                 cls
clus               0  1
  HMGCR MUTATED    3  3
  HMGCR WILD-TYPE 32 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      3    3
  HMGCR WILD-TYPE   32   86
   clus
vv  HMGCR MUTATED HMGCR WILD-TYPE
  0             3              32
  1             3              86
[1] 2 2
[1] FALSE
D553V6, binary
                 cls
clus               0  1
  HMGCR MUTATED    4  0
  HMGCR WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      4    0
  HMGCR WILD-TYPE   53    3
   clus
vv  HMGCR MUTATED HMGCR WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D553V7, binary
                 cls
clus               0  1
  HMGCR MUTATED    3  3
  HMGCR WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      3    3
  HMGCR WILD-TYPE   48   72
        clus
vv       HMGCR MUTATED HMGCR WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D553V8, binary
                 cls
clus               0  1
  HMGCR MUTATED    2  4
  HMGCR WILD-TYPE 86 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      2    4
  HMGCR WILD-TYPE   86   26
     clus
vv    HMGCR MUTATED HMGCR WILD-TYPE
  NO              2              86
  YES             4              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HMGCR MUTATED                                     5
  HMGCR WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HMGCR MUTATED                                       1
  HMGCR WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HMGCR MUTATED                                                  0
  HMGCR WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HMGCR MUTATED                                     0
  HMGCR WILD-TYPE                                   1
D553V9, multiclass
                                                  clus
vv                                                 HMGCR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HMGCR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V10, continuous
D553V11, continuous
                 vv
clus              R0 R1 R2 RX
  HMGCR MUTATED    5  1  0  0
  HMGCR WILD-TYPE 75 34  4  2
D553V12, multiclass
    clus
vv   HMGCR MUTATED HMGCR WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMGCR MUTATED       0                         0     6
  HMGCR WILD-TYPE     6                         5   108
D553V14, multiclass
                           clus
vv                          HMGCR MUTATED HMGCR WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V15, binary
                 cls
clus               0  1
  HMGCR MUTATED    1  4
  HMGCR WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMGCR MUTATED      1    4
  HMGCR WILD-TYPE    4   87
                        clus
vv                       HMGCR MUTATED HMGCR WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(554) Variable = ITPR2 MUTATION ANALYSIS
D554V1, survival
                 sevent
clus2              0  1
  ITPR2 MUTATED    2  3
  ITPR2 WILD-TYPE 61 59
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              5             120 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              3              59 
$`ITPR2 MUTATED`
TCGA-2L-AAQJ TCGA-F2-A8YN TCGA-HZ-8637 TCGA-HZ-A8P1 TCGA-IB-7651 
       12.95        17.00        17.00         0.23        19.82 

$`ITPR2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A9TJ 
       31.86        20.19        10.13         5.26        10.85        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           0.23            0.26 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
          19.82           90.12 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         17.000          15.205 
[1] "0.2 - 19.8 (17.0)" "0.3 - 90.1 (15.2)"
[1] "hr=" "1.5"
D554V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ITPR2 MUTATED         0        0        1         1         2         1
  ITPR2 WILD-TYPE       1        3       11        18        80         3
                 vv
clus              STAGE IV
  ITPR2 MUTATED          0
  ITPR2 WILD-TYPE        3
D554V3, multiclass
           clus
vv          ITPR2 MUTATED ITPR2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ITPR2 MUTATED    0  1     4
  ITPR2 WILD-TYPE  5 16    98
D554V4, multiclass
       clus
vv      ITPR2 MUTATED ITPR2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V5, binary
                 cls
clus               0  1
  ITPR2 MUTATED    3  2
  ITPR2 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      3    2
  ITPR2 WILD-TYPE   32   87
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D554V6, binary
                 cls
clus               0  1
  ITPR2 MUTATED    2  0
  ITPR2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      2    0
  ITPR2 WILD-TYPE   55    3
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D554V7, binary
                 cls
clus               0  1
  ITPR2 MUTATED    3  2
  ITPR2 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      3    2
  ITPR2 WILD-TYPE   48   73
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D554V8, binary
                 cls
clus               0  1
  ITPR2 MUTATED    3  1
  ITPR2 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      3    1
  ITPR2 WILD-TYPE   85   29
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ITPR2 MUTATED                                     5
  ITPR2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ITPR2 MUTATED                                       0
  ITPR2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ITPR2 MUTATED                                                  0
  ITPR2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ITPR2 MUTATED                                     0
  ITPR2 WILD-TYPE                                   1
D554V9, multiclass
                                                  clus
vv                                                 ITPR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ITPR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V10, continuous
D554V11, continuous
[1] "Remove cluster labels:" "ITPR2 MUTATED"         
clus
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-IB-7885      TCGA-IB-8126 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" "ITPR2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ITPR2 MUTATED    3  2  0  0
  ITPR2 WILD-TYPE 77 33  4  2
D554V12, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITPR2 MUTATED       0                         0     5
  ITPR2 WILD-TYPE     6                         5   109
D554V14, multiclass
                           clus
vv                          ITPR2 MUTATED ITPR2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V15, binary
                 cls
clus               0  1
  ITPR2 MUTATED    1  3
  ITPR2 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED      1    3
  ITPR2 WILD-TYPE    4   88
                        clus
vv                       ITPR2 MUTATED ITPR2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(555) Variable = FZD7 MUTATION ANALYSIS
D555V1, survival
                sevent
clus2             0  1
  FZD7 MUTATED    4  0
  FZD7 WILD-TYPE 59 62
  FZD7 MUTATED FZD7 WILD-TYPE 
             4            121 
  FZD7 MUTATED FZD7 WILD-TYPE 
             0             62 
$`FZD7 MUTATED`
TCGA-3A-A9IR TCGA-HV-AA8V TCGA-HZ-A77P TCGA-HZ-A8P1 
       50.70        30.25        10.85         0.23 

$`FZD7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        32.15        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A9TJ 
       31.86        20.19        17.00        10.13         5.26        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  FZD7 MUTATED FZD7 WILD-TYPE 
          0.23           0.26 
  FZD7 MUTATED FZD7 WILD-TYPE 
         50.70          90.12 
  FZD7 MUTATED FZD7 WILD-TYPE 
         20.55          15.22 
[1] "0.2 - 50.7 (20.6)" "0.3 - 90.1 (15.2)"
[1] "hr="     "2.6e+07"
D555V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FZD7 MUTATED         0        0        2         0         2         0
  FZD7 WILD-TYPE       1        3       10        19        80         4
                vv
clus             STAGE IV
  FZD7 MUTATED          0
  FZD7 WILD-TYPE        3
D555V3, multiclass
           clus
vv          FZD7 MUTATED FZD7 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             2             10
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  FZD7 MUTATED     0   2     2
  FZD7 WILD-TYPE   5  15   100
D555V4, multiclass
       clus
vv      FZD7 MUTATED FZD7 WILD-TYPE
  T1               0              5
  T2               2             15
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V5, binary
                cls
clus              0  1
  FZD7 MUTATED    2  2
  FZD7 WILD-TYPE 33 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD7 MUTATED      2    2
  FZD7 WILD-TYPE   33   87
   clus
vv  FZD7 MUTATED FZD7 WILD-TYPE
  0            2             33
  1            2             87
[1] 2 2
[1] FALSE
D555V6, binary
                cls
clus              0  1
  FZD7 MUTATED    0  0
  FZD7 WILD-TYPE 57  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD7 MUTATED      0    0
  FZD7 WILD-TYPE   57    3
D555V7, binary
                cls
clus              0  1
  FZD7 MUTATED    1  3
  FZD7 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD7 MUTATED      1    3
  FZD7 WILD-TYPE   50   72
        clus
vv       FZD7 MUTATED FZD7 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D555V8, binary
                cls
clus              0  1
  FZD7 MUTATED    3  0
  FZD7 WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD7 MUTATED      3    0
  FZD7 WILD-TYPE   85   30
     clus
vv    FZD7 MUTATED FZD7 WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FZD7 MUTATED                                     2
  FZD7 WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FZD7 MUTATED                                       2
  FZD7 WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FZD7 MUTATED                                                  0
  FZD7 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  FZD7 MUTATED                                     0
  FZD7 WILD-TYPE                                   1
D555V9, multiclass
                                                  clus
vv                                                 FZD7 MUTATED FZD7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V10, continuous
[1] "Remove cluster labels:" "FZD7 MUTATED"          
clus
  FZD7 MUTATED FZD7 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-IB-7651 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-YY-A8LH 
"FZD7 WILD-TYPE" 
D555V11, continuous
[1] "Remove cluster labels:" "FZD7 MUTATED"          
clus
  FZD7 MUTATED FZD7 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IX 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"FZD7 WILD-TYPE" "FZD7 WILD-TYPE" "FZD7 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  FZD7 MUTATED    3  0  1  0
  FZD7 WILD-TYPE 77 35  3  2
D555V12, multiclass
    clus
vv   FZD7 MUTATED FZD7 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            1              3
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FZD7 MUTATED       1                         0     3
  FZD7 WILD-TYPE     5                         5   111
D555V14, multiclass
                           clus
vv                          FZD7 MUTATED FZD7 WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V15, binary
                cls
clus              0  1
  FZD7 MUTATED    0  3
  FZD7 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD7 MUTATED      0    3
  FZD7 WILD-TYPE    5   88
                        clus
vv                       FZD7 MUTATED FZD7 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(556) Variable = TGFBR1 MUTATION ANALYSIS
D556V1, survival
                  sevent
clus2               0  1
  TGFBR1 MUTATED    2  4
  TGFBR1 WILD-TYPE 61 58
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               6              119 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               4               58 
$`TGFBR1 MUTATED`
TCGA-3E-AAAY TCGA-FZ-5922 TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUU TCGA-LB-A9Q5 
       75.12        36.20        19.82        12.00         8.05        10.29 

$`TGFBR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       15.06        36.26        34.09        10.13        24.43        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        15.19        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY 
        7.40        13.28         7.56        12.46         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            8.05             0.23 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
           75.12            90.12 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
           15.91            15.22 
[1] "8.1 - 75.1 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D556V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TGFBR1 MUTATED         0        0        0         1         5         0
  TGFBR1 WILD-TYPE       1        3       12        18        77         4
                  vv
clus               STAGE IV
  TGFBR1 MUTATED          0
  TGFBR1 WILD-TYPE        3
D556V3, multiclass
           clus
vv          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              5               77
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  TGFBR1 MUTATED    0  0     6
  TGFBR1 WILD-TYPE  5 17    96
D556V4, multiclass
       clus
vv      TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              6               96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V5, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    1  5
  TGFBR1 WILD-TYPE 34 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      1    5
  TGFBR1 WILD-TYPE   34   84
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              1               34
  1              5               84
[1] 2 2
[1] FALSE
D556V6, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    4  0
  TGFBR1 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      4    0
  TGFBR1 WILD-TYPE   53    3
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D556V7, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    2  4
  TGFBR1 WILD-TYPE 49 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      2    4
  TGFBR1 WILD-TYPE   49   71
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  FEMALE              2               49
  MALE                4               71
[1] 2 2
[1] FALSE
D556V8, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    5  1
  TGFBR1 WILD-TYPE 83 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      5    1
  TGFBR1 WILD-TYPE   83   29
     clus
vv    TGFBR1 MUTATED TGFBR1 WILD-TYPE
  NO               5               83
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR1 MUTATED                                     6
  TGFBR1 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR1 MUTATED                                       0
  TGFBR1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR1 MUTATED                                                  0
  TGFBR1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TGFBR1 MUTATED                                     0
  TGFBR1 WILD-TYPE                                   1
D556V9, multiclass
                                                  clus
vv                                                 TGFBR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TGFBR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V10, continuous
D556V11, continuous
[1] "Remove cluster labels:" "TGFBR1 MUTATED"        
clus
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-OE-A75W 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" "TGFBR1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TGFBR1 MUTATED    5  0  0  0
  TGFBR1 WILD-TYPE 75 35  4  2
D556V12, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR1 MUTATED       0                         0     6
  TGFBR1 WILD-TYPE     6                         5   108
D556V14, multiclass
                           clus
vv                          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V15, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    0  5
  TGFBR1 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      0    5
  TGFBR1 WILD-TYPE    5   86
                        clus
vv                       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(557) Variable = LRRC41 MUTATION ANALYSIS
D557V1, survival
                  sevent
clus2               0  1
  LRRC41 MUTATED    2  1
  LRRC41 WILD-TYPE 61 61
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               3              122 
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               1               61 
$`LRRC41 MUTATED`
TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-XD-AAUI 
       22.06        32.15        12.03 

$`LRRC41 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       36.20        20.35        17.79         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LRRC41 MUTATED LRRC41 WILD-TYPE 
           12.03             0.23 
  LRRC41 MUTATED LRRC41 WILD-TYPE 
           32.15            90.12 
  LRRC41 MUTATED LRRC41 WILD-TYPE 
          22.060           15.205 
[1] "12.0 - 32.1 (22.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2"  
D557V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LRRC41 MUTATED         0        0        0         1         2         0
  LRRC41 WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  LRRC41 MUTATED          0
  LRRC41 WILD-TYPE        3
D557V3, multiclass
           clus
vv          LRRC41 MUTATED LRRC41 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  LRRC41 MUTATED    0  0     3
  LRRC41 WILD-TYPE  5 17    99
D557V4, multiclass
       clus
vv      LRRC41 MUTATED LRRC41 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V5, binary
                  cls
clus                0  1
  LRRC41 MUTATED    1  2
  LRRC41 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC41 MUTATED      1    2
  LRRC41 WILD-TYPE   34   87
   clus
vv  LRRC41 MUTATED LRRC41 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D557V6, binary
                  cls
clus                0  1
  LRRC41 MUTATED    1  0
  LRRC41 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC41 MUTATED      1    0
  LRRC41 WILD-TYPE   56    3
   clus
vv  LRRC41 MUTATED LRRC41 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D557V7, binary
                  cls
clus                0  1
  LRRC41 MUTATED    1  2
  LRRC41 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC41 MUTATED      1    2
  LRRC41 WILD-TYPE   50   73
        clus
vv       LRRC41 MUTATED LRRC41 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D557V8, binary
                  cls
clus                0  1
  LRRC41 MUTATED    2  1
  LRRC41 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC41 MUTATED      2    1
  LRRC41 WILD-TYPE   86   29
     clus
vv    LRRC41 MUTATED LRRC41 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LRRC41 MUTATED                                     1
  LRRC41 WILD-TYPE                                 104
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LRRC41 MUTATED                                       2
  LRRC41 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LRRC41 MUTATED                                                  0
  LRRC41 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  LRRC41 MUTATED                                     0
  LRRC41 WILD-TYPE                                   1
D557V9, multiclass
                                                  clus
vv                                                 LRRC41 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 LRRC41 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V10, continuous
[1] "Remove cluster labels:" "LRRC41 MUTATED"        
clus
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
D557V11, continuous
[1] "Remove cluster labels:" "LRRC41 MUTATED"        
clus
  LRRC41 MUTATED LRRC41 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XN-A8T5       TCGA-YY-A8LH 
"LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" "LRRC41 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LRRC41 MUTATED    2  1  0  0
  LRRC41 WILD-TYPE 78 34  4  2
D557V12, multiclass
    clus
vv   LRRC41 MUTATED LRRC41 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRRC41 MUTATED       1                         0     2
  LRRC41 WILD-TYPE     5                         5   112
D557V14, multiclass
                           clus
vv                          LRRC41 MUTATED LRRC41 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V15, binary
                  cls
clus                0  1
  LRRC41 MUTATED    0  2
  LRRC41 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC41 MUTATED      0    2
  LRRC41 WILD-TYPE    5   89
                        clus
vv                       LRRC41 MUTATED LRRC41 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(558) Variable = STAG3 MUTATION ANALYSIS
D558V1, survival
                 sevent
clus2              0  1
  STAG3 MUTATED    2  3
  STAG3 WILD-TYPE 61 59
  STAG3 MUTATED STAG3 WILD-TYPE 
              5             120 
  STAG3 MUTATED STAG3 WILD-TYPE 
              3              59 
$`STAG3 MUTATED`
TCGA-2L-AAQE TCGA-IB-7651 TCGA-IB-A5SO TCGA-RL-AAAS TCGA-YH-A8SY 
       22.49        19.82        12.00         0.30        12.76 

$`STAG3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        11.51        66.28        15.35 

  STAG3 MUTATED STAG3 WILD-TYPE 
           0.30            0.23 
  STAG3 MUTATED STAG3 WILD-TYPE 
          22.49           90.12 
  STAG3 MUTATED STAG3 WILD-TYPE 
          12.76           15.27 
[1] "0.3 - 22.5 (12.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.5"
D558V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  STAG3 MUTATED         0        0        1         0         3         1
  STAG3 WILD-TYPE       1        3       11        19        79         3
                 vv
clus              STAGE IV
  STAG3 MUTATED          0
  STAG3 WILD-TYPE        3
D558V3, multiclass
           clus
vv          STAG3 MUTATED STAG3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  STAG3 MUTATED    0  1     4
  STAG3 WILD-TYPE  5 16    98
D558V4, multiclass
       clus
vv      STAG3 MUTATED STAG3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V5, binary
                 cls
clus               0  1
  STAG3 MUTATED    1  4
  STAG3 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG3 MUTATED      1    4
  STAG3 WILD-TYPE   34   85
   clus
vv  STAG3 MUTATED STAG3 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D558V6, binary
                 cls
clus               0  1
  STAG3 MUTATED    4  0
  STAG3 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG3 MUTATED      4    0
  STAG3 WILD-TYPE   53    3
   clus
vv  STAG3 MUTATED STAG3 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D558V7, binary
                 cls
clus               0  1
  STAG3 MUTATED    3  2
  STAG3 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG3 MUTATED      3    2
  STAG3 WILD-TYPE   48   73
        clus
vv       STAG3 MUTATED STAG3 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D558V8, binary
                 cls
clus               0  1
  STAG3 MUTATED    4  1
  STAG3 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG3 MUTATED      4    1
  STAG3 WILD-TYPE   84   29
     clus
vv    STAG3 MUTATED STAG3 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STAG3 MUTATED                                     4
  STAG3 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STAG3 MUTATED                                       0
  STAG3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STAG3 MUTATED                                                  0
  STAG3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  STAG3 MUTATED                                     0
  STAG3 WILD-TYPE                                   1
D558V9, multiclass
                                                  clus
vv                                                 STAG3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 STAG3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V10, continuous
[1] "Remove cluster labels:" "STAG3 MUTATED"         
clus
  STAG3 MUTATED STAG3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-YY-A8LH 
"STAG3 WILD-TYPE" 
D558V11, continuous
[1] "Remove cluster labels:" "STAG3 MUTATED"         
clus
  STAG3 MUTATED STAG3 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" "STAG3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  STAG3 MUTATED    4  0  0  0
  STAG3 WILD-TYPE 76 35  4  2
D558V12, multiclass
    clus
vv   STAG3 MUTATED STAG3 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG3 MUTATED       0                         0     5
  STAG3 WILD-TYPE     6                         5   109
D558V14, multiclass
                           clus
vv                          STAG3 MUTATED STAG3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V15, binary
                 cls
clus               0  1
  STAG3 MUTATED    0  3
  STAG3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG3 MUTATED      0    3
  STAG3 WILD-TYPE    5   88
                        clus
vv                       STAG3 MUTATED STAG3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(559) Variable = PSME4 MUTATION ANALYSIS
D559V1, survival
                 sevent
clus2              0  1
  PSME4 MUTATED    3  2
  PSME4 WILD-TYPE 60 60
  PSME4 MUTATED PSME4 WILD-TYPE 
              5             120 
  PSME4 MUTATED PSME4 WILD-TYPE 
              2              60 
$`PSME4 MUTATED`
TCGA-3A-A9IB TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-AAUR TCGA-YB-A89D 
        7.36         8.28        19.82        11.11        11.51 

$`PSME4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        23.67        12.76        66.28        15.35 

  PSME4 MUTATED PSME4 WILD-TYPE 
           7.36            0.23 
  PSME4 MUTATED PSME4 WILD-TYPE 
          19.82           90.12 
  PSME4 MUTATED PSME4 WILD-TYPE 
         11.110          15.335 
[1] "7.4 - 19.8 (11.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.3"
D559V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PSME4 MUTATED         0        0        0         1         4         0
  PSME4 WILD-TYPE       1        3       12        18        78         4
                 vv
clus              STAGE IV
  PSME4 MUTATED          0
  PSME4 WILD-TYPE        3
D559V3, multiclass
           clus
vv          PSME4 MUTATED PSME4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PSME4 MUTATED    0  0     5
  PSME4 WILD-TYPE  5 17    97
D559V4, multiclass
       clus
vv      PSME4 MUTATED PSME4 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V5, binary
                 cls
clus               0  1
  PSME4 MUTATED    1  4
  PSME4 WILD-TYPE 34 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      1    4
  PSME4 WILD-TYPE   34   85
   clus
vv  PSME4 MUTATED PSME4 WILD-TYPE
  0             1              34
  1             4              85
[1] 2 2
[1] FALSE
D559V6, binary
                 cls
clus               0  1
  PSME4 MUTATED    2  0
  PSME4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      2    0
  PSME4 WILD-TYPE   55    3
   clus
vv  PSME4 MUTATED PSME4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D559V7, binary
                 cls
clus               0  1
  PSME4 MUTATED    2  3
  PSME4 WILD-TYPE 49 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      2    3
  PSME4 WILD-TYPE   49   72
        clus
vv       PSME4 MUTATED PSME4 WILD-TYPE
  FEMALE             2              49
  MALE               3              72
[1] 2 2
[1] FALSE
D559V8, binary
                 cls
clus               0  1
  PSME4 MUTATED    4  1
  PSME4 WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      4    1
  PSME4 WILD-TYPE   84   29
     clus
vv    PSME4 MUTATED PSME4 WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PSME4 MUTATED                                     5
  PSME4 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PSME4 MUTATED                                       0
  PSME4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PSME4 MUTATED                                                  0
  PSME4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PSME4 MUTATED                                     0
  PSME4 WILD-TYPE                                   1
D559V9, multiclass
                                                  clus
vv                                                 PSME4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PSME4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V10, continuous
[1] "Remove cluster labels:" "PSME4 MUTATED"         
clus
  PSME4 MUTATED PSME4 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IX 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-YY-A8LH 
"PSME4 WILD-TYPE" 
D559V11, continuous
[1] "Remove cluster labels:" "PSME4 MUTATED"         
clus
  PSME4 MUTATED PSME4 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IR      TCGA-3A-A9IX 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PSME4 WILD-TYPE" "PSME4 WILD-TYPE" "PSME4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PSME4 MUTATED    3  1  1  0
  PSME4 WILD-TYPE 77 34  3  2
D559V12, multiclass
    clus
vv   PSME4 MUTATED PSME4 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSME4 MUTATED       1                         0     4
  PSME4 WILD-TYPE     5                         5   110
D559V14, multiclass
                           clus
vv                          PSME4 MUTATED PSME4 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V15, binary
                 cls
clus               0  1
  PSME4 MUTATED    0  4
  PSME4 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSME4 MUTATED      0    4
  PSME4 WILD-TYPE    5   87
                        clus
vv                       PSME4 MUTATED PSME4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(560) Variable = LILRA2 MUTATION ANALYSIS
D560V1, survival
                  sevent
clus2               0  1
  LILRA2 MUTATED    2  3
  LILRA2 WILD-TYPE 61 59
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               5              120 
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               3               59 
$`LILRA2 MUTATED`
TCGA-FB-AAPQ TCGA-FB-AAQ1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-RL-AAAS 
       37.15         4.04        19.82        19.82         0.30 

$`LILRA2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ2 
       15.95         7.50        12.53        23.54        15.55         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 
        8.78        13.68         3.12        15.32         9.40        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  LILRA2 MUTATED LILRA2 WILD-TYPE 
            0.30             0.23 
  LILRA2 MUTATED LILRA2 WILD-TYPE 
           37.15            90.12 
  LILRA2 MUTATED LILRA2 WILD-TYPE 
          19.820           15.205 
[1] "0.3 - 37.1 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D560V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LILRA2 MUTATED         0        0        1         0         3         0
  LILRA2 WILD-TYPE       1        3       11        19        79         4
                  vv
clus               STAGE IV
  LILRA2 MUTATED          1
  LILRA2 WILD-TYPE        2
D560V3, multiclass
           clus
vv          LILRA2 MUTATED LILRA2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  LILRA2 MUTATED    0  1     4
  LILRA2 WILD-TYPE  5 16    98
D560V4, multiclass
       clus
vv      LILRA2 MUTATED LILRA2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V5, binary
                  cls
clus                0  1
  LILRA2 MUTATED    2  3
  LILRA2 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA2 MUTATED      2    3
  LILRA2 WILD-TYPE   33   86
   clus
vv  LILRA2 MUTATED LILRA2 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D560V6, binary
                  cls
clus                0  1
  LILRA2 MUTATED    2  1
  LILRA2 WILD-TYPE 55  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA2 MUTATED      2    1
  LILRA2 WILD-TYPE   55    2
   clus
vv  LILRA2 MUTATED LILRA2 WILD-TYPE
  0              2               55
  1              1                2
[1] 2 2
[1] FALSE
D560V7, binary
                  cls
clus                0  1
  LILRA2 MUTATED    2  3
  LILRA2 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA2 MUTATED      2    3
  LILRA2 WILD-TYPE   49   72
        clus
vv       LILRA2 MUTATED LILRA2 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D560V8, binary
                  cls
clus                0  1
  LILRA2 MUTATED    5  0
  LILRA2 WILD-TYPE 83 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA2 MUTATED      5    0
  LILRA2 WILD-TYPE   83   30
     clus
vv    LILRA2 MUTATED LILRA2 WILD-TYPE
  NO               5               83
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LILRA2 MUTATED                                     4
  LILRA2 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LILRA2 MUTATED                                       1
  LILRA2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LILRA2 MUTATED                                                  0
  LILRA2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  LILRA2 MUTATED                                     0
  LILRA2 WILD-TYPE                                   1
D560V9, multiclass
                                                  clus
vv                                                 LILRA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 LILRA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V10, continuous
[1] "Remove cluster labels:" "LILRA2 MUTATED"        
clus
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-YY-A8LH 
"LILRA2 WILD-TYPE" 
D560V11, continuous
[1] "Remove cluster labels:" "LILRA2 MUTATED"        
clus
  LILRA2 MUTATED LILRA2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" "LILRA2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LILRA2 MUTATED    4  1  0  0
  LILRA2 WILD-TYPE 76 34  4  2
D560V12, multiclass
    clus
vv   LILRA2 MUTATED LILRA2 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LILRA2 MUTATED       0                         0     5
  LILRA2 WILD-TYPE     6                         5   109
D560V14, multiclass
                           clus
vv                          LILRA2 MUTATED LILRA2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V15, binary
                  cls
clus                0  1
  LILRA2 MUTATED    0  5
  LILRA2 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA2 MUTATED      0    5
  LILRA2 WILD-TYPE    5   86
                        clus
vv                       LILRA2 MUTATED LILRA2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(561) Variable = ATP2C2 MUTATION ANALYSIS
D561V1, survival
                  sevent
clus2               0  1
  ATP2C2 MUTATED    2  2
  ATP2C2 WILD-TYPE 61 60
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              121 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               60 
$`ATP2C2 MUTATED`
TCGA-3A-A9IH TCGA-FB-AAPS TCGA-IB-7651 TCGA-US-A77G 
       33.57         7.50        19.82         0.39 

$`ATP2C2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
            0.39             0.23 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
           33.57            90.12 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
           13.66            15.22 
[1] "0.4 - 33.6 (13.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D561V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP2C2 MUTATED         0        1        0         0         3         0
  ATP2C2 WILD-TYPE       1        2       12        19        79         4
                  vv
clus               STAGE IV
  ATP2C2 MUTATED          0
  ATP2C2 WILD-TYPE        3
D561V3, multiclass
           clus
vv          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP2C2 MUTATED     1   1     2
  ATP2C2 WILD-TYPE   4  16   100
D561V4, multiclass
       clus
vv      ATP2C2 MUTATED ATP2C2 WILD-TYPE
  T1                 1                4
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V5, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    1  3
  ATP2C2 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    3
  ATP2C2 WILD-TYPE   34   86
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D561V6, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    1  0
  ATP2C2 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    0
  ATP2C2 WILD-TYPE   56    3
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D561V7, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    3  1
  ATP2C2 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      3    1
  ATP2C2 WILD-TYPE   48   74
        clus
vv       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D561V8, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    3  1
  ATP2C2 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      3    1
  ATP2C2 WILD-TYPE   85   29
     clus
vv    ATP2C2 MUTATED ATP2C2 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2C2 MUTATED                                     4
  ATP2C2 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2C2 MUTATED                                       0
  ATP2C2 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2C2 MUTATED                                                  0
  ATP2C2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP2C2 MUTATED                                     0
  ATP2C2 WILD-TYPE                                   1
D561V9, multiclass
                                                  clus
vv                                                 ATP2C2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ATP2C2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V10, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" 
D561V11, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATP2C2 MUTATED    4  0  0  0
  ATP2C2 WILD-TYPE 76 35  4  2
D561V12, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2C2 MUTATED       0                         0     4
  ATP2C2 WILD-TYPE     6                         5   110
D561V14, multiclass
                           clus
vv                          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V15, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    0  4
  ATP2C2 WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      0    4
  ATP2C2 WILD-TYPE    5   87
                        clus
vv                       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(562) Variable = KIAA1211 MUTATION ANALYSIS
D562V1, survival
                    sevent
clus2                 0  1
  KIAA1211 MUTATED    2  3
  KIAA1211 WILD-TYPE 61 59
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 5                120 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 3                 59 
$`KIAA1211 MUTATED`
TCGA-2J-AABE TCGA-2J-AABP TCGA-HZ-8637 TCGA-IB-7651 TCGA-IB-A5SQ 
       22.22        15.22        17.00        19.82         7.20 

$`KIAA1211 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
              7.20               0.23 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
             22.22              90.12 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
            17.000             15.155 
[1] "7.2 - 22.2 (17.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D562V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KIAA1211 MUTATED         0        0        1         1         3         0
  KIAA1211 WILD-TYPE       1        3       11        18        79         4
                    vv
clus                 STAGE IV
  KIAA1211 MUTATED          0
  KIAA1211 WILD-TYPE        3
D562V3, multiclass
           clus
vv          KIAA1211 MUTATED KIAA1211 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  KIAA1211 MUTATED    0  1     4
  KIAA1211 WILD-TYPE  5 16    98
D562V4, multiclass
       clus
vv      KIAA1211 MUTATED KIAA1211 WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V5, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    2  3
  KIAA1211 WILD-TYPE 33 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      2    3
  KIAA1211 WILD-TYPE   33   86
   clus
vv  KIAA1211 MUTATED KIAA1211 WILD-TYPE
  0                2                 33
  1                3                 86
[1] 2 2
[1] FALSE
D562V6, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    4  0
  KIAA1211 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      4    0
  KIAA1211 WILD-TYPE   53    3
   clus
vv  KIAA1211 MUTATED KIAA1211 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D562V7, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    4  1
  KIAA1211 WILD-TYPE 47 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      4    1
  KIAA1211 WILD-TYPE   47   74
        clus
vv       KIAA1211 MUTATED KIAA1211 WILD-TYPE
  FEMALE                4                 47
  MALE                  1                 74
[1] 2 2
[1] FALSE
D562V8, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    3  2
  KIAA1211 WILD-TYPE 85 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      3    2
  KIAA1211 WILD-TYPE   85   28
     clus
vv    KIAA1211 MUTATED KIAA1211 WILD-TYPE
  NO                 3                 85
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA1211 MUTATED                                     4
  KIAA1211 WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA1211 MUTATED                                       0
  KIAA1211 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA1211 MUTATED                                                  0
  KIAA1211 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  KIAA1211 MUTATED                                     1
  KIAA1211 WILD-TYPE                                   0
D562V9, multiclass
                                                  clus
vv                                                 KIAA1211 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
                                                  clus
vv                                                 KIAA1211 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V10, continuous
[1] "Remove cluster labels:" "KIAA1211 MUTATED"      
clus
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABF 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-YY-A8LH 
"KIAA1211 WILD-TYPE" 
D562V11, continuous
[1] "Remove cluster labels:" "KIAA1211 MUTATED"      
clus
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABF         TCGA-2J-AABO 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-YY-A8LH 
"KIAA1211 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  KIAA1211 MUTATED    5  0  0  0
  KIAA1211 WILD-TYPE 75 35  4  2
D562V12, multiclass
    clus
vv   KIAA1211 MUTATED KIAA1211 WILD-TYPE
  R0                5                 75
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1211 MUTATED       0                         0     5
  KIAA1211 WILD-TYPE     6                         5   109
D562V14, multiclass
                           clus
vv                          KIAA1211 MUTATED KIAA1211 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V15, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    1  2
  KIAA1211 WILD-TYPE  4 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      1    2
  KIAA1211 WILD-TYPE    4   89
                        clus
vv                       KIAA1211 MUTATED KIAA1211 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(563) Variable = LPIN3 MUTATION ANALYSIS
D563V1, survival
                 sevent
clus2              0  1
  LPIN3 MUTATED    3  1
  LPIN3 WILD-TYPE 60 61
  LPIN3 MUTATED LPIN3 WILD-TYPE 
              4             121 
  LPIN3 MUTATED LPIN3 WILD-TYPE 
              1              61 
$`LPIN3 MUTATED`
TCGA-2L-AAQM TCGA-3A-A9I9 TCGA-3A-A9IV TCGA-F2-A8YN 
       45.47        20.84        36.26        17.00 

$`LPIN3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39        12.95         9.60        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IX 
       33.57        63.85        50.70        32.81        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  LPIN3 MUTATED LPIN3 WILD-TYPE 
          17.00            0.23 
  LPIN3 MUTATED LPIN3 WILD-TYPE 
          45.47           90.12 
  LPIN3 MUTATED LPIN3 WILD-TYPE 
          28.55           15.12 
[1] "17.0 - 45.5 (28.5)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3.4"
D563V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LPIN3 MUTATED         0        0        1         2         1         0
  LPIN3 WILD-TYPE       1        3       11        17        81         4
                 vv
clus              STAGE IV
  LPIN3 MUTATED          0
  LPIN3 WILD-TYPE        3
D563V3, multiclass
           clus
vv          LPIN3 MUTATED LPIN3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             2              17
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LPIN3 MUTATED    0  1     3
  LPIN3 WILD-TYPE  5 16    99
D563V4, multiclass
       clus
vv      LPIN3 MUTATED LPIN3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V5, binary
                 cls
clus               0  1
  LPIN3 MUTATED    3  1
  LPIN3 WILD-TYPE 32 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN3 MUTATED      3    1
  LPIN3 WILD-TYPE   32   88
   clus
vv  LPIN3 MUTATED LPIN3 WILD-TYPE
  0             3              32
  1             1              88
[1] 2 2
[1] FALSE
D563V6, binary
                 cls
clus               0  1
  LPIN3 MUTATED    1  0
  LPIN3 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN3 MUTATED      1    0
  LPIN3 WILD-TYPE   56    3
   clus
vv  LPIN3 MUTATED LPIN3 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D563V7, binary
                 cls
clus               0  1
  LPIN3 MUTATED    1  3
  LPIN3 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN3 MUTATED      1    3
  LPIN3 WILD-TYPE   50   72
        clus
vv       LPIN3 MUTATED LPIN3 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D563V8, binary
                 cls
clus               0  1
  LPIN3 MUTATED    3  1
  LPIN3 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN3 MUTATED      3    1
  LPIN3 WILD-TYPE   85   29
     clus
vv    LPIN3 MUTATED LPIN3 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LPIN3 MUTATED                                     2
  LPIN3 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LPIN3 MUTATED                                       2
  LPIN3 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LPIN3 MUTATED                                                  0
  LPIN3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LPIN3 MUTATED                                     0
  LPIN3 WILD-TYPE                                   1
D563V9, multiclass
                                                  clus
vv                                                 LPIN3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LPIN3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V10, continuous
[1] "Remove cluster labels:" "LPIN3 MUTATED"         
clus
  LPIN3 MUTATED LPIN3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9IB      TCGA-3A-A9IX 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1      TCGA-IB-7651 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" "LPIN3 WILD-TYPE" 
     TCGA-YY-A8LH 
"LPIN3 WILD-TYPE" 
D563V11, continuous
                 vv
clus              R0 R1 R2 RX
  LPIN3 MUTATED    2  2  0  0
  LPIN3 WILD-TYPE 78 33  4  2
D563V12, multiclass
    clus
vv   LPIN3 MUTATED LPIN3 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LPIN3 MUTATED       0                         0     4
  LPIN3 WILD-TYPE     6                         5   110
D563V14, multiclass
                           clus
vv                          LPIN3 MUTATED LPIN3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V15, binary
                 cls
clus               0  1
  LPIN3 MUTATED    0  3
  LPIN3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN3 MUTATED      0    3
  LPIN3 WILD-TYPE    5   88
                        clus
vv                       LPIN3 MUTATED LPIN3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(564) Variable = WDR8 MUTATION ANALYSIS
D564V1, survival
                sevent
clus2             0  1
  WDR8 MUTATED    1  3
  WDR8 WILD-TYPE 62 59
  WDR8 MUTATED WDR8 WILD-TYPE 
             4            121 
  WDR8 MUTATED WDR8 WILD-TYPE 
             3             59 
$`WDR8 MUTATED`
TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-IB-7651 TCGA-US-A77J 
        9.63         2.63        19.82        18.67 

$`WDR8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB9 TCGA-2J-AABA 
       14.14        16.37         2.17        23.97        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  WDR8 MUTATED WDR8 WILD-TYPE 
          2.63           0.23 
  WDR8 MUTATED WDR8 WILD-TYPE 
         19.82          90.12 
  WDR8 MUTATED WDR8 WILD-TYPE 
         14.15          15.22 
[1] "2.6 - 19.8 (14.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.1"
D564V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  WDR8 MUTATED         0        0        0         1         3         0
  WDR8 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  WDR8 MUTATED          0
  WDR8 WILD-TYPE        3
D564V3, multiclass
           clus
vv          WDR8 MUTATED WDR8 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  WDR8 MUTATED    0  0     4
  WDR8 WILD-TYPE  5 17    98
D564V4, multiclass
       clus
vv      WDR8 MUTATED WDR8 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V5, binary
                cls
clus              0  1
  WDR8 MUTATED    1  3
  WDR8 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR8 MUTATED      1    3
  WDR8 WILD-TYPE   34   86
   clus
vv  WDR8 MUTATED WDR8 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D564V6, binary
                cls
clus              0  1
  WDR8 MUTATED    3  0
  WDR8 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR8 MUTATED      3    0
  WDR8 WILD-TYPE   54    3
   clus
vv  WDR8 MUTATED WDR8 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D564V7, binary
                cls
clus              0  1
  WDR8 MUTATED    2  2
  WDR8 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR8 MUTATED      2    2
  WDR8 WILD-TYPE   49   73
        clus
vv       WDR8 MUTATED WDR8 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D564V8, binary
                cls
clus              0  1
  WDR8 MUTATED    2  0
  WDR8 WILD-TYPE 86 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR8 MUTATED      2    0
  WDR8 WILD-TYPE   86   30
     clus
vv    WDR8 MUTATED WDR8 WILD-TYPE
  NO             2             86
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDR8 MUTATED                                     4
  WDR8 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDR8 MUTATED                                       0
  WDR8 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDR8 MUTATED                                                  0
  WDR8 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  WDR8 MUTATED                                     0
  WDR8 WILD-TYPE                                   1
D564V9, multiclass
                                                  clus
vv                                                 WDR8 MUTATED WDR8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V10, continuous
[1] "Remove cluster labels:" "WDR8 MUTATED"          
clus
  WDR8 MUTATED WDR8 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
D564V11, continuous
[1] "Remove cluster labels:" "WDR8 MUTATED"          
clus
  WDR8 MUTATED WDR8 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" "WDR8 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  WDR8 MUTATED    3  1  0  0
  WDR8 WILD-TYPE 77 34  4  2
D564V12, multiclass
    clus
vv   WDR8 MUTATED WDR8 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR8 MUTATED       0                         0     4
  WDR8 WILD-TYPE     6                         5   110
D564V14, multiclass
                           clus
vv                          WDR8 MUTATED WDR8 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V15, binary
                cls
clus              0  1
  WDR8 MUTATED    0  2
  WDR8 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR8 MUTATED      0    2
  WDR8 WILD-TYPE    5   89
                        clus
vv                       WDR8 MUTATED WDR8 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(565) Variable = ASH1L MUTATION ANALYSIS
D565V1, survival
                 sevent
clus2              0  1
  ASH1L MUTATED    3  3
  ASH1L WILD-TYPE 60 59
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             119 
  ASH1L MUTATED ASH1L WILD-TYPE 
              3              59 
$`ASH1L MUTATED`
TCGA-HZ-A77Q TCGA-2L-AAQL TCGA-3A-A9IH TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-YB-A89D 
        1.08         9.60        33.57        15.55        19.82        11.51 

$`ASH1L WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       12.53        23.54         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  ASH1L MUTATED ASH1L WILD-TYPE 
           1.08            0.23 
  ASH1L MUTATED ASH1L WILD-TYPE 
          33.57           90.12 
  ASH1L MUTATED ASH1L WILD-TYPE 
          13.53           15.22 
[1] "1.1 - 33.6 (13.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D565V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ASH1L MUTATED         0        1        0         1         4         0
  ASH1L WILD-TYPE       1        2       12        18        78         4
                 vv
clus              STAGE IV
  ASH1L MUTATED          0
  ASH1L WILD-TYPE        3
D565V3, multiclass
           clus
vv          ASH1L MUTATED ASH1L WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  ASH1L MUTATED    1  0     5
  ASH1L WILD-TYPE  4 17    97
D565V4, multiclass
       clus
vv      ASH1L MUTATED ASH1L WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V5, binary
                 cls
clus               0  1
  ASH1L MUTATED    2  4
  ASH1L WILD-TYPE 33 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      2    4
  ASH1L WILD-TYPE   33   85
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             2              33
  1             4              85
[1] 2 2
[1] FALSE
D565V6, binary
                 cls
clus               0  1
  ASH1L MUTATED    1  0
  ASH1L WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      1    0
  ASH1L WILD-TYPE   56    3
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D565V7, binary
                 cls
clus               0  1
  ASH1L MUTATED    3  3
  ASH1L WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      3    3
  ASH1L WILD-TYPE   48   72
        clus
vv       ASH1L MUTATED ASH1L WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D565V8, binary
                 cls
clus               0  1
  ASH1L MUTATED    4  1
  ASH1L WILD-TYPE 84 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      4    1
  ASH1L WILD-TYPE   84   29
     clus
vv    ASH1L MUTATED ASH1L WILD-TYPE
  NO              4              84
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASH1L MUTATED                                     5
  ASH1L WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASH1L MUTATED                                       1
  ASH1L WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASH1L MUTATED                                                  0
  ASH1L WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ASH1L MUTATED                                     0
  ASH1L WILD-TYPE                                   1
D565V9, multiclass
                                                  clus
vv                                                 ASH1L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ASH1L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V10, continuous
[1] "Remove cluster labels:" "ASH1L MUTATED"         
clus
  ASH1L MUTATED ASH1L WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-YY-A8LH 
"ASH1L WILD-TYPE" 
D565V11, continuous
[1] "Remove cluster labels:" "ASH1L MUTATED"         
clus
  ASH1L MUTATED ASH1L WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ASH1L WILD-TYPE" "ASH1L WILD-TYPE" "ASH1L WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ASH1L MUTATED    5  0  0  1
  ASH1L WILD-TYPE 75 35  4  1
D565V12, multiclass
    clus
vv   ASH1L MUTATED ASH1L WILD-TYPE
  R0             5              75
  R1             0              35
  R2             0               4
  RX             1               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASH1L MUTATED       0                         0     6
  ASH1L WILD-TYPE     6                         5   108
D565V14, multiclass
                           clus
vv                          ASH1L MUTATED ASH1L WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V15, binary
                 cls
clus               0  1
  ASH1L MUTATED    0  5
  ASH1L WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      0    5
  ASH1L WILD-TYPE    5   86
                        clus
vv                       ASH1L MUTATED ASH1L WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(566) Variable = SPINT1 MUTATION ANALYSIS
D566V1, survival
                  sevent
clus2               0  1
  SPINT1 MUTATED    2  1
  SPINT1 WILD-TYPE 61 61
  SPINT1 MUTATED SPINT1 WILD-TYPE 
               3              122 
  SPINT1 MUTATED SPINT1 WILD-TYPE 
               1               61 
$`SPINT1 MUTATED`
TCGA-IB-7652 TCGA-IB-AAUP TCGA-US-A779 
       36.69        14.17        16.80 

$`SPINT1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        19.82        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        39.98         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SPINT1 MUTATED SPINT1 WILD-TYPE 
           14.17             0.23 
  SPINT1 MUTATED SPINT1 WILD-TYPE 
           36.69            90.12 
  SPINT1 MUTATED SPINT1 WILD-TYPE 
          16.800           15.205 
[1] "14.2 - 36.7 (16.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.9"
D566V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SPINT1 MUTATED         0        0        0         0         3         0
  SPINT1 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  SPINT1 MUTATED          0
  SPINT1 WILD-TYPE        3
D566V3, multiclass
           clus
vv          SPINT1 MUTATED SPINT1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SPINT1 MUTATED    0  0     3
  SPINT1 WILD-TYPE  5 17    99
D566V4, multiclass
       clus
vv      SPINT1 MUTATED SPINT1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V5, binary
                  cls
clus                0  1
  SPINT1 MUTATED    0  3
  SPINT1 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT1 MUTATED      0    3
  SPINT1 WILD-TYPE   35   86
   clus
vv  SPINT1 MUTATED SPINT1 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D566V6, binary
                  cls
clus                0  1
  SPINT1 MUTATED    2  0
  SPINT1 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT1 MUTATED      2    0
  SPINT1 WILD-TYPE   55    3
   clus
vv  SPINT1 MUTATED SPINT1 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D566V7, binary
                  cls
clus                0  1
  SPINT1 MUTATED    2  1
  SPINT1 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT1 MUTATED      2    1
  SPINT1 WILD-TYPE   49   74
        clus
vv       SPINT1 MUTATED SPINT1 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D566V8, binary
                  cls
clus                0  1
  SPINT1 MUTATED    2  0
  SPINT1 WILD-TYPE 86 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT1 MUTATED      2    0
  SPINT1 WILD-TYPE   86   30
     clus
vv    SPINT1 MUTATED SPINT1 WILD-TYPE
  NO               2               86
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPINT1 MUTATED                                     3
  SPINT1 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPINT1 MUTATED                                       0
  SPINT1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPINT1 MUTATED                                                  0
  SPINT1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SPINT1 MUTATED                                     0
  SPINT1 WILD-TYPE                                   1
D566V9, multiclass
                                                  clus
vv                                                 SPINT1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SPINT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V10, continuous
D566V11, continuous
                  vv
clus               R0 R1 R2 RX
  SPINT1 MUTATED    1  2  0  0
  SPINT1 WILD-TYPE 79 33  4  2
D566V12, multiclass
    clus
vv   SPINT1 MUTATED SPINT1 WILD-TYPE
  R0              1               79
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPINT1 MUTATED       1                         0     2
  SPINT1 WILD-TYPE     5                         5   112
D566V14, multiclass
                           clus
vv                          SPINT1 MUTATED SPINT1 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V15, binary
                  cls
clus                0  1
  SPINT1 MUTATED    0  3
  SPINT1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT1 MUTATED      0    3
  SPINT1 WILD-TYPE    5   88
                        clus
vv                       SPINT1 MUTATED SPINT1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(567) Variable = SARS2 MUTATION ANALYSIS
D567V1, survival
                 sevent
clus2              0  1
  SARS2 MUTATED    0  4
  SARS2 WILD-TYPE 63 58
  SARS2 MUTATED SARS2 WILD-TYPE 
              4             121 
  SARS2 MUTATED SARS2 WILD-TYPE 
              4              58 
$`SARS2 MUTATED`
TCGA-LB-A7SX TCGA-2J-AAB1 TCGA-FB-A78T TCGA-RB-A7B8 
       12.92         2.17        12.33        15.32 

$`SARS2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SARS2 MUTATED SARS2 WILD-TYPE 
           2.17            0.23 
  SARS2 MUTATED SARS2 WILD-TYPE 
          15.32           90.12 
  SARS2 MUTATED SARS2 WILD-TYPE 
         12.625          15.350 
[1] "2.2 - 15.3 (12.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "4"  
D567V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SARS2 MUTATED         0        0        0         0         4         0
  SARS2 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  SARS2 MUTATED          0
  SARS2 WILD-TYPE        3
D567V3, multiclass
           clus
vv          SARS2 MUTATED SARS2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  SARS2 MUTATED    0  0     4
  SARS2 WILD-TYPE  5 17    98
D567V4, multiclass
       clus
vv      SARS2 MUTATED SARS2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V5, binary
                 cls
clus               0  1
  SARS2 MUTATED    0  4
  SARS2 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    4
  SARS2 WILD-TYPE   35   85
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D567V6, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  0
  SARS2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    0
  SARS2 WILD-TYPE   55    3
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D567V7, binary
                 cls
clus               0  1
  SARS2 MUTATED    3  1
  SARS2 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      3    1
  SARS2 WILD-TYPE   48   74
        clus
vv       SARS2 MUTATED SARS2 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D567V8, binary
                 cls
clus               0  1
  SARS2 MUTATED    4  0
  SARS2 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      4    0
  SARS2 WILD-TYPE   84   30
     clus
vv    SARS2 MUTATED SARS2 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SARS2 MUTATED                                     2
  SARS2 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SARS2 MUTATED                                       2
  SARS2 WILD-TYPE                                    16
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SARS2 MUTATED                                                  0
  SARS2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SARS2 MUTATED                                     0
  SARS2 WILD-TYPE                                   1
D567V9, multiclass
                                                  clus
vv                                                 SARS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SARS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V10, continuous
D567V11, continuous
                 vv
clus              R0 R1 R2 RX
  SARS2 MUTATED    3  1  0  0
  SARS2 WILD-TYPE 77 34  4  2
D567V12, multiclass
    clus
vv   SARS2 MUTATED SARS2 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SARS2 MUTATED       0                         1     3
  SARS2 WILD-TYPE     6                         4   111
D567V14, multiclass
                           clus
vv                          SARS2 MUTATED SARS2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V15, binary
                 cls
clus               0  1
  SARS2 MUTATED    0  3
  SARS2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    3
  SARS2 WILD-TYPE    5   88
                        clus
vv                       SARS2 MUTATED SARS2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(568) Variable = DNAH7 MUTATION ANALYSIS
D568V1, survival
                 sevent
clus2              0  1
  DNAH7 MUTATED    3  5
  DNAH7 WILD-TYPE 60 57
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              8             117 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              5              57 
$`DNAH7 MUTATED`
TCGA-HZ-A77Q TCGA-2L-AAQA TCGA-FB-AAPZ TCGA-FZ-5919 TCGA-FZ-5920 TCGA-HZ-A77O 
        1.08         4.70        23.54        24.36         2.01         5.26 
TCGA-IB-7651 TCGA-RB-AA9M 
       19.82         9.40 

$`DNAH7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        12.53        15.55         4.04         5.03         1.02 
TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL 
        5.10        36.20        20.35        17.79        22.06         8.28 
TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
       32.15        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  DNAH7 MUTATED DNAH7 WILD-TYPE 
           1.08            0.23 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          24.36           90.12 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
           7.33           15.32 
[1] "1.1 - 24.4 (7.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.8"
D568V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DNAH7 MUTATED         0        0        0         0         8         0
  DNAH7 WILD-TYPE       1        3       12        19        74         4
                 vv
clus              STAGE IV
  DNAH7 MUTATED          0
  DNAH7 WILD-TYPE        3
D568V3, multiclass
           clus
vv          DNAH7 MUTATED DNAH7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             8              74
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DNAH7 MUTATED    1  2     5
  DNAH7 WILD-TYPE  4 15    97
D568V4, multiclass
       clus
vv      DNAH7 MUTATED DNAH7 WILD-TYPE
  T1                1               4
  T2                2              15
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V5, binary
                 cls
clus               0  1
  DNAH7 MUTATED    0  8
  DNAH7 WILD-TYPE 35 81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    8
  DNAH7 WILD-TYPE   35   81
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             0              35
  1             8              81
[1] 2 2
[1] FALSE
D568V6, binary
                 cls
clus               0  1
  DNAH7 MUTATED    2  0
  DNAH7 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      2    0
  DNAH7 WILD-TYPE   55    3
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D568V7, binary
                 cls
clus               0  1
  DNAH7 MUTATED    4  4
  DNAH7 WILD-TYPE 47 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      4    4
  DNAH7 WILD-TYPE   47   71
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE             4              47
  MALE               4              71
[1] 2 2
[1] FALSE
D568V8, binary
                 cls
clus               0  1
  DNAH7 MUTATED    6  1
  DNAH7 WILD-TYPE 82 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      6    1
  DNAH7 WILD-TYPE   82   29
     clus
vv    DNAH7 MUTATED DNAH7 WILD-TYPE
  NO              6              82
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DNAH7 MUTATED                                     7
  DNAH7 WILD-TYPE                                  98
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DNAH7 MUTATED                                       1
  DNAH7 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DNAH7 MUTATED                                                  0
  DNAH7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DNAH7 MUTATED                                     0
  DNAH7 WILD-TYPE                                   1
D568V9, multiclass
                                                  clus
vv                                                 DNAH7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DNAH7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V10, continuous
D568V11, continuous
[1] "Remove cluster labels:" "DNAH7 MUTATED"         
clus
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" "DNAH7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DNAH7 MUTATED    6  1  0  0
  DNAH7 WILD-TYPE 74 34  4  2
D568V12, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  R0             6              74
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH7 MUTATED       0                         1     7
  DNAH7 WILD-TYPE     6                         4   107
D568V14, multiclass
                           clus
vv                          DNAH7 MUTATED DNAH7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V15, binary
                 cls
clus               0  1
  DNAH7 MUTATED    0  7
  DNAH7 WILD-TYPE  5 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    7
  DNAH7 WILD-TYPE    5   84
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              84
[1] 2 2
[1] FALSE

Clustering(569) Variable = XIRP2 MUTATION ANALYSIS
D569V1, survival
                 sevent
clus2              0  1
  XIRP2 MUTATED    2  4
  XIRP2 WILD-TYPE 61 58
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              6             119 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              4              58 
$`XIRP2 MUTATED`
TCGA-FZ-5924 TCGA-F2-A8YN TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-XD-AAUI 
       15.78        17.00         5.26        10.85        19.82        12.03 

$`XIRP2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        20.19        17.00        10.13         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XN-A8T3 
       16.80         0.39        18.67        13.81        12.99        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  XIRP2 MUTATED XIRP2 WILD-TYPE 
           5.26            0.23 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
          19.82           90.12 
  XIRP2 MUTATED XIRP2 WILD-TYPE 
         13.905          15.220 
[1] "5.3 - 19.8 (13.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D569V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  XIRP2 MUTATED         0        0        0         2         4         0
  XIRP2 WILD-TYPE       1        3       12        17        78         4
                 vv
clus              STAGE IV
  XIRP2 MUTATED          0
  XIRP2 WILD-TYPE        3
D569V3, multiclass
           clus
vv          XIRP2 MUTATED XIRP2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             2              17
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  XIRP2 MUTATED    0  1     5
  XIRP2 WILD-TYPE  5 16    97
D569V4, multiclass
       clus
vv      XIRP2 MUTATED XIRP2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V5, binary
                 cls
clus               0  1
  XIRP2 MUTATED    1  5
  XIRP2 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      1    5
  XIRP2 WILD-TYPE   34   84
   clus
vv  XIRP2 MUTATED XIRP2 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D569V6, binary
                 cls
clus               0  1
  XIRP2 MUTATED    3  0
  XIRP2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      3    0
  XIRP2 WILD-TYPE   54    3
   clus
vv  XIRP2 MUTATED XIRP2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D569V7, binary
                 cls
clus               0  1
  XIRP2 MUTATED    3  3
  XIRP2 WILD-TYPE 48 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      3    3
  XIRP2 WILD-TYPE   48   72
        clus
vv       XIRP2 MUTATED XIRP2 WILD-TYPE
  FEMALE             3              48
  MALE               3              72
[1] 2 2
[1] FALSE
D569V8, binary
                 cls
clus               0  1
  XIRP2 MUTATED    6  0
  XIRP2 WILD-TYPE 82 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      6    0
  XIRP2 WILD-TYPE   82   30
     clus
vv    XIRP2 MUTATED XIRP2 WILD-TYPE
  NO              6              82
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XIRP2 MUTATED                                     5
  XIRP2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XIRP2 MUTATED                                       1
  XIRP2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XIRP2 MUTATED                                                  0
  XIRP2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  XIRP2 MUTATED                                     0
  XIRP2 WILD-TYPE                                   1
D569V9, multiclass
                                                  clus
vv                                                 XIRP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 XIRP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V10, continuous
[1] "Remove cluster labels:" "XIRP2 MUTATED"         
clus
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-YY-A8LH 
"XIRP2 WILD-TYPE" 
D569V11, continuous
[1] "Remove cluster labels:" "XIRP2 MUTATED"         
clus
  XIRP2 MUTATED XIRP2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XN-A8T5      TCGA-YY-A8LH 
"XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" "XIRP2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  XIRP2 MUTATED    4  2  0  0
  XIRP2 WILD-TYPE 76 33  4  2
D569V12, multiclass
    clus
vv   XIRP2 MUTATED XIRP2 WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XIRP2 MUTATED       0                         0     6
  XIRP2 WILD-TYPE     6                         5   108
D569V14, multiclass
                           clus
vv                          XIRP2 MUTATED XIRP2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V15, binary
                 cls
clus               0  1
  XIRP2 MUTATED    0  6
  XIRP2 WILD-TYPE  5 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XIRP2 MUTATED      0    6
  XIRP2 WILD-TYPE    5   85
                        clus
vv                       XIRP2 MUTATED XIRP2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              85
[1] 2 2
[1] FALSE

Clustering(570) Variable = SLC4A5 MUTATION ANALYSIS
D570V1, survival
                  sevent
clus2               0  1
  SLC4A5 MUTATED    0  4
  SLC4A5 WILD-TYPE 63 58
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               4              121 
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               4               58 
$`SLC4A5 MUTATED`
TCGA-F2-A7TX TCGA-HZ-A49I TCGA-HZ-A77O TCGA-IB-7651 
        3.12        10.13         5.26        19.82 

$`SLC4A5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77P TCGA-HZ-A8P1 
       17.49        31.86        20.19        17.00        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
            3.12             0.23 
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
           19.82            90.12 
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
           7.695           15.320 
[1] "3.1 - 19.8 (7.7)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.1"
D570V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC4A5 MUTATED         0        0        0         0         4         0
  SLC4A5 WILD-TYPE       1        3       12        19        78         4
                  vv
clus               STAGE IV
  SLC4A5 MUTATED          0
  SLC4A5 WILD-TYPE        3
D570V3, multiclass
           clus
vv          SLC4A5 MUTATED SLC4A5 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SLC4A5 MUTATED    0  1     3
  SLC4A5 WILD-TYPE  5 16    99
D570V4, multiclass
       clus
vv      SLC4A5 MUTATED SLC4A5 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V5, binary
                  cls
clus                0  1
  SLC4A5 MUTATED    0  4
  SLC4A5 WILD-TYPE 35 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A5 MUTATED      0    4
  SLC4A5 WILD-TYPE   35   85
   clus
vv  SLC4A5 MUTATED SLC4A5 WILD-TYPE
  0              0               35
  1              4               85
[1] 2 2
[1] FALSE
D570V6, binary
                  cls
clus                0  1
  SLC4A5 MUTATED    2  0
  SLC4A5 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A5 MUTATED      2    0
  SLC4A5 WILD-TYPE   55    3
   clus
vv  SLC4A5 MUTATED SLC4A5 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D570V7, binary
                  cls
clus                0  1
  SLC4A5 MUTATED    2  2
  SLC4A5 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A5 MUTATED      2    2
  SLC4A5 WILD-TYPE   49   73
        clus
vv       SLC4A5 MUTATED SLC4A5 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D570V8, binary
                  cls
clus                0  1
  SLC4A5 MUTATED    3  1
  SLC4A5 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A5 MUTATED      3    1
  SLC4A5 WILD-TYPE   85   29
     clus
vv    SLC4A5 MUTATED SLC4A5 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC4A5 MUTATED                                     4
  SLC4A5 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC4A5 MUTATED                                       0
  SLC4A5 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC4A5 MUTATED                                                  0
  SLC4A5 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC4A5 MUTATED                                     0
  SLC4A5 WILD-TYPE                                   1
D570V9, multiclass
                                                  clus
vv                                                 SLC4A5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SLC4A5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V10, continuous
[1] "Remove cluster labels:" "SLC4A5 MUTATED"        
clus
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
D570V11, continuous
[1] "Remove cluster labels:" "SLC4A5 MUTATED"        
clus
  SLC4A5 MUTATED SLC4A5 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" "SLC4A5 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SLC4A5 MUTATED    2  2  0  0
  SLC4A5 WILD-TYPE 78 33  4  2
D570V12, multiclass
    clus
vv   SLC4A5 MUTATED SLC4A5 WILD-TYPE
  R0              2               78
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC4A5 MUTATED       0                         0     4
  SLC4A5 WILD-TYPE     6                         5   110
D570V14, multiclass
                           clus
vv                          SLC4A5 MUTATED SLC4A5 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V15, binary
                  cls
clus                0  1
  SLC4A5 MUTATED    0  3
  SLC4A5 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A5 MUTATED      0    3
  SLC4A5 WILD-TYPE    5   88
                        clus
vv                       SLC4A5 MUTATED SLC4A5 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(571) Variable = BTN2A2 MUTATION ANALYSIS
D571V1, survival
                  sevent
clus2               0  1
  BTN2A2 MUTATED    2  1
  BTN2A2 WILD-TYPE 61 61
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               3              122 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               1               61 
$`BTN2A2 MUTATED`
TCGA-2J-AABR TCGA-F2-A8YN TCGA-IB-AAUO 
       14.40        17.00         7.86 

$`BTN2A2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
            7.86             0.23 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
           17.00            90.12 
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
           14.40            15.27 
[1] "7.9 - 17.0 (14.4)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D571V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BTN2A2 MUTATED         0        0        0         2         1         0
  BTN2A2 WILD-TYPE       1        3       12        17        81         4
                  vv
clus               STAGE IV
  BTN2A2 MUTATED          0
  BTN2A2 WILD-TYPE        3
D571V3, multiclass
           clus
vv          BTN2A2 MUTATED BTN2A2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  BTN2A2 MUTATED    0  0     3
  BTN2A2 WILD-TYPE  5 17    99
D571V4, multiclass
       clus
vv      BTN2A2 MUTATED BTN2A2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V5, binary
                  cls
clus                0  1
  BTN2A2 MUTATED    2  1
  BTN2A2 WILD-TYPE 33 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      2    1
  BTN2A2 WILD-TYPE   33   88
   clus
vv  BTN2A2 MUTATED BTN2A2 WILD-TYPE
  0              2               33
  1              1               88
[1] 2 2
[1] FALSE
D571V6, binary
                  cls
clus                0  1
  BTN2A2 MUTATED    3  0
  BTN2A2 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      3    0
  BTN2A2 WILD-TYPE   54    3
   clus
vv  BTN2A2 MUTATED BTN2A2 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D571V7, binary
                  cls
clus                0  1
  BTN2A2 MUTATED    2  1
  BTN2A2 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      2    1
  BTN2A2 WILD-TYPE   49   74
        clus
vv       BTN2A2 MUTATED BTN2A2 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D571V8, binary
                  cls
clus                0  1
  BTN2A2 MUTATED    3  0
  BTN2A2 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      3    0
  BTN2A2 WILD-TYPE   85   30
     clus
vv    BTN2A2 MUTATED BTN2A2 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BTN2A2 MUTATED                                     3
  BTN2A2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BTN2A2 MUTATED                                       0
  BTN2A2 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BTN2A2 MUTATED                                                  0
  BTN2A2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  BTN2A2 MUTATED                                     0
  BTN2A2 WILD-TYPE                                   1
D571V9, multiclass
                                                  clus
vv                                                 BTN2A2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 BTN2A2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V10, continuous
[1] "Remove cluster labels:" "BTN2A2 MUTATED"        
clus
  BTN2A2 MUTATED BTN2A2 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"BTN2A2 WILD-TYPE" "BTN2A2 WILD-TYPE" 
D571V11, continuous
                  vv
clus               R0 R1 R2 RX
  BTN2A2 MUTATED    1  2  0  0
  BTN2A2 WILD-TYPE 79 33  4  2
D571V12, multiclass
    clus
vv   BTN2A2 MUTATED BTN2A2 WILD-TYPE
  R0              1               79
  R1              2               33
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTN2A2 MUTATED       0                         0     3
  BTN2A2 WILD-TYPE     6                         5   111
D571V14, multiclass
                           clus
vv                          BTN2A2 MUTATED BTN2A2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V15, binary
                  cls
clus                0  1
  BTN2A2 MUTATED    0  2
  BTN2A2 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A2 MUTATED      0    2
  BTN2A2 WILD-TYPE    5   89
                        clus
vv                       BTN2A2 MUTATED BTN2A2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(572) Variable = SV2A MUTATION ANALYSIS
D572V1, survival
                sevent
clus2             0  1
  SV2A MUTATED    1  2
  SV2A WILD-TYPE 62 60
  SV2A MUTATED SV2A WILD-TYPE 
             3            122 
  SV2A MUTATED SV2A WILD-TYPE 
             2             60 
$`SV2A MUTATED`
TCGA-2J-AAB1 TCGA-F2-7273 TCGA-HV-A7OP 
        2.17        19.46        32.15 

$`SV2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SV2A MUTATED SV2A WILD-TYPE 
          2.17           0.23 
  SV2A MUTATED SV2A WILD-TYPE 
         32.15          90.12 
  SV2A MUTATED SV2A WILD-TYPE 
        19.460         15.205 
[1] "2.2 - 32.1 (19.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D572V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SV2A MUTATED         0        0        0         0         4         0
  SV2A WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  SV2A MUTATED          0
  SV2A WILD-TYPE        3
D572V3, multiclass
           clus
vv          SV2A MUTATED SV2A WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  SV2A MUTATED    0  0     4
  SV2A WILD-TYPE  5 17    98
D572V4, multiclass
       clus
vv      SV2A MUTATED SV2A WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V5, binary
                cls
clus              0  1
  SV2A MUTATED    0  4
  SV2A WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED      0    4
  SV2A WILD-TYPE   35   85
   clus
vv  SV2A MUTATED SV2A WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D572V6, binary
                cls
clus              0  1
  SV2A MUTATED    3  0
  SV2A WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED      3    0
  SV2A WILD-TYPE   54    3
   clus
vv  SV2A MUTATED SV2A WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D572V7, binary
                cls
clus              0  1
  SV2A MUTATED    0  4
  SV2A WILD-TYPE 51 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED      0    4
  SV2A WILD-TYPE   51   71
        clus
vv       SV2A MUTATED SV2A WILD-TYPE
  FEMALE            0             51
  MALE              4             71
[1] 2 2
[1] FALSE
D572V8, binary
                cls
clus              0  1
  SV2A MUTATED    1  2
  SV2A WILD-TYPE 87 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED      1    2
  SV2A WILD-TYPE   87   28
     clus
vv    SV2A MUTATED SV2A WILD-TYPE
  NO             1             87
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SV2A MUTATED                                     2
  SV2A WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SV2A MUTATED                                       2
  SV2A WILD-TYPE                                    16
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SV2A MUTATED                                                  0
  SV2A WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  SV2A MUTATED                                     0
  SV2A WILD-TYPE                                   1
D572V9, multiclass
                                                  clus
vv                                                 SV2A MUTATED SV2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V10, continuous
[1] "Remove cluster labels:" "SV2A MUTATED"          
clus
  SV2A MUTATED SV2A WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1     TCGA-IB-7651 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-YY-A8LH 
"SV2A WILD-TYPE" 
D572V11, continuous
[1] "Remove cluster labels:" "SV2A MUTATED"          
clus
  SV2A MUTATED SV2A WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-IB-A5SS     TCGA-LB-A7SX 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX     TCGA-FB-A5VM 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"SV2A WILD-TYPE" "SV2A WILD-TYPE" "SV2A WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  SV2A MUTATED    3  1  0  0
  SV2A WILD-TYPE 77 34  4  2
D572V12, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SV2A MUTATED       1                         1     2
  SV2A WILD-TYPE     5                         4   112
D572V14, multiclass
                           clus
vv                          SV2A MUTATED SV2A WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                2            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V15, binary
                cls
clus              0  1
  SV2A MUTATED    0  2
  SV2A WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED      0    2
  SV2A WILD-TYPE    5   89
                        clus
vv                       SV2A MUTATED SV2A WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(573) Variable = MORC3 MUTATION ANALYSIS
D573V1, survival
                 sevent
clus2              0  1
  MORC3 MUTATED    2  1
  MORC3 WILD-TYPE 61 61
  MORC3 MUTATED MORC3 WILD-TYPE 
              3             122 
  MORC3 MUTATED MORC3 WILD-TYPE 
              1              61 
$`MORC3 MUTATED`
TCGA-IB-7651 TCGA-IB-A7M4 TCGA-YH-A8SY 
       19.82        15.88        12.76 

$`MORC3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MORC3 MUTATED MORC3 WILD-TYPE 
          12.76            0.23 
  MORC3 MUTATED MORC3 WILD-TYPE 
          19.82           90.12 
  MORC3 MUTATED MORC3 WILD-TYPE 
         15.880          15.205 
[1] "12.8 - 19.8 (15.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D573V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MORC3 MUTATED         0        0        0         0         2         1
  MORC3 WILD-TYPE       1        3       12        19        80         3
                 vv
clus              STAGE IV
  MORC3 MUTATED          0
  MORC3 WILD-TYPE        3
D573V3, multiclass
           clus
vv          MORC3 MUTATED MORC3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  MORC3 MUTATED    0  0     3
  MORC3 WILD-TYPE  5 17    99
D573V4, multiclass
       clus
vv      MORC3 MUTATED MORC3 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V5, binary
                 cls
clus               0  1
  MORC3 MUTATED    0  3
  MORC3 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      0    3
  MORC3 WILD-TYPE   35   86
   clus
vv  MORC3 MUTATED MORC3 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D573V6, binary
                 cls
clus               0  1
  MORC3 MUTATED    1  0
  MORC3 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      1    0
  MORC3 WILD-TYPE   56    3
   clus
vv  MORC3 MUTATED MORC3 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D573V7, binary
                 cls
clus               0  1
  MORC3 MUTATED    2  1
  MORC3 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      2    1
  MORC3 WILD-TYPE   49   74
        clus
vv       MORC3 MUTATED MORC3 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D573V8, binary
                 cls
clus               0  1
  MORC3 MUTATED    2  1
  MORC3 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      2    1
  MORC3 WILD-TYPE   86   29
     clus
vv    MORC3 MUTATED MORC3 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MORC3 MUTATED                                     2
  MORC3 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MORC3 MUTATED                                       0
  MORC3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MORC3 MUTATED                                                  0
  MORC3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  MORC3 MUTATED                                     0
  MORC3 WILD-TYPE                                   1
D573V9, multiclass
[1] "Remove cluster labels:" "MORC3 MUTATED"         
clus
  MORC3 MUTATED MORC3 WILD-TYPE 
              2             123 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IV      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3E-AAAY      TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FZ-5919      TCGA-FZ-5920      TCGA-FZ-5921      TCGA-FZ-5922 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7652 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
D573V10, continuous
[1] "Remove cluster labels:" "MORC3 MUTATED"         
clus
  MORC3 MUTATED MORC3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-YY-A8LH 
"MORC3 WILD-TYPE" 
D573V11, continuous
[1] "Remove cluster labels:" "MORC3 MUTATED"         
clus
  MORC3 MUTATED MORC3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-AAUQ 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MORC3 MUTATED    2  0  0  0
  MORC3 WILD-TYPE 78 35  4  2
D573V12, multiclass
[1] "Remove cluster labels:" "MORC3 MUTATED"         
clus
  MORC3 MUTATED MORC3 WILD-TYPE 
              2             119 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-3A-A9IV      TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7652 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"MORC3 WILD-TYPE" "MORC3 WILD-TYPE" "MORC3 WILD-TYPE" 
D573V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MORC3 MUTATED       0                         0     3
  MORC3 WILD-TYPE     6                         5   111
D573V14, multiclass
                           clus
vv                          MORC3 MUTATED MORC3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V15, binary
                 cls
clus               0  1
  MORC3 MUTATED    0  3
  MORC3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC3 MUTATED      0    3
  MORC3 WILD-TYPE    5   88
                        clus
vv                       MORC3 MUTATED MORC3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(574) Variable = HABP4 MUTATION ANALYSIS
D574V1, survival
                 sevent
clus2              0  1
  HABP4 MUTATED    1  3
  HABP4 WILD-TYPE 62 59
  HABP4 MUTATED HABP4 WILD-TYPE 
              4             121 
  HABP4 MUTATED HABP4 WILD-TYPE 
              3              59 
$`HABP4 MUTATED`
TCGA-HV-AA8X TCGA-IB-7651 TCGA-IB-A5ST TCGA-IB-AAUN 
       17.49        19.82        20.88         4.73 

$`HABP4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HABP4 MUTATED HABP4 WILD-TYPE 
           4.73            0.23 
  HABP4 MUTATED HABP4 WILD-TYPE 
          20.88           90.12 
  HABP4 MUTATED HABP4 WILD-TYPE 
         18.655          15.190 
[1] "4.7 - 20.9 (18.7)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D574V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HABP4 MUTATED         0        0        1         0         3         0
  HABP4 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  HABP4 MUTATED          0
  HABP4 WILD-TYPE        3
D574V3, multiclass
           clus
vv          HABP4 MUTATED HABP4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  HABP4 MUTATED     0   2     2
  HABP4 WILD-TYPE   5  15   100
D574V4, multiclass
       clus
vv      HABP4 MUTATED HABP4 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V5, binary
                 cls
clus               0  1
  HABP4 MUTATED    1  3
  HABP4 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HABP4 MUTATED      1    3
  HABP4 WILD-TYPE   34   86
   clus
vv  HABP4 MUTATED HABP4 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D574V6, binary
                 cls
clus               0  1
  HABP4 MUTATED    3  0
  HABP4 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HABP4 MUTATED      3    0
  HABP4 WILD-TYPE   54    3
   clus
vv  HABP4 MUTATED HABP4 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D574V7, binary
                 cls
clus               0  1
  HABP4 MUTATED    4  0
  HABP4 WILD-TYPE 47 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HABP4 MUTATED      4    0
  HABP4 WILD-TYPE   47   75
        clus
vv       HABP4 MUTATED HABP4 WILD-TYPE
  FEMALE             4              47
  MALE               0              75
[1] 2 2
[1] FALSE
D574V8, binary
                 cls
clus               0  1
  HABP4 MUTATED    4  0
  HABP4 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HABP4 MUTATED      4    0
  HABP4 WILD-TYPE   84   30
     clus
vv    HABP4 MUTATED HABP4 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HABP4 MUTATED                                     4
  HABP4 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HABP4 MUTATED                                       0
  HABP4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HABP4 MUTATED                                                  0
  HABP4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  HABP4 MUTATED                                     0
  HABP4 WILD-TYPE                                   1
D574V9, multiclass
                                                  clus
vv                                                 HABP4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 HABP4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V10, continuous
[1] "Remove cluster labels:" "HABP4 MUTATED"         
clus
  HABP4 MUTATED HABP4 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
D574V11, continuous
[1] "Remove cluster labels:" "HABP4 MUTATED"         
clus
  HABP4 MUTATED HABP4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" "HABP4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HABP4 MUTATED    2  1  1  0
  HABP4 WILD-TYPE 78 34  3  2
D574V12, multiclass
    clus
vv   HABP4 MUTATED HABP4 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HABP4 MUTATED       1                         0     3
  HABP4 WILD-TYPE     5                         5   111
D574V14, multiclass
                           clus
vv                          HABP4 MUTATED HABP4 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V15, binary
                 cls
clus               0  1
  HABP4 MUTATED    0  3
  HABP4 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HABP4 MUTATED      0    3
  HABP4 WILD-TYPE    5   88
                        clus
vv                       HABP4 MUTATED HABP4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(575) Variable = SLC5A3 MUTATION ANALYSIS
D575V1, survival
                  sevent
clus2               0  1
  SLC5A3 MUTATED    0  4
  SLC5A3 WILD-TYPE 63 58
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               4              121 
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               4               58 
$`SLC5A3 MUTATED`
TCGA-2J-AABU TCGA-FZ-5922 TCGA-IB-7651 TCGA-IB-A5SQ 
        9.11        36.20        19.82         7.20 

$`SLC5A3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
            7.20             0.23 
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
           36.20            90.12 
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
          14.465           15.220 
[1] "7.2 - 36.2 (14.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.1"
D575V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLC5A3 MUTATED         0        0        1         1         2         0
  SLC5A3 WILD-TYPE       1        3       11        18        80         4
                  vv
clus               STAGE IV
  SLC5A3 MUTATED          0
  SLC5A3 WILD-TYPE        3
D575V3, multiclass
           clus
vv          SLC5A3 MUTATED SLC5A3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SLC5A3 MUTATED    0  1     3
  SLC5A3 WILD-TYPE  5 16    99
D575V4, multiclass
       clus
vv      SLC5A3 MUTATED SLC5A3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V5, binary
                  cls
clus                0  1
  SLC5A3 MUTATED    2  2
  SLC5A3 WILD-TYPE 33 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC5A3 MUTATED      2    2
  SLC5A3 WILD-TYPE   33   87
   clus
vv  SLC5A3 MUTATED SLC5A3 WILD-TYPE
  0              2               33
  1              2               87
[1] 2 2
[1] FALSE
D575V6, binary
                  cls
clus                0  1
  SLC5A3 MUTATED    4  0
  SLC5A3 WILD-TYPE 53  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC5A3 MUTATED      4    0
  SLC5A3 WILD-TYPE   53    3
   clus
vv  SLC5A3 MUTATED SLC5A3 WILD-TYPE
  0              4               53
  1              0                3
[1] 2 2
[1] FALSE
D575V7, binary
                  cls
clus                0  1
  SLC5A3 MUTATED    2  2
  SLC5A3 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC5A3 MUTATED      2    2
  SLC5A3 WILD-TYPE   49   73
        clus
vv       SLC5A3 MUTATED SLC5A3 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D575V8, binary
                  cls
clus                0  1
  SLC5A3 MUTATED    4  0
  SLC5A3 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC5A3 MUTATED      4    0
  SLC5A3 WILD-TYPE   84   30
     clus
vv    SLC5A3 MUTATED SLC5A3 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC5A3 MUTATED                                     4
  SLC5A3 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC5A3 MUTATED                                       0
  SLC5A3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC5A3 MUTATED                                                  0
  SLC5A3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLC5A3 MUTATED                                     0
  SLC5A3 WILD-TYPE                                   1
D575V9, multiclass
                                                  clus
vv                                                 SLC5A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SLC5A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V10, continuous
[1] "Remove cluster labels:" "SLC5A3 MUTATED"        
clus
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
D575V11, continuous
[1] "Remove cluster labels:" "SLC5A3 MUTATED"        
clus
  SLC5A3 MUTATED SLC5A3 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" "SLC5A3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SLC5A3 MUTATED    4  0  0  0
  SLC5A3 WILD-TYPE 76 35  4  2
D575V12, multiclass
    clus
vv   SLC5A3 MUTATED SLC5A3 WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC5A3 MUTATED       0                         0     4
  SLC5A3 WILD-TYPE     6                         5   110
D575V14, multiclass
                           clus
vv                          SLC5A3 MUTATED SLC5A3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V15, binary
                  cls
clus                0  1
  SLC5A3 MUTATED    0  3
  SLC5A3 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC5A3 MUTATED      0    3
  SLC5A3 WILD-TYPE    5   88
                        clus
vv                       SLC5A3 MUTATED SLC5A3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(576) Variable = TGOLN2 MUTATION ANALYSIS
D576V1, survival
                  sevent
clus2               0  1
  TGOLN2 MUTATED    1  2
  TGOLN2 WILD-TYPE 62 60
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               3              122 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
               2               60 
$`TGOLN2 MUTATED`
TCGA-IB-A5SQ TCGA-IB-A7LX TCGA-YB-A89D 
        7.20         8.22        11.51 

$`TGOLN2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 
        5.26        10.85         0.23        19.82        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF 
       41.33        15.19        12.00        15.85        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        23.67        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
            7.20             0.23 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
           11.51            90.12 
  TGOLN2 MUTATED TGOLN2 WILD-TYPE 
           8.220           15.335 
[1] "7.2 - 11.5 (8.2)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "3.5"
D576V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TGOLN2 MUTATED         0        0        1         0         2         0
  TGOLN2 WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  TGOLN2 MUTATED          0
  TGOLN2 WILD-TYPE        3
D576V3, multiclass
           clus
vv          TGOLN2 MUTATED TGOLN2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  TGOLN2 MUTATED     0   1     2
  TGOLN2 WILD-TYPE   5  16   100
D576V4, multiclass
       clus
vv      TGOLN2 MUTATED TGOLN2 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V5, binary
                  cls
clus                0  1
  TGOLN2 MUTATED    1  2
  TGOLN2 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      1    2
  TGOLN2 WILD-TYPE   34   87
   clus
vv  TGOLN2 MUTATED TGOLN2 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D576V6, binary
                  cls
clus                0  1
  TGOLN2 MUTATED    1  0
  TGOLN2 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      1    0
  TGOLN2 WILD-TYPE   56    3
   clus
vv  TGOLN2 MUTATED TGOLN2 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D576V7, binary
                  cls
clus                0  1
  TGOLN2 MUTATED    1  2
  TGOLN2 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      1    2
  TGOLN2 WILD-TYPE   50   73
        clus
vv       TGOLN2 MUTATED TGOLN2 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D576V8, binary
                  cls
clus                0  1
  TGOLN2 MUTATED    2  1
  TGOLN2 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      2    1
  TGOLN2 WILD-TYPE   86   29
     clus
vv    TGOLN2 MUTATED TGOLN2 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGOLN2 MUTATED                                     3
  TGOLN2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGOLN2 MUTATED                                       0
  TGOLN2 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGOLN2 MUTATED                                                  0
  TGOLN2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  TGOLN2 MUTATED                                     0
  TGOLN2 WILD-TYPE                                   1
D576V9, multiclass
                                                  clus
vv                                                 TGOLN2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 TGOLN2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V10, continuous
D576V11, continuous
                  vv
clus               R0 R1 R2 RX
  TGOLN2 MUTATED    3  0  0  0
  TGOLN2 WILD-TYPE 77 35  4  2
D576V12, multiclass
    clus
vv   TGOLN2 MUTATED TGOLN2 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGOLN2 MUTATED       0                         0     3
  TGOLN2 WILD-TYPE     6                         5   111
D576V14, multiclass
                           clus
vv                          TGOLN2 MUTATED TGOLN2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V15, binary
                  cls
clus                0  1
  TGOLN2 MUTATED    0  3
  TGOLN2 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGOLN2 MUTATED      0    3
  TGOLN2 WILD-TYPE    5   88
                        clus
vv                       TGOLN2 MUTATED TGOLN2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(577) Variable = HIST1H1E MUTATION ANALYSIS
D577V1, survival
                    sevent
clus2                 0  1
  HIST1H1E MUTATED    2  1
  HIST1H1E WILD-TYPE 61 61
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 3                122 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 1                 61 
$`HIST1H1E MUTATED`
TCGA-3A-A9IJ TCGA-HV-A7OP TCGA-IB-7651 
       60.95        32.15        19.82 

$`HIST1H1E WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             19.82               0.23 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             60.95              90.12 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
            32.150             15.155 
[1] "19.8 - 61.0 (32.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.7"
D577V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIST1H1E MUTATED         0        0        1         0         2         0
  HIST1H1E WILD-TYPE       1        3       11        19        80         4
                    vv
clus                 STAGE IV
  HIST1H1E MUTATED          0
  HIST1H1E WILD-TYPE        3
D577V3, multiclass
           clus
vv          HIST1H1E MUTATED HIST1H1E WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 1                 11
  STAGE IIA                0                 19
  STAGE IIB                2                 80
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  HIST1H1E MUTATED     0   1     2
  HIST1H1E WILD-TYPE   5  16   100
D577V4, multiclass
       clus
vv      HIST1H1E MUTATED HIST1H1E WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                2                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V5, binary
                    cls
clus                  0  1
  HIST1H1E MUTATED    1  2
  HIST1H1E WILD-TYPE 34 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      1    2
  HIST1H1E WILD-TYPE   34   87
   clus
vv  HIST1H1E MUTATED HIST1H1E WILD-TYPE
  0                1                 34
  1                2                 87
[1] 2 2
[1] FALSE
D577V6, binary
                    cls
clus                  0  1
  HIST1H1E MUTATED    2  0
  HIST1H1E WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      2    0
  HIST1H1E WILD-TYPE   55    3
   clus
vv  HIST1H1E MUTATED HIST1H1E WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D577V7, binary
                    cls
clus                  0  1
  HIST1H1E MUTATED    1  2
  HIST1H1E WILD-TYPE 50 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      1    2
  HIST1H1E WILD-TYPE   50   73
        clus
vv       HIST1H1E MUTATED HIST1H1E WILD-TYPE
  FEMALE                1                 50
  MALE                  2                 73
[1] 2 2
[1] FALSE
D577V8, binary
                    cls
clus                  0  1
  HIST1H1E MUTATED    2  1
  HIST1H1E WILD-TYPE 86 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      2    1
  HIST1H1E WILD-TYPE   86   29
     clus
vv    HIST1H1E MUTATED HIST1H1E WILD-TYPE
  NO                 2                 86
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H1E MUTATED                                     1
  HIST1H1E WILD-TYPE                                 104
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H1E MUTATED                                       2
  HIST1H1E WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H1E MUTATED                                                  0
  HIST1H1E WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIST1H1E MUTATED                                     0
  HIST1H1E WILD-TYPE                                   1
D577V9, multiclass
                                                  clus
vv                                                 HIST1H1E MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 HIST1H1E WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V10, continuous
[1] "Remove cluster labels:" "HIST1H1E MUTATED"      
clus
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 2                 37 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-IB-A5SS 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-XD-AAUL         TCGA-2J-AAB1 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-YY-A8LH 
"HIST1H1E WILD-TYPE" 
D577V11, continuous
[1] "Remove cluster labels:" "HIST1H1E MUTATED"      
clus
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 2                 31 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-IB-A5SS 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-XD-AAUL         TCGA-2J-AAB1 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" "HIST1H1E WILD-TYPE" 
        TCGA-YY-A8LH 
"HIST1H1E WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  HIST1H1E MUTATED    3  0  0  0
  HIST1H1E WILD-TYPE 77 35  4  2
D577V12, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  R0                3                 77
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1E MUTATED       1                         0     2
  HIST1H1E WILD-TYPE     5                         5   112
D577V14, multiclass
                           clus
vv                          HIST1H1E MUTATED HIST1H1E WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    2                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V15, binary
                    cls
clus                  0  1
  HIST1H1E MUTATED    0  2
  HIST1H1E WILD-TYPE  5 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      0    2
  HIST1H1E WILD-TYPE    5   89
                        clus
vv                       HIST1H1E MUTATED HIST1H1E WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(578) Variable = APOA1BP MUTATION ANALYSIS
D578V1, survival
                   sevent
clus2                0  1
  APOA1BP MUTATED    2  2
  APOA1BP WILD-TYPE 61 60
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                4               121 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                2                60 
$`APOA1BP MUTATED`
TCGA-2J-AABK TCGA-2L-AAQI TCGA-HV-A7OP TCGA-IB-7651 
       15.91         3.39        32.15        19.82 

$`APOA1BP WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABO 
       20.61        19.96        22.22        22.72        42.31        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  APOA1BP MUTATED APOA1BP WILD-TYPE 
             3.39              0.23 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
            32.15             90.12 
  APOA1BP MUTATED APOA1BP WILD-TYPE 
           17.865            15.190 
[1] "3.4 - 32.1 (17.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D578V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  APOA1BP MUTATED         0        0        0         0         4         0
  APOA1BP WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  APOA1BP MUTATED          0
  APOA1BP WILD-TYPE        3
D578V3, multiclass
           clus
vv          APOA1BP MUTATED APOA1BP WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  APOA1BP MUTATED    0  0     4
  APOA1BP WILD-TYPE  5 17    98
D578V4, multiclass
       clus
vv      APOA1BP MUTATED APOA1BP WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V5, binary
                   cls
clus                 0  1
  APOA1BP MUTATED    0  4
  APOA1BP WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      0    4
  APOA1BP WILD-TYPE   35   85
   clus
vv  APOA1BP MUTATED APOA1BP WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D578V6, binary
                   cls
clus                 0  1
  APOA1BP MUTATED    3  0
  APOA1BP WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      3    0
  APOA1BP WILD-TYPE   54    3
   clus
vv  APOA1BP MUTATED APOA1BP WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D578V7, binary
                   cls
clus                 0  1
  APOA1BP MUTATED    1  3
  APOA1BP WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      1    3
  APOA1BP WILD-TYPE   50   72
        clus
vv       APOA1BP MUTATED APOA1BP WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D578V8, binary
                   cls
clus                 0  1
  APOA1BP MUTATED    2  2
  APOA1BP WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      2    2
  APOA1BP WILD-TYPE   86   28
     clus
vv    APOA1BP MUTATED APOA1BP WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  APOA1BP MUTATED                                     3
  APOA1BP WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  APOA1BP MUTATED                                       1
  APOA1BP WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  APOA1BP MUTATED                                                  0
  APOA1BP WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  APOA1BP MUTATED                                     0
  APOA1BP WILD-TYPE                                   1
D578V9, multiclass
                                                  clus
vv                                                 APOA1BP MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 APOA1BP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V10, continuous
[1] "Remove cluster labels:" "APOA1BP MUTATED"       
clus
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
D578V11, continuous
[1] "Remove cluster labels:" "APOA1BP MUTATED"       
clus
  APOA1BP MUTATED APOA1BP WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" "APOA1BP WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  APOA1BP MUTATED    2  2  0  0
  APOA1BP WILD-TYPE 78 33  4  2
D578V12, multiclass
    clus
vv   APOA1BP MUTATED APOA1BP WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APOA1BP MUTATED       1                         0     3
  APOA1BP WILD-TYPE     5                         5   111
D578V14, multiclass
                           clus
vv                          APOA1BP MUTATED APOA1BP WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V15, binary
                   cls
clus                 0  1
  APOA1BP MUTATED    0  1
  APOA1BP WILD-TYPE  5 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOA1BP MUTATED      0    1
  APOA1BP WILD-TYPE    5   90
                        clus
vv                       APOA1BP MUTATED APOA1BP WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               1                90
[1] 2 2
[1] FALSE

Clustering(579) Variable = AKNAD1 MUTATION ANALYSIS
D579V1, survival
                  sevent
clus2               0  1
  AKNAD1 MUTATED    2  1
  AKNAD1 WILD-TYPE 61 61
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               3              122 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               1               61 
$`AKNAD1 MUTATED`
TCGA-HZ-A77Q TCGA-IB-7651 TCGA-YH-A8SY 
        1.08        19.82        12.76 

$`AKNAD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
            1.08             0.23 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
           19.82            90.12 
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
           12.76            15.27 
[1] "1.1 - 19.8 (12.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1"  
D579V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AKNAD1 MUTATED         0        0        0         0         2         1
  AKNAD1 WILD-TYPE       1        3       12        19        80         3
                  vv
clus               STAGE IV
  AKNAD1 MUTATED          0
  AKNAD1 WILD-TYPE        3
D579V3, multiclass
           clus
vv          AKNAD1 MUTATED AKNAD1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  AKNAD1 MUTATED    0  0     3
  AKNAD1 WILD-TYPE  5 17    99
D579V4, multiclass
       clus
vv      AKNAD1 MUTATED AKNAD1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V5, binary
                  cls
clus                0  1
  AKNAD1 MUTATED    0  3
  AKNAD1 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      0    3
  AKNAD1 WILD-TYPE   35   86
   clus
vv  AKNAD1 MUTATED AKNAD1 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D579V6, binary
                  cls
clus                0  1
  AKNAD1 MUTATED    1  0
  AKNAD1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      1    0
  AKNAD1 WILD-TYPE   56    3
   clus
vv  AKNAD1 MUTATED AKNAD1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D579V7, binary
                  cls
clus                0  1
  AKNAD1 MUTATED    3  0
  AKNAD1 WILD-TYPE 48 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      3    0
  AKNAD1 WILD-TYPE   48   75
        clus
vv       AKNAD1 MUTATED AKNAD1 WILD-TYPE
  FEMALE              3               48
  MALE                0               75
[1] 2 2
[1] FALSE
D579V8, binary
                  cls
clus                0  1
  AKNAD1 MUTATED    1  1
  AKNAD1 WILD-TYPE 87 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      1    1
  AKNAD1 WILD-TYPE   87   29
     clus
vv    AKNAD1 MUTATED AKNAD1 WILD-TYPE
  NO               1               87
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AKNAD1 MUTATED                                     1
  AKNAD1 WILD-TYPE                                 104
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AKNAD1 MUTATED                                       1
  AKNAD1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AKNAD1 MUTATED                                                  0
  AKNAD1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  AKNAD1 MUTATED                                     0
  AKNAD1 WILD-TYPE                                   1
D579V9, multiclass
[1] "Remove cluster labels:" "AKNAD1 MUTATED"        
clus
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               2              123 
      TCGA-2J-AABR       TCGA-2J-AABT       TCGA-3A-A9I5       TCGA-3A-A9IJ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IL       TCGA-F2-A44G       TCGA-FB-AAQ6       TCGA-FZ-5924 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX       TCGA-S4-A8RO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-US-A77E       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AAB4 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AAB6       TCGA-2J-AAB8       TCGA-2J-AAB9       TCGA-2J-AABA 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABH       TCGA-2J-AABK 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABP       TCGA-2J-AABU       TCGA-2J-AABV 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-2L-AAQI       TCGA-2L-AAQJ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2L-AAQL       TCGA-2L-AAQM       TCGA-3A-A9I7       TCGA-3A-A9I9 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IC       TCGA-3A-A9IH       TCGA-3A-A9IO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IR       TCGA-3A-A9IS       TCGA-3A-A9IU       TCGA-3A-A9IV 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-3A-A9IZ       TCGA-3A-A9J0       TCGA-3E-AAAY 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3E-AAAZ       TCGA-F2-7273       TCGA-F2-A7TX       TCGA-F2-A8YN 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPP       TCGA-FB-AAPQ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPU       TCGA-FB-AAPZ       TCGA-FB-AAQ0 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAQ1       TCGA-FB-AAQ2       TCGA-FB-AAQ3       TCGA-FZ-5919 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FZ-5920       TCGA-FZ-5921       TCGA-FZ-5922       TCGA-FZ-5923 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FZ-5926       TCGA-H8-A6C1       TCGA-HV-A7OL       TCGA-HV-A7OP 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HV-AA8V       TCGA-HV-AA8X       TCGA-HZ-7918       TCGA-HZ-7925 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-8637       TCGA-HZ-A49I       TCGA-HZ-A77O       TCGA-HZ-A77P 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-HZ-A9TJ       TCGA-IB-7652       TCGA-IB-7885 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SO       TCGA-IB-A5SP       TCGA-IB-A5SQ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A5ST       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7LX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUM       TCGA-IB-AAUN       TCGA-IB-AAUO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUP       TCGA-IB-AAUQ       TCGA-IB-AAUR       TCGA-IB-AAUS 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-IB-AAUW       TCGA-LB-A8F3 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-Q3-A5QY       TCGA-Q3-AA2A 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-RB-A7B8       TCGA-RB-AA9M       TCGA-RL-AAAS       TCGA-US-A776 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-US-A779       TCGA-US-A77G       TCGA-US-A77J       TCGA-XD-AAUG 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-XD-AAUH       TCGA-XD-AAUI       TCGA-XN-A8T3       TCGA-XN-A8T5 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-YB-A89D       TCGA-YY-A8LH       TCGA-Z5-AAPL 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
D579V10, continuous
[1] "Remove cluster labels:" "AKNAD1 MUTATED"        
clus
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-YY-A8LH 
"AKNAD1 WILD-TYPE" 
D579V11, continuous
[1] "Remove cluster labels:" "AKNAD1 MUTATED"        
clus
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  AKNAD1 MUTATED    2  0  0  0
  AKNAD1 WILD-TYPE 78 35  4  2
D579V12, multiclass
[1] "Remove cluster labels:" "AKNAD1 MUTATED"        
clus
  AKNAD1 MUTATED AKNAD1 WILD-TYPE 
               2              119 
      TCGA-2J-AABR       TCGA-2J-AABT       TCGA-3A-A9I5       TCGA-3A-A9IJ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IL       TCGA-F2-A44G       TCGA-FB-AAQ6       TCGA-FZ-5924 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX       TCGA-S4-A8RO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-US-A77E       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AAB4 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AAB6       TCGA-2J-AAB8       TCGA-2J-AAB9       TCGA-2J-AABA 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABH       TCGA-2J-AABK 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-2J-AABP       TCGA-2J-AABU       TCGA-2J-AABV 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-2L-AAQI       TCGA-2L-AAQJ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-2L-AAQL       TCGA-2L-AAQM       TCGA-3A-A9I7       TCGA-3A-A9I9 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IC       TCGA-3A-A9IH       TCGA-3A-A9IO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IR       TCGA-3A-A9IS       TCGA-3A-A9IU       TCGA-3A-A9IV 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-3A-A9IZ       TCGA-3A-A9J0       TCGA-F2-7273 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-F2-A7TX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAPP       TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-FB-AAPU 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAPZ       TCGA-FB-AAQ0       TCGA-FB-AAQ1       TCGA-FB-AAQ2 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FB-AAQ3       TCGA-FZ-5920       TCGA-FZ-5922       TCGA-FZ-5923 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-FZ-5926       TCGA-H8-A6C1       TCGA-HV-A7OL       TCGA-HV-A7OP 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HV-AA8V       TCGA-HV-AA8X       TCGA-HZ-7918       TCGA-HZ-7925 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-8637       TCGA-HZ-A49I       TCGA-HZ-A77O       TCGA-HZ-A77P 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-HZ-A9TJ       TCGA-IB-7652       TCGA-IB-7885 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SO       TCGA-IB-A5SP       TCGA-IB-A5SQ 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A5ST       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7LX 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUM       TCGA-IB-AAUN       TCGA-IB-AAUO 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUP       TCGA-IB-AAUQ       TCGA-IB-AAUR       TCGA-IB-AAUS 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-IB-AAUW       TCGA-LB-A8F3 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-Q3-A5QY       TCGA-Q3-AA2A 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-RB-A7B8       TCGA-RB-AA9M       TCGA-RL-AAAS       TCGA-US-A776 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-US-A779       TCGA-US-A77G       TCGA-US-A77J       TCGA-XD-AAUG 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-XD-AAUH       TCGA-XD-AAUI       TCGA-XN-A8T3       TCGA-XN-A8T5 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
      TCGA-YB-A89D       TCGA-YY-A8LH       TCGA-Z5-AAPL 
"AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" "AKNAD1 WILD-TYPE" 
D579V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKNAD1 MUTATED       0                         0     3
  AKNAD1 WILD-TYPE     6                         5   111
D579V14, multiclass
                           clus
vv                          AKNAD1 MUTATED AKNAD1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V15, binary
                  cls
clus                0  1
  AKNAD1 MUTATED    0  3
  AKNAD1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKNAD1 MUTATED      0    3
  AKNAD1 WILD-TYPE    5   88
                        clus
vv                       AKNAD1 MUTATED AKNAD1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(580) Variable = MMP9 MUTATION ANALYSIS
D580V1, survival
                sevent
clus2             0  1
  MMP9 MUTATED    0  3
  MMP9 WILD-TYPE 63 59
  MMP9 MUTATED MMP9 WILD-TYPE 
             3            122 
  MMP9 MUTATED MMP9 WILD-TYPE 
             3             59 
$`MMP9 MUTATED`
TCGA-2L-AAQL TCGA-HZ-A77O TCGA-IB-7651 
        9.60         5.26        19.82 

$`MMP9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MMP9 MUTATED MMP9 WILD-TYPE 
          5.26           0.23 
  MMP9 MUTATED MMP9 WILD-TYPE 
         19.82          90.12 
  MMP9 MUTATED MMP9 WILD-TYPE 
          9.60          15.27 
[1] "5.3 - 19.8 (9.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "3.3"
D580V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MMP9 MUTATED         0        0        0         0         3         0
  MMP9 WILD-TYPE       1        3       12        19        79         4
                vv
clus             STAGE IV
  MMP9 MUTATED          0
  MMP9 WILD-TYPE        3
D580V3, multiclass
           clus
vv          MMP9 MUTATED MMP9 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2 T3+T4
  MMP9 MUTATED     0   1     2
  MMP9 WILD-TYPE   5  16   100
D580V4, multiclass
       clus
vv      MMP9 MUTATED MMP9 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            2            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V5, binary
                cls
clus              0  1
  MMP9 MUTATED    0  3
  MMP9 WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP9 MUTATED      0    3
  MMP9 WILD-TYPE   35   86
   clus
vv  MMP9 MUTATED MMP9 WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D580V6, binary
                cls
clus              0  1
  MMP9 MUTATED    1  0
  MMP9 WILD-TYPE 56  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP9 MUTATED      1    0
  MMP9 WILD-TYPE   56    3
   clus
vv  MMP9 MUTATED MMP9 WILD-TYPE
  0            1             56
  1            0              3
[1] 2 2
[1] FALSE
D580V7, binary
                cls
clus              0  1
  MMP9 MUTATED    2  1
  MMP9 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP9 MUTATED      2    1
  MMP9 WILD-TYPE   49   74
        clus
vv       MMP9 MUTATED MMP9 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D580V8, binary
                cls
clus              0  1
  MMP9 MUTATED    3  0
  MMP9 WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP9 MUTATED      3    0
  MMP9 WILD-TYPE   85   30
     clus
vv    MMP9 MUTATED MMP9 WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP9 MUTATED                                     3
  MMP9 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP9 MUTATED                                       0
  MMP9 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP9 MUTATED                                                  0
  MMP9 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  MMP9 MUTATED                                     0
  MMP9 WILD-TYPE                                   1
D580V9, multiclass
                                                  clus
vv                                                 MMP9 MUTATED MMP9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V10, continuous
[1] "Remove cluster labels:" "MMP9 MUTATED"          
clus
  MMP9 MUTATED MMP9 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
D580V11, continuous
[1] "Remove cluster labels:" "MMP9 MUTATED"          
clus
  MMP9 MUTATED MMP9 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" "MMP9 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MMP9 MUTATED    2  0  0  1
  MMP9 WILD-TYPE 78 35  4  1
D580V12, multiclass
    clus
vv   MMP9 MUTATED MMP9 WILD-TYPE
  R0            2             78
  R1            0             35
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP9 MUTATED       0                         0     3
  MMP9 WILD-TYPE     6                         5   111
D580V14, multiclass
                           clus
vv                          MMP9 MUTATED MMP9 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V15, binary
                cls
clus              0  1
  MMP9 MUTATED    0  2
  MMP9 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP9 MUTATED      0    2
  MMP9 WILD-TYPE    5   89
                        clus
vv                       MMP9 MUTATED MMP9 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(581) Variable = SCAND3 MUTATION ANALYSIS
D581V1, survival
                  sevent
clus2               0  1
  SCAND3 MUTATED    4  1
  SCAND3 WILD-TYPE 59 61
  SCAND3 MUTATED SCAND3 WILD-TYPE 
               5              120 
  SCAND3 MUTATED SCAND3 WILD-TYPE 
               1               61 
$`SCAND3 MUTATED`
TCGA-HZ-A77Q TCGA-XD-AAUL TCGA-H8-A6C1 TCGA-IB-7651 TCGA-RB-AA9M 
        1.08        16.37        22.06        19.82         9.40 

$`SCAND3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 
        8.78        13.68         3.12        15.32         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SCAND3 MUTATED SCAND3 WILD-TYPE 
            1.08             0.23 
  SCAND3 MUTATED SCAND3 WILD-TYPE 
           22.06            90.12 
  SCAND3 MUTATED SCAND3 WILD-TYPE 
          16.370           15.205 
[1] "1.1 - 22.1 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.2"
D581V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SCAND3 MUTATED         0        0        0         2         3         0
  SCAND3 WILD-TYPE       1        3       12        17        79         4
                  vv
clus               STAGE IV
  SCAND3 MUTATED          0
  SCAND3 WILD-TYPE        3
D581V3, multiclass
           clus
vv          SCAND3 MUTATED SCAND3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              2               17
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  SCAND3 MUTATED    1  0     4
  SCAND3 WILD-TYPE  4 17    98
D581V4, multiclass
       clus
vv      SCAND3 MUTATED SCAND3 WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V5, binary
                  cls
clus                0  1
  SCAND3 MUTATED    2  3
  SCAND3 WILD-TYPE 33 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAND3 MUTATED      2    3
  SCAND3 WILD-TYPE   33   86
   clus
vv  SCAND3 MUTATED SCAND3 WILD-TYPE
  0              2               33
  1              3               86
[1] 2 2
[1] FALSE
D581V6, binary
                  cls
clus                0  1
  SCAND3 MUTATED    1  0
  SCAND3 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAND3 MUTATED      1    0
  SCAND3 WILD-TYPE   56    3
   clus
vv  SCAND3 MUTATED SCAND3 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D581V7, binary
                  cls
clus                0  1
  SCAND3 MUTATED    2  3
  SCAND3 WILD-TYPE 49 72
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAND3 MUTATED      2    3
  SCAND3 WILD-TYPE   49   72
        clus
vv       SCAND3 MUTATED SCAND3 WILD-TYPE
  FEMALE              2               49
  MALE                3               72
[1] 2 2
[1] FALSE
D581V8, binary
                  cls
clus                0  1
  SCAND3 MUTATED    3  1
  SCAND3 WILD-TYPE 85 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAND3 MUTATED      3    1
  SCAND3 WILD-TYPE   85   29
     clus
vv    SCAND3 MUTATED SCAND3 WILD-TYPE
  NO               3               85
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SCAND3 MUTATED                                     3
  SCAND3 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SCAND3 MUTATED                                       2
  SCAND3 WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SCAND3 MUTATED                                                  0
  SCAND3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SCAND3 MUTATED                                     0
  SCAND3 WILD-TYPE                                   1
D581V9, multiclass
                                                  clus
vv                                                 SCAND3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SCAND3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V10, continuous
D581V11, continuous
                  vv
clus               R0 R1 R2 RX
  SCAND3 MUTATED    5  0  0  0
  SCAND3 WILD-TYPE 75 35  4  2
D581V12, multiclass
    clus
vv   SCAND3 MUTATED SCAND3 WILD-TYPE
  R0              5               75
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCAND3 MUTATED       0                         0     5
  SCAND3 WILD-TYPE     6                         5   109
D581V14, multiclass
                           clus
vv                          SCAND3 MUTATED SCAND3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V15, binary
                  cls
clus                0  1
  SCAND3 MUTATED    0  5
  SCAND3 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCAND3 MUTATED      0    5
  SCAND3 WILD-TYPE    5   86
                        clus
vv                       SCAND3 MUTATED SCAND3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(582) Variable = RNGTT MUTATION ANALYSIS
D582V1, survival
                 sevent
clus2              0  1
  RNGTT MUTATED    2  1
  RNGTT WILD-TYPE 61 61
  RNGTT MUTATED RNGTT WILD-TYPE 
              3             122 
  RNGTT MUTATED RNGTT WILD-TYPE 
              1              61 
$`RNGTT MUTATED`
TCGA-3A-A9IV TCGA-FZ-5919 TCGA-YH-A8SY 
       36.26        24.36        12.76 

$`RNGTT WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03         1.02         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RNGTT MUTATED RNGTT WILD-TYPE 
          12.76            0.23 
  RNGTT MUTATED RNGTT WILD-TYPE 
          36.26           90.12 
  RNGTT MUTATED RNGTT WILD-TYPE 
         24.360          15.205 
[1] "12.8 - 36.3 (24.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.3"
D582V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RNGTT MUTATED         0        0        1         0         1         1
  RNGTT WILD-TYPE       1        3       11        19        81         3
                 vv
clus              STAGE IV
  RNGTT MUTATED          0
  RNGTT WILD-TYPE        3
D582V3, multiclass
           clus
vv          RNGTT MUTATED RNGTT WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             1              81
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  RNGTT MUTATED     0   1     2
  RNGTT WILD-TYPE   5  16   100
D582V4, multiclass
       clus
vv      RNGTT MUTATED RNGTT WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V5, binary
                 cls
clus               0  1
  RNGTT MUTATED    1  2
  RNGTT WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNGTT MUTATED      1    2
  RNGTT WILD-TYPE   34   87
   clus
vv  RNGTT MUTATED RNGTT WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D582V6, binary
                 cls
clus               0  1
  RNGTT MUTATED    0  0
  RNGTT WILD-TYPE 57  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNGTT MUTATED      0    0
  RNGTT WILD-TYPE   57    3
D582V7, binary
                 cls
clus               0  1
  RNGTT MUTATED    3  0
  RNGTT WILD-TYPE 48 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNGTT MUTATED      3    0
  RNGTT WILD-TYPE   48   75
        clus
vv       RNGTT MUTATED RNGTT WILD-TYPE
  FEMALE             3              48
  MALE               0              75
[1] 2 2
[1] FALSE
D582V8, binary
                 cls
clus               0  1
  RNGTT MUTATED    2  1
  RNGTT WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNGTT MUTATED      2    1
  RNGTT WILD-TYPE   86   29
     clus
vv    RNGTT MUTATED RNGTT WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNGTT MUTATED                                     1
  RNGTT WILD-TYPE                                 104
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNGTT MUTATED                                       1
  RNGTT WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNGTT MUTATED                                                  0
  RNGTT WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  RNGTT MUTATED                                     0
  RNGTT WILD-TYPE                                   1
D582V9, multiclass
[1] "Remove cluster labels:" "RNGTT MUTATED"         
clus
  RNGTT MUTATED RNGTT WILD-TYPE 
              2             123 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5920 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923      TCGA-FZ-5926 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP      TCGA-HV-AA8V 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652      TCGA-IB-7885 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
D582V10, continuous
D582V11, continuous
                 vv
clus              R0 R1 R2 RX
  RNGTT MUTATED    1  0  0  0
  RNGTT WILD-TYPE 79 35  4  2
D582V12, multiclass
[1] "Remove cluster labels:" "RNGTT MUTATED"         
clus
  RNGTT MUTATED RNGTT WILD-TYPE 
              1             120 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-2L-AAQJ      TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IO      TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-F2-7273 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922      TCGA-FZ-5923 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7651      TCGA-IB-7652 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-US-A776      TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" "RNGTT WILD-TYPE" 
D582V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNGTT MUTATED       0                         0     3
  RNGTT WILD-TYPE     6                         5   111
D582V14, multiclass
                           clus
vv                          RNGTT MUTATED RNGTT WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V15, binary
                 cls
clus               0  1
  RNGTT MUTATED    0  3
  RNGTT WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNGTT MUTATED      0    3
  RNGTT WILD-TYPE    5   88
                        clus
vv                       RNGTT MUTATED RNGTT WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(583) Variable = C1QTNF7 MUTATION ANALYSIS
D583V1, survival
                   sevent
clus2                0  1
  C1QTNF7 MUTATED    1  3
  C1QTNF7 WILD-TYPE 62 59
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                4               121 
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                3                59 
$`C1QTNF7 MUTATED`
TCGA-2J-AAB9 TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-AAUS 
       20.61         5.26        19.82         7.40 

$`C1QTNF7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
             5.26              0.23 
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
            20.61             90.12 
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
            13.61             15.22 
[1] "5.3 - 20.6 (13.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D583V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C1QTNF7 MUTATED         0        0        0         0         4         0
  C1QTNF7 WILD-TYPE       1        3       12        19        78         4
                   vv
clus                STAGE IV
  C1QTNF7 MUTATED          0
  C1QTNF7 WILD-TYPE        3
D583V3, multiclass
           clus
vv          C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               4                78
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  C1QTNF7 MUTATED    0  1     3
  C1QTNF7 WILD-TYPE  5 16    99
D583V4, multiclass
       clus
vv      C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V5, binary
                   cls
clus                 0  1
  C1QTNF7 MUTATED    0  4
  C1QTNF7 WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF7 MUTATED      0    4
  C1QTNF7 WILD-TYPE   35   85
   clus
vv  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D583V6, binary
                   cls
clus                 0  1
  C1QTNF7 MUTATED    3  0
  C1QTNF7 WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF7 MUTATED      3    0
  C1QTNF7 WILD-TYPE   54    3
   clus
vv  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D583V7, binary
                   cls
clus                 0  1
  C1QTNF7 MUTATED    4  0
  C1QTNF7 WILD-TYPE 47 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF7 MUTATED      4    0
  C1QTNF7 WILD-TYPE   47   75
        clus
vv       C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  FEMALE               4                47
  MALE                 0                75
[1] 2 2
[1] FALSE
D583V8, binary
                   cls
clus                 0  1
  C1QTNF7 MUTATED    3  1
  C1QTNF7 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF7 MUTATED      3    1
  C1QTNF7 WILD-TYPE   85   29
     clus
vv    C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C1QTNF7 MUTATED                                     4
  C1QTNF7 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C1QTNF7 MUTATED                                       0
  C1QTNF7 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C1QTNF7 MUTATED                                                  0
  C1QTNF7 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  C1QTNF7 MUTATED                                     0
  C1QTNF7 WILD-TYPE                                   1
D583V9, multiclass
                                                  clus
vv                                                 C1QTNF7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 C1QTNF7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V10, continuous
[1] "Remove cluster labels:" "C1QTNF7 MUTATED"       
clus
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUU 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-YY-A8LH 
"C1QTNF7 WILD-TYPE" 
D583V11, continuous
[1] "Remove cluster labels:" "C1QTNF7 MUTATED"       
clus
  C1QTNF7 MUTATED C1QTNF7 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" "C1QTNF7 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  C1QTNF7 MUTATED    3  1  0  0
  C1QTNF7 WILD-TYPE 77 34  4  2
D583V12, multiclass
    clus
vv   C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QTNF7 MUTATED       0                         0     4
  C1QTNF7 WILD-TYPE     6                         5   110
D583V14, multiclass
                           clus
vv                          C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V15, binary
                   cls
clus                 0  1
  C1QTNF7 MUTATED    0  3
  C1QTNF7 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF7 MUTATED      0    3
  C1QTNF7 WILD-TYPE    5   88
                        clus
vv                       C1QTNF7 MUTATED C1QTNF7 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(584) Variable = CHMP2A MUTATION ANALYSIS
D584V1, survival
                  sevent
clus2               0  1
  CHMP2A MUTATED    1  3
  CHMP2A WILD-TYPE 62 59
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               4              121 
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               3               59 
$`CHMP2A MUTATED`
TCGA-F2-A7TX TCGA-HZ-A77O TCGA-IB-7651 TCGA-RL-AAAS 
        3.12         5.26        19.82         0.30 

$`CHMP2A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CHMP2A MUTATED CHMP2A WILD-TYPE 
            0.30             0.23 
  CHMP2A MUTATED CHMP2A WILD-TYPE 
           19.82            90.12 
  CHMP2A MUTATED CHMP2A WILD-TYPE 
            4.19            15.32 
[1] "0.3 - 19.8 (4.2)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4"  
D584V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CHMP2A MUTATED         0        0        1         0         3         0
  CHMP2A WILD-TYPE       1        3       11        19        79         4
                  vv
clus               STAGE IV
  CHMP2A MUTATED          0
  CHMP2A WILD-TYPE        3
D584V3, multiclass
           clus
vv          CHMP2A MUTATED CHMP2A WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  CHMP2A MUTATED     0   2     2
  CHMP2A WILD-TYPE   5  15   100
D584V4, multiclass
       clus
vv      CHMP2A MUTATED CHMP2A WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V5, binary
                  cls
clus                0  1
  CHMP2A MUTATED    1  3
  CHMP2A WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP2A MUTATED      1    3
  CHMP2A WILD-TYPE   34   86
   clus
vv  CHMP2A MUTATED CHMP2A WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D584V6, binary
                  cls
clus                0  1
  CHMP2A MUTATED    3  0
  CHMP2A WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP2A MUTATED      3    0
  CHMP2A WILD-TYPE   54    3
   clus
vv  CHMP2A MUTATED CHMP2A WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D584V7, binary
                  cls
clus                0  1
  CHMP2A MUTATED    3  1
  CHMP2A WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP2A MUTATED      3    1
  CHMP2A WILD-TYPE   48   74
        clus
vv       CHMP2A MUTATED CHMP2A WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D584V8, binary
                  cls
clus                0  1
  CHMP2A MUTATED    4  0
  CHMP2A WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP2A MUTATED      4    0
  CHMP2A WILD-TYPE   84   30
     clus
vv    CHMP2A MUTATED CHMP2A WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHMP2A MUTATED                                     4
  CHMP2A WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHMP2A MUTATED                                       0
  CHMP2A WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHMP2A MUTATED                                                  0
  CHMP2A WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  CHMP2A MUTATED                                     0
  CHMP2A WILD-TYPE                                   1
D584V9, multiclass
                                                  clus
vv                                                 CHMP2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 CHMP2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V10, continuous
[1] "Remove cluster labels:" "CHMP2A MUTATED"        
clus
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
D584V11, continuous
[1] "Remove cluster labels:" "CHMP2A MUTATED"        
clus
  CHMP2A MUTATED CHMP2A WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" "CHMP2A WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CHMP2A MUTATED    3  1  0  0
  CHMP2A WILD-TYPE 77 34  4  2
D584V12, multiclass
    clus
vv   CHMP2A MUTATED CHMP2A WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHMP2A MUTATED       0                         0     4
  CHMP2A WILD-TYPE     6                         5   110
D584V14, multiclass
                           clus
vv                          CHMP2A MUTATED CHMP2A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V15, binary
                  cls
clus                0  1
  CHMP2A MUTATED    0  3
  CHMP2A WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP2A MUTATED      0    3
  CHMP2A WILD-TYPE    5   88
                        clus
vv                       CHMP2A MUTATED CHMP2A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(585) Variable = ATP6V0A4 MUTATION ANALYSIS
D585V1, survival
                    sevent
clus2                 0  1
  ATP6V0A4 MUTATED    2  4
  ATP6V0A4 WILD-TYPE 61 58
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 6                119 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 4                 58 
$`ATP6V0A4 MUTATED`
TCGA-F2-A44G TCGA-2J-AABA TCGA-2J-AABV TCGA-3A-A9IX TCGA-HV-AA8V TCGA-IB-7651 
        7.66        19.96        21.44        34.09        30.25        19.82 

$`ATP6V0A4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        36.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        32.15        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 
       10.13         5.26        10.85         0.23        19.82        36.69 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST 
       41.33        15.19        12.00        15.85         7.20        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
              7.66               0.23 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             34.09              90.12 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             20.70              15.12 
[1] "7.7 - 34.1 (20.7)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1"  
D585V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP6V0A4 MUTATED         0        1        0         0         5         0
  ATP6V0A4 WILD-TYPE       1        2       12        19        77         4
                    vv
clus                 STAGE IV
  ATP6V0A4 MUTATED          0
  ATP6V0A4 WILD-TYPE        3
D585V3, multiclass
           clus
vv          ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  2
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                5                 77
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  ATP6V0A4 MUTATED    1  0     5
  ATP6V0A4 WILD-TYPE  4 17    97
D585V4, multiclass
       clus
vv      ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  T1                   1                  4
  T2                   0                 17
  T3+T4                5                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V5, binary
                    cls
clus                  0  1
  ATP6V0A4 MUTATED    1  5
  ATP6V0A4 WILD-TYPE 34 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      1    5
  ATP6V0A4 WILD-TYPE   34   84
   clus
vv  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  0                1                 34
  1                5                 84
[1] 2 2
[1] FALSE
D585V6, binary
                    cls
clus                  0  1
  ATP6V0A4 MUTATED    4  0
  ATP6V0A4 WILD-TYPE 53  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      4    0
  ATP6V0A4 WILD-TYPE   53    3
   clus
vv  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  0                4                 53
  1                0                  3
[1] 2 2
[1] FALSE
D585V7, binary
                    cls
clus                  0  1
  ATP6V0A4 MUTATED    2  4
  ATP6V0A4 WILD-TYPE 49 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      2    4
  ATP6V0A4 WILD-TYPE   49   71
        clus
vv       ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  FEMALE                2                 49
  MALE                  4                 71
[1] 2 2
[1] FALSE
D585V8, binary
                    cls
clus                  0  1
  ATP6V0A4 MUTATED    4  2
  ATP6V0A4 WILD-TYPE 84 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      4    2
  ATP6V0A4 WILD-TYPE   84   28
     clus
vv    ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  NO                 4                 84
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP6V0A4 MUTATED                                     6
  ATP6V0A4 WILD-TYPE                                  99
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP6V0A4 MUTATED                                       0
  ATP6V0A4 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP6V0A4 MUTATED                                                  0
  ATP6V0A4 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP6V0A4 MUTATED                                     0
  ATP6V0A4 WILD-TYPE                                   1
D585V9, multiclass
                                                  clus
vv                                                 ATP6V0A4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 ATP6V0A4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V10, continuous
D585V11, continuous
[1] "Remove cluster labels:" "ATP6V0A4 MUTATED"      
clus
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" "ATP6V0A4 WILD-TYPE" 
        TCGA-YY-A8LH 
"ATP6V0A4 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  ATP6V0A4 MUTATED    2  3  1  0
  ATP6V0A4 WILD-TYPE 78 32  3  2
D585V12, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  R0                2                 78
  R1                3                 32
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP6V0A4 MUTATED       1                         0     5
  ATP6V0A4 WILD-TYPE     5                         5   109
D585V14, multiclass
                           clus
vv                          ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V15, binary
                    cls
clus                  0  1
  ATP6V0A4 MUTATED    0  3
  ATP6V0A4 WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      0    3
  ATP6V0A4 WILD-TYPE    5   88
                        clus
vv                       ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(586) Variable = FANCD2 MUTATION ANALYSIS
D586V1, survival
                  sevent
clus2               0  1
  FANCD2 MUTATED    3  4
  FANCD2 WILD-TYPE 60 58
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               7              118 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               4               58 
$`FANCD2 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IB TCGA-HZ-8637 TCGA-HZ-A49I TCGA-IB-7651 TCGA-XD-AAUG 
        1.08         7.36        17.00        10.13        19.82        13.81 
TCGA-YB-A89D 
       11.51 

$`FANCD2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC 
       12.95         9.60        45.47        43.50        20.84        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       31.86        20.19         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
       16.80         0.39        18.67        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  FANCD2 MUTATED FANCD2 WILD-TYPE 
            1.08             0.23 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           19.82            90.12 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
          11.510           15.335 
[1] "1.1 - 19.8 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.9"
D586V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FANCD2 MUTATED         0        0        0         0         6         0
  FANCD2 WILD-TYPE       1        3       12        19        76         4
                  vv
clus               STAGE IV
  FANCD2 MUTATED          1
  FANCD2 WILD-TYPE        2
D586V3, multiclass
           clus
vv          FANCD2 MUTATED FANCD2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              6               76
  STAGE III              0                4
  STAGE IV               1                2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  FANCD2 MUTATED    0  0     7
  FANCD2 WILD-TYPE  5 17    95
D586V4, multiclass
       clus
vv      FANCD2 MUTATED FANCD2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              7               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V5, binary
                  cls
clus                0  1
  FANCD2 MUTATED    0  7
  FANCD2 WILD-TYPE 35 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      0    7
  FANCD2 WILD-TYPE   35   82
   clus
vv  FANCD2 MUTATED FANCD2 WILD-TYPE
  0              0               35
  1              7               82
[1] 2 2
[1] FALSE
D586V6, binary
                  cls
clus                0  1
  FANCD2 MUTATED    1  1
  FANCD2 WILD-TYPE 56  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      1    1
  FANCD2 WILD-TYPE   56    2
   clus
vv  FANCD2 MUTATED FANCD2 WILD-TYPE
  0              1               56
  1              1                2
[1] 2 2
[1] FALSE
D586V7, binary
                  cls
clus                0  1
  FANCD2 MUTATED    5  2
  FANCD2 WILD-TYPE 46 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      5    2
  FANCD2 WILD-TYPE   46   73
        clus
vv       FANCD2 MUTATED FANCD2 WILD-TYPE
  FEMALE              5               46
  MALE                2               73
[1] 2 2
[1] FALSE
D586V8, binary
                  cls
clus                0  1
  FANCD2 MUTATED    3  3
  FANCD2 WILD-TYPE 85 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      3    3
  FANCD2 WILD-TYPE   85   27
     clus
vv    FANCD2 MUTATED FANCD2 WILD-TYPE
  NO               3               85
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FANCD2 MUTATED                                     6
  FANCD2 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FANCD2 MUTATED                                       1
  FANCD2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FANCD2 MUTATED                                                  0
  FANCD2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  FANCD2 MUTATED                                     0
  FANCD2 WILD-TYPE                                   1
D586V9, multiclass
                                                  clus
vv                                                 FANCD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 FANCD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V10, continuous
D586V11, continuous
                  vv
clus               R0 R1 R2 RX
  FANCD2 MUTATED    6  1  0  0
  FANCD2 WILD-TYPE 74 34  4  2
D586V12, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  R0              6               74
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FANCD2 MUTATED       0                         0     7
  FANCD2 WILD-TYPE     6                         5   107
D586V14, multiclass
                           clus
vv                          FANCD2 MUTATED FANCD2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V15, binary
                  cls
clus                0  1
  FANCD2 MUTATED    1  6
  FANCD2 WILD-TYPE  4 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      1    6
  FANCD2 WILD-TYPE    4   85
                        clus
vv                       FANCD2 MUTATED FANCD2 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              6               85
[1] 2 2
[1] FALSE

Clustering(587) Variable = ZCCHC11 MUTATION ANALYSIS
D587V1, survival
                   sevent
clus2                0  1
  ZCCHC11 MUTATED    3  5
  ZCCHC11 WILD-TYPE 60 57
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                8               117 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
                5                57 
$`ZCCHC11 MUTATED`
TCGA-2J-AABP TCGA-3A-A9IZ TCGA-IB-7651 TCGA-IB-AAUO TCGA-IB-AAUW TCGA-OE-A75W 
       15.22        10.13        19.82         7.86         7.56         8.78 
TCGA-XN-A8T3 TCGA-XN-A8T5 
       31.27        23.67 

$`ZCCHC11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        34.09        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY 
        7.40         8.05        13.28        12.46        10.29        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-YB-A89D 
        0.39        18.67        13.81        12.99        12.03        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
             7.56              0.23 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
            31.27             90.12 
  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE 
           12.675            15.320 
[1] "7.6 - 31.3 (12.7)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.4"
D587V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZCCHC11 MUTATED         0        0        2         1         5         0
  ZCCHC11 WILD-TYPE       1        3       10        18        77         4
                   vv
clus                STAGE IV
  ZCCHC11 MUTATED          0
  ZCCHC11 WILD-TYPE        3
D587V3, multiclass
           clus
vv          ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                2                10
  STAGE IIA               1                18
  STAGE IIB               5                77
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  ZCCHC11 MUTATED    0  2     6
  ZCCHC11 WILD-TYPE  5 15    96
D587V4, multiclass
       clus
vv      ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  T1                  0                 5
  T2                  2                15
  T3+T4               6                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V5, binary
                   cls
clus                 0  1
  ZCCHC11 MUTATED    3  5
  ZCCHC11 WILD-TYPE 32 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      3    5
  ZCCHC11 WILD-TYPE   32   84
   clus
vv  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  0               3                32
  1               5                84
[1] 2 2
[1] FALSE
D587V6, binary
                   cls
clus                 0  1
  ZCCHC11 MUTATED    7  0
  ZCCHC11 WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      7    0
  ZCCHC11 WILD-TYPE   50    3
   clus
vv  ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  0               7                50
  1               0                 3
[1] 2 2
[1] FALSE
D587V7, binary
                   cls
clus                 0  1
  ZCCHC11 MUTATED    5  3
  ZCCHC11 WILD-TYPE 46 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      5    3
  ZCCHC11 WILD-TYPE   46   72
        clus
vv       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  FEMALE               5                46
  MALE                 3                72
[1] 2 2
[1] FALSE
D587V8, binary
                   cls
clus                 0  1
  ZCCHC11 MUTATED    5  3
  ZCCHC11 WILD-TYPE 83 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      5    3
  ZCCHC11 WILD-TYPE   83   27
     clus
vv    ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  NO                5                83
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZCCHC11 MUTATED                                     6
  ZCCHC11 WILD-TYPE                                  99
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZCCHC11 MUTATED                                       1
  ZCCHC11 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZCCHC11 MUTATED                                                  0
  ZCCHC11 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZCCHC11 MUTATED                                     1
  ZCCHC11 WILD-TYPE                                   0
D587V9, multiclass
                                                  clus
vv                                                 ZCCHC11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
                                                  clus
vv                                                 ZCCHC11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V10, continuous
D587V11, continuous
                   vv
clus                R0 R1 R2 RX
  ZCCHC11 MUTATED    4  4  0  0
  ZCCHC11 WILD-TYPE 76 31  4  2
D587V12, multiclass
    clus
vv   ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  R0               4                76
  R1               4                31
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZCCHC11 MUTATED       0                         0     8
  ZCCHC11 WILD-TYPE     6                         5   106
D587V14, multiclass
                           clus
vv                          ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   8               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V15, binary
                   cls
clus                 0  1
  ZCCHC11 MUTATED    3  4
  ZCCHC11 WILD-TYPE  2 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZCCHC11 MUTATED      3    4
  ZCCHC11 WILD-TYPE    2   87
                        clus
vv                       ZCCHC11 MUTATED ZCCHC11 WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(588) Variable = GRM1 MUTATION ANALYSIS
D588V1, survival
                sevent
clus2             0  1
  GRM1 MUTATED    4  4
  GRM1 WILD-TYPE 59 58
  GRM1 MUTATED GRM1 WILD-TYPE 
             8            117 
  GRM1 MUTATED GRM1 WILD-TYPE 
             4             58 
$`GRM1 MUTATED`
TCGA-LB-A7SX TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-RB-AA9M 
       12.92        10.85        19.82        15.85         7.20         9.40 
TCGA-US-A776 TCGA-US-A77J 
       39.98        18.67 

$`GRM1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G 
       13.68         3.12        15.32         0.30        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  GRM1 MUTATED GRM1 WILD-TYPE 
          7.20           0.23 
  GRM1 MUTATED GRM1 WILD-TYPE 
         39.98          90.12 
  GRM1 MUTATED GRM1 WILD-TYPE 
        14.385         15.220 
[1] "7.2 - 40.0 (14.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.1"
D588V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GRM1 MUTATED         0        0        1         2         5         0
  GRM1 WILD-TYPE       1        3       11        17        77         4
                vv
clus             STAGE IV
  GRM1 MUTATED          0
  GRM1 WILD-TYPE        3
D588V3, multiclass
           clus
vv          GRM1 MUTATED GRM1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            2             17
  STAGE IIB            5             77
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  GRM1 MUTATED    1  1     6
  GRM1 WILD-TYPE  4 16    96
D588V4, multiclass
       clus
vv      GRM1 MUTATED GRM1 WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V5, binary
                cls
clus              0  1
  GRM1 MUTATED    3  5
  GRM1 WILD-TYPE 32 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED      3    5
  GRM1 WILD-TYPE   32   84
   clus
vv  GRM1 MUTATED GRM1 WILD-TYPE
  0            3             32
  1            5             84
[1] 2 2
[1] FALSE
D588V6, binary
                cls
clus              0  1
  GRM1 MUTATED    3  0
  GRM1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED      3    0
  GRM1 WILD-TYPE   54    3
   clus
vv  GRM1 MUTATED GRM1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D588V7, binary
                cls
clus              0  1
  GRM1 MUTATED    4  4
  GRM1 WILD-TYPE 47 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED      4    4
  GRM1 WILD-TYPE   47   71
        clus
vv       GRM1 MUTATED GRM1 WILD-TYPE
  FEMALE            4             47
  MALE              4             71
[1] 2 2
[1] FALSE
D588V8, binary
                cls
clus              0  1
  GRM1 MUTATED    6  1
  GRM1 WILD-TYPE 82 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED      6    1
  GRM1 WILD-TYPE   82   29
     clus
vv    GRM1 MUTATED GRM1 WILD-TYPE
  NO             6             82
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GRM1 MUTATED                                     6
  GRM1 WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GRM1 MUTATED                                       1
  GRM1 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GRM1 MUTATED                                                  1
  GRM1 WILD-TYPE                                                0
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  GRM1 MUTATED                                     0
  GRM1 WILD-TYPE                                   1
D588V9, multiclass
                                                  clus
vv                                                 GRM1 MUTATED GRM1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            1              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V10, continuous
[1] "Remove cluster labels:" "GRM1 MUTATED"          
clus
  GRM1 MUTATED GRM1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-YY-A8LH 
"GRM1 WILD-TYPE" 
D588V11, continuous
[1] "Remove cluster labels:" "GRM1 MUTATED"          
clus
  GRM1 MUTATED GRM1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"GRM1 WILD-TYPE" "GRM1 WILD-TYPE" "GRM1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  GRM1 MUTATED    6  2  0  0
  GRM1 WILD-TYPE 74 33  4  2
D588V12, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  R0            6             74
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GRM1 MUTATED       0                         1     7
  GRM1 WILD-TYPE     6                         4   107
D588V14, multiclass
                           clus
vv                          GRM1 MUTATED GRM1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                7            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V15, binary
                cls
clus              0  1
  GRM1 MUTATED    0  7
  GRM1 WILD-TYPE  5 84
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED      0    7
  GRM1 WILD-TYPE    5   84
                        clus
vv                       GRM1 MUTATED GRM1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7             84
[1] 2 2
[1] FALSE

Clustering(589) Variable = TNFRSF11A MUTATION ANALYSIS
D589V1, survival
                     sevent
clus2                  0  1
  TNFRSF11A MUTATED    2  2
  TNFRSF11A WILD-TYPE 61 60
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  4                 121 
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  2                  60 
$`TNFRSF11A MUTATED`
TCGA-3A-A9IS TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-A5ST 
       32.81        71.74        19.82        20.88 

$`TNFRSF11A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU 
        7.36        24.26        33.57        63.85        50.70        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
              19.82                0.23 
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
              71.74               90.12 
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
             26.845              15.120 
[1] "19.8 - 71.7 (26.8)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.9"
D589V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TNFRSF11A MUTATED         0        0        1         1         2         0
  TNFRSF11A WILD-TYPE       1        3       11        18        80         4
                     vv
clus                  STAGE IV
  TNFRSF11A MUTATED          0
  TNFRSF11A WILD-TYPE        3
D589V3, multiclass
           clus
vv          TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  0                   3
  STAGE IB                  1                  11
  STAGE IIA                 1                  18
  STAGE IIB                 2                  80
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3+T4
  TNFRSF11A MUTATED    0  1     3
  TNFRSF11A WILD-TYPE  5 16    99
D589V4, multiclass
       clus
vv      TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  T1                    0                   5
  T2                    1                  16
  T3+T4                 3                  99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V5, binary
                     cls
clus                   0  1
  TNFRSF11A MUTATED    2  2
  TNFRSF11A WILD-TYPE 33 87
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF11A MUTATED      2    2
  TNFRSF11A WILD-TYPE   33   87
   clus
vv  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  0                 2                  33
  1                 2                  87
[1] 2 2
[1] FALSE
D589V6, binary
                     cls
clus                   0  1
  TNFRSF11A MUTATED    2  0
  TNFRSF11A WILD-TYPE 55  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF11A MUTATED      2    0
  TNFRSF11A WILD-TYPE   55    3
   clus
vv  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  0                 2                  55
  1                 0                   3
[1] 2 2
[1] FALSE
D589V7, binary
                     cls
clus                   0  1
  TNFRSF11A MUTATED    2  2
  TNFRSF11A WILD-TYPE 49 73
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF11A MUTATED      2    2
  TNFRSF11A WILD-TYPE   49   73
        clus
vv       TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  FEMALE                 2                  49
  MALE                   2                  73
[1] 2 2
[1] FALSE
D589V8, binary
                     cls
clus                   0  1
  TNFRSF11A MUTATED    3  0
  TNFRSF11A WILD-TYPE 85 30
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF11A MUTATED      3    0
  TNFRSF11A WILD-TYPE   85   30
     clus
vv    TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  NO                  3                  85
  YES                 0                  30
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNFRSF11A MUTATED                                     3
  TNFRSF11A WILD-TYPE                                 102
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNFRSF11A MUTATED                                       1
  TNFRSF11A WILD-TYPE                                    17
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNFRSF11A MUTATED                                                  0
  TNFRSF11A WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  TNFRSF11A MUTATED                                     0
  TNFRSF11A WILD-TYPE                                   1
D589V9, multiclass
                                                  clus
vv                                                 TNFRSF11A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 TNFRSF11A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V10, continuous
[1] "Remove cluster labels:" "TNFRSF11A MUTATED"     
clus
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  1                  38 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2J-AABV 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-2L-AAQA          TCGA-2L-AAQE          TCGA-3A-A9I9 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-3A-A9IB          TCGA-3A-A9IX          TCGA-F2-A8YN 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-FB-A5VM          TCGA-FB-A78T          TCGA-FB-AAPQ 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-FB-AAPS          TCGA-H8-A6C1          TCGA-HV-AA8V 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUU 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-AAUV          TCGA-LB-A9Q5          TCGA-OE-A75W 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
D589V11, continuous
[1] "Remove cluster labels:" "TNFRSF11A MUTATED"     
clus
  TNFRSF11A MUTATED TNFRSF11A WILD-TYPE 
                  1                  32 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABE          TCGA-2J-AABF 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-2J-AABO          TCGA-3A-A9IB          TCGA-3A-A9IR 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-FB-A5VM          TCGA-FB-A78T 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-FB-AAPQ          TCGA-FB-AAPS          TCGA-H8-A6C1 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-HZ-A8P1          TCGA-IB-7885          TCGA-IB-8126 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUV 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-LB-A9Q5          TCGA-OE-A75W          TCGA-XD-AAUI 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"TNFRSF11A WILD-TYPE" "TNFRSF11A WILD-TYPE" 
                     vv
clus                  R0 R1 R2 RX
  TNFRSF11A MUTATED    3  0  0  0
  TNFRSF11A WILD-TYPE 77 35  4  2
D589V12, multiclass
    clus
vv   TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  R0                 3                  77
  R1                 0                  35
  R2                 0                   4
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNFRSF11A MUTATED       0                         0     4
  TNFRSF11A WILD-TYPE     6                         5   110
D589V14, multiclass
                           clus
vv                          TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     4                 110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V15, binary
                     cls
clus                   0  1
  TNFRSF11A MUTATED    1  3
  TNFRSF11A WILD-TYPE  4 88
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF11A MUTATED      1    3
  TNFRSF11A WILD-TYPE    4   88
                        clus
vv                       TNFRSF11A MUTATED TNFRSF11A WILD-TYPE
  HISPANIC OR LATINO                     1                   4
  NOT HISPANIC OR LATINO                 3                  88
[1] 2 2
[1] FALSE

Clustering(590) Variable = ANKRD30A MUTATION ANALYSIS
D590V1, survival
                    sevent
clus2                 0  1
  ANKRD30A MUTATED    3  4
  ANKRD30A WILD-TYPE 60 58
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 7                118 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 4                 58 
$`ANKRD30A MUTATED`
TCGA-3A-A9IC TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-RB-AA9M 
       24.26        10.85        19.82         1.35        15.88         9.40 
TCGA-US-A779 
       16.80 

$`ANKRD30A WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM 
       15.85         7.20        20.88        21.90         8.22         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G 
       13.68         3.12        15.32         0.30        39.98         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              1.35               0.23 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             24.26              90.12 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            15.880             15.205 
[1] "1.4 - 24.3 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D590V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ANKRD30A MUTATED         0        0        0         0         7         0
  ANKRD30A WILD-TYPE       1        3       12        19        75         4
                    vv
clus                 STAGE IV
  ANKRD30A MUTATED          0
  ANKRD30A WILD-TYPE        3
D590V3, multiclass
           clus
vv          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                7                 75
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  ANKRD30A MUTATED    1  0     6
  ANKRD30A WILD-TYPE  4 17    96
D590V4, multiclass
       clus
vv      ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                   1                  4
  T2                   0                 17
  T3+T4                6                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V5, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    0  7
  ANKRD30A WILD-TYPE 35 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    7
  ANKRD30A WILD-TYPE   35   82
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                0                 35
  1                7                 82
[1] 2 2
[1] FALSE
D590V6, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    2  0
  ANKRD30A WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      2    0
  ANKRD30A WILD-TYPE   55    3
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D590V7, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    3  4
  ANKRD30A WILD-TYPE 48 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      3    4
  ANKRD30A WILD-TYPE   48   71
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  FEMALE                3                 48
  MALE                  4                 71
[1] 2 2
[1] FALSE
D590V8, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    4  2
  ANKRD30A WILD-TYPE 84 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      4    2
  ANKRD30A WILD-TYPE   84   28
     clus
vv    ANKRD30A MUTATED ANKRD30A WILD-TYPE
  NO                 4                 84
  YES                2                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD30A MUTATED                                     6
  ANKRD30A WILD-TYPE                                  99
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD30A MUTATED                                       1
  ANKRD30A WILD-TYPE                                    17
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD30A MUTATED                                                  0
  ANKRD30A WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  ANKRD30A MUTATED                                     0
  ANKRD30A WILD-TYPE                                   1
D590V9, multiclass
                                                  clus
vv                                                 ANKRD30A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 ANKRD30A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V10, continuous
D590V11, continuous
                    vv
clus                 R0 R1 R2 RX
  ANKRD30A MUTATED    6  1  0  0
  ANKRD30A WILD-TYPE 74 34  4  2
D590V12, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0                6                 74
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD30A MUTATED       0                         0     7
  ANKRD30A WILD-TYPE     6                         5   107
D590V14, multiclass
                           clus
vv                          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    7                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V15, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    0  7
  ANKRD30A WILD-TYPE  5 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    7
  ANKRD30A WILD-TYPE    5   84
                        clus
vv                       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                7                 84
[1] 2 2
[1] FALSE

Clustering(591) Variable = SNX32 MUTATION ANALYSIS
D591V1, survival
                 sevent
clus2              0  1
  SNX32 MUTATED    2  2
  SNX32 WILD-TYPE 61 60
  SNX32 MUTATED SNX32 WILD-TYPE 
              4             121 
  SNX32 MUTATED SNX32 WILD-TYPE 
              2              60 
$`SNX32 MUTATED`
TCGA-3A-A9IV TCGA-HZ-A77O TCGA-IB-7651 TCGA-Q3-A5QY 
       36.26         5.26        19.82        13.68 

$`SNX32 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P 
       17.49        31.86        20.19        17.00        10.13        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SNX32 MUTATED SNX32 WILD-TYPE 
           5.26            0.23 
  SNX32 MUTATED SNX32 WILD-TYPE 
          36.26           90.12 
  SNX32 MUTATED SNX32 WILD-TYPE 
          16.75           15.22 
[1] "5.3 - 36.3 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D591V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SNX32 MUTATED         0        0        1         0         3         0
  SNX32 WILD-TYPE       1        3       11        19        79         4
                 vv
clus              STAGE IV
  SNX32 MUTATED          0
  SNX32 WILD-TYPE        3
D591V3, multiclass
           clus
vv          SNX32 MUTATED SNX32 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SNX32 MUTATED     0   2     2
  SNX32 WILD-TYPE   5  15   100
D591V4, multiclass
       clus
vv      SNX32 MUTATED SNX32 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V5, binary
                 cls
clus               0  1
  SNX32 MUTATED    1  3
  SNX32 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX32 MUTATED      1    3
  SNX32 WILD-TYPE   34   86
   clus
vv  SNX32 MUTATED SNX32 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D591V6, binary
                 cls
clus               0  1
  SNX32 MUTATED    1  0
  SNX32 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX32 MUTATED      1    0
  SNX32 WILD-TYPE   56    3
   clus
vv  SNX32 MUTATED SNX32 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D591V7, binary
                 cls
clus               0  1
  SNX32 MUTATED    3  1
  SNX32 WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX32 MUTATED      3    1
  SNX32 WILD-TYPE   48   74
        clus
vv       SNX32 MUTATED SNX32 WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D591V8, binary
                 cls
clus               0  1
  SNX32 MUTATED    4  0
  SNX32 WILD-TYPE 84 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX32 MUTATED      4    0
  SNX32 WILD-TYPE   84   30
     clus
vv    SNX32 MUTATED SNX32 WILD-TYPE
  NO              4              84
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SNX32 MUTATED                                     3
  SNX32 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SNX32 MUTATED                                       1
  SNX32 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SNX32 MUTATED                                                  0
  SNX32 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SNX32 MUTATED                                     0
  SNX32 WILD-TYPE                                   1
D591V9, multiclass
                                                  clus
vv                                                 SNX32 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SNX32 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V10, continuous
[1] "Remove cluster labels:" "SNX32 MUTATED"         
clus
  SNX32 MUTATED SNX32 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
D591V11, continuous
[1] "Remove cluster labels:" "SNX32 MUTATED"         
clus
  SNX32 MUTATED SNX32 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" "SNX32 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SNX32 MUTATED    4  0  0  0
  SNX32 WILD-TYPE 76 35  4  2
D591V12, multiclass
    clus
vv   SNX32 MUTATED SNX32 WILD-TYPE
  R0             4              76
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SNX32 MUTATED       0                         0     4
  SNX32 WILD-TYPE     6                         5   110
D591V14, multiclass
                           clus
vv                          SNX32 MUTATED SNX32 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V15, binary
                 cls
clus               0  1
  SNX32 MUTATED    0  4
  SNX32 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX32 MUTATED      0    4
  SNX32 WILD-TYPE    5   87
                        clus
vv                       SNX32 MUTATED SNX32 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(592) Variable = BRF1 MUTATION ANALYSIS
D592V1, survival
                sevent
clus2             0  1
  BRF1 MUTATED    1  3
  BRF1 WILD-TYPE 62 59
  BRF1 MUTATED BRF1 WILD-TYPE 
             4            121 
  BRF1 MUTATED BRF1 WILD-TYPE 
             3             59 
$`BRF1 MUTATED`
TCGA-FZ-5924 TCGA-IB-7651 TCGA-IB-AAUU TCGA-XD-AAUI 
       15.78        19.82         8.05        12.03 

$`BRF1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  BRF1 MUTATED BRF1 WILD-TYPE 
          8.05           0.23 
  BRF1 MUTATED BRF1 WILD-TYPE 
         19.82          90.12 
  BRF1 MUTATED BRF1 WILD-TYPE 
        13.905         15.220 
[1] "8.1 - 19.8 (13.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2"  
D592V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BRF1 MUTATED         0        0        0         1         3         0
  BRF1 WILD-TYPE       1        3       12        18        79         4
                vv
clus             STAGE IV
  BRF1 MUTATED          0
  BRF1 WILD-TYPE        3
D592V3, multiclass
           clus
vv          BRF1 MUTATED BRF1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  BRF1 MUTATED    0  0     4
  BRF1 WILD-TYPE  5 17    98
D592V4, multiclass
       clus
vv      BRF1 MUTATED BRF1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V5, binary
                cls
clus              0  1
  BRF1 MUTATED    0  4
  BRF1 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      0    4
  BRF1 WILD-TYPE   35   85
   clus
vv  BRF1 MUTATED BRF1 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D592V6, binary
                cls
clus              0  1
  BRF1 MUTATED    3  0
  BRF1 WILD-TYPE 54  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      3    0
  BRF1 WILD-TYPE   54    3
   clus
vv  BRF1 MUTATED BRF1 WILD-TYPE
  0            3             54
  1            0              3
[1] 2 2
[1] FALSE
D592V7, binary
                cls
clus              0  1
  BRF1 MUTATED    2  2
  BRF1 WILD-TYPE 49 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      2    2
  BRF1 WILD-TYPE   49   73
        clus
vv       BRF1 MUTATED BRF1 WILD-TYPE
  FEMALE            2             49
  MALE              2             73
[1] 2 2
[1] FALSE
D592V8, binary
                cls
clus              0  1
  BRF1 MUTATED    4  0
  BRF1 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      4    0
  BRF1 WILD-TYPE   84   30
     clus
vv    BRF1 MUTATED BRF1 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRF1 MUTATED                                     4
  BRF1 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRF1 MUTATED                                       0
  BRF1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRF1 MUTATED                                                  0
  BRF1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  BRF1 MUTATED                                     0
  BRF1 WILD-TYPE                                   1
D592V9, multiclass
                                                  clus
vv                                                 BRF1 MUTATED BRF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V10, continuous
[1] "Remove cluster labels:" "BRF1 MUTATED"          
clus
  BRF1 MUTATED BRF1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-YY-A8LH 
"BRF1 WILD-TYPE" 
D592V11, continuous
[1] "Remove cluster labels:" "BRF1 MUTATED"          
clus
  BRF1 MUTATED BRF1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XN-A8T5     TCGA-YY-A8LH 
"BRF1 WILD-TYPE" "BRF1 WILD-TYPE" "BRF1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BRF1 MUTATED    3  1  0  0
  BRF1 WILD-TYPE 77 34  4  2
D592V12, multiclass
    clus
vv   BRF1 MUTATED BRF1 WILD-TYPE
  R0            3             77
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRF1 MUTATED       0                         0     4
  BRF1 WILD-TYPE     6                         5   110
D592V14, multiclass
                           clus
vv                          BRF1 MUTATED BRF1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V15, binary
                cls
clus              0  1
  BRF1 MUTATED    0  4
  BRF1 WILD-TYPE  5 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRF1 MUTATED      0    4
  BRF1 WILD-TYPE    5   87
                        clus
vv                       BRF1 MUTATED BRF1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4             87
[1] 2 2
[1] FALSE

Clustering(593) Variable = TPTE MUTATION ANALYSIS
D593V1, survival
                sevent
clus2             0  1
  TPTE MUTATED    5  4
  TPTE WILD-TYPE 58 58
  TPTE MUTATED TPTE WILD-TYPE 
             9            116 
  TPTE MUTATED TPTE WILD-TYPE 
             4             58 
$`TPTE MUTATED`
TCGA-S4-A8RO TCGA-2J-AAB6 TCGA-3A-A9IX TCGA-FB-AAPP TCGA-HV-A7OP TCGA-HZ-A77P 
       17.26         9.63        34.09        15.95        32.15        10.85 
TCGA-IB-7651 TCGA-IB-A5SP TCGA-RB-A7B8 
       19.82        15.85        15.32 

$`TPTE WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-US-A77E 
        8.02        15.78         1.08        15.12        12.92        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
       16.37         2.17        23.97         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        12.33        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
       10.13         5.26         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TPTE MUTATED TPTE WILD-TYPE 
          9.63           0.23 
  TPTE MUTATED TPTE WILD-TYPE 
         34.09          90.12 
  TPTE MUTATED TPTE WILD-TYPE 
         15.95          15.09 
[1] "9.6 - 34.1 (15.9)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.2"
D593V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TPTE MUTATED         0        1        0         2         6         0
  TPTE WILD-TYPE       1        2       12        17        76         4
                vv
clus             STAGE IV
  TPTE MUTATED          0
  TPTE WILD-TYPE        3
D593V3, multiclass
           clus
vv          TPTE MUTATED TPTE WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            6             76
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  TPTE MUTATED    1  0     8
  TPTE WILD-TYPE  4 17    94
D593V4, multiclass
       clus
vv      TPTE MUTATED TPTE WILD-TYPE
  T1               1              4
  T2               0             17
  T3+T4            8             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V5, binary
                cls
clus              0  1
  TPTE MUTATED    3  6
  TPTE WILD-TYPE 32 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      3    6
  TPTE WILD-TYPE   32   83
   clus
vv  TPTE MUTATED TPTE WILD-TYPE
  0            3             32
  1            6             83
[1] 2 2
[1] FALSE
D593V6, binary
                cls
clus              0  1
  TPTE MUTATED    4  0
  TPTE WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      4    0
  TPTE WILD-TYPE   53    3
   clus
vv  TPTE MUTATED TPTE WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D593V7, binary
                cls
clus              0  1
  TPTE MUTATED    3  6
  TPTE WILD-TYPE 48 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      3    6
  TPTE WILD-TYPE   48   69
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  FEMALE            3             48
  MALE              6             69
[1] 2 2
[1] FALSE
D593V8, binary
                cls
clus              0  1
  TPTE MUTATED    5  4
  TPTE WILD-TYPE 83 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      5    4
  TPTE WILD-TYPE   83   26
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  NO             5             83
  YES            4             26
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TPTE MUTATED                                     6
  TPTE WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TPTE MUTATED                                       3
  TPTE WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TPTE MUTATED                                                  0
  TPTE WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  TPTE MUTATED                                     0
  TPTE WILD-TYPE                                   1
D593V9, multiclass
                                                  clus
vv                                                 TPTE MUTATED TPTE WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V10, continuous
[1] "Remove cluster labels:" "TPTE MUTATED"          
clus
  TPTE MUTATED TPTE WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V     TCGA-HZ-A8P1 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-YY-A8LH 
"TPTE WILD-TYPE" 
D593V11, continuous
[1] "Remove cluster labels:" "TPTE MUTATED"          
clus
  TPTE MUTATED TPTE WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TPTE MUTATED    7  2  0  0
  TPTE WILD-TYPE 73 33  4  2
D593V12, multiclass
    clus
vv   TPTE MUTATED TPTE WILD-TYPE
  R0            7             73
  R1            2             33
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE MUTATED       1                         0     8
  TPTE WILD-TYPE     5                         5   106
D593V14, multiclass
                           clus
vv                          TPTE MUTATED TPTE WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V15, binary
                cls
clus              0  1
  TPTE MUTATED    0  6
  TPTE WILD-TYPE  5 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      0    6
  TPTE WILD-TYPE    5   85
                        clus
vv                       TPTE MUTATED TPTE WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             85
[1] 2 2
[1] FALSE

Clustering(594) Variable = EXOSC10 MUTATION ANALYSIS
D594V1, survival
                   sevent
clus2                0  1
  EXOSC10 MUTATED    1  2
  EXOSC10 WILD-TYPE 62 60
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                3               122 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                2                60 
$`EXOSC10 MUTATED`
TCGA-3A-A9IU TCGA-HZ-A77P TCGA-IB-7651 
       15.06        10.85        19.82 

$`EXOSC10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            10.85              0.23 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            19.82             90.12 
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
            15.06             15.27 
[1] "10.8 - 19.8 (15.1)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.6"
D594V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EXOSC10 MUTATED         0        0        0         0         3         0
  EXOSC10 WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  EXOSC10 MUTATED          0
  EXOSC10 WILD-TYPE        3
D594V3, multiclass
           clus
vv          EXOSC10 MUTATED EXOSC10 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  EXOSC10 MUTATED    0  0     3
  EXOSC10 WILD-TYPE  5 17    99
D594V4, multiclass
       clus
vv      EXOSC10 MUTATED EXOSC10 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V5, binary
                   cls
clus                 0  1
  EXOSC10 MUTATED    0  3
  EXOSC10 WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      0    3
  EXOSC10 WILD-TYPE   35   86
   clus
vv  EXOSC10 MUTATED EXOSC10 WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D594V6, binary
                   cls
clus                 0  1
  EXOSC10 MUTATED    1  0
  EXOSC10 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      1    0
  EXOSC10 WILD-TYPE   56    3
   clus
vv  EXOSC10 MUTATED EXOSC10 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D594V7, binary
                   cls
clus                 0  1
  EXOSC10 MUTATED    1  2
  EXOSC10 WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      1    2
  EXOSC10 WILD-TYPE   50   73
        clus
vv       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  FEMALE               1                50
  MALE                 2                73
[1] 2 2
[1] FALSE
D594V8, binary
                   cls
clus                 0  1
  EXOSC10 MUTATED    3  0
  EXOSC10 WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      3    0
  EXOSC10 WILD-TYPE   85   30
     clus
vv    EXOSC10 MUTATED EXOSC10 WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EXOSC10 MUTATED                                     2
  EXOSC10 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EXOSC10 MUTATED                                       1
  EXOSC10 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EXOSC10 MUTATED                                                  0
  EXOSC10 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  EXOSC10 MUTATED                                     0
  EXOSC10 WILD-TYPE                                   1
D594V9, multiclass
                                                  clus
vv                                                 EXOSC10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 EXOSC10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V10, continuous
[1] "Remove cluster labels:" "EXOSC10 MUTATED"       
clus
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
D594V11, continuous
[1] "Remove cluster labels:" "EXOSC10 MUTATED"       
clus
  EXOSC10 MUTATED EXOSC10 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" "EXOSC10 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  EXOSC10 MUTATED    3  0  0  0
  EXOSC10 WILD-TYPE 77 35  4  2
D594V12, multiclass
    clus
vv   EXOSC10 MUTATED EXOSC10 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EXOSC10 MUTATED       0                         0     3
  EXOSC10 WILD-TYPE     6                         5   111
D594V14, multiclass
                           clus
vv                          EXOSC10 MUTATED EXOSC10 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V15, binary
                   cls
clus                 0  1
  EXOSC10 MUTATED    0  3
  EXOSC10 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EXOSC10 MUTATED      0    3
  EXOSC10 WILD-TYPE    5   88
                        clus
vv                       EXOSC10 MUTATED EXOSC10 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(595) Variable = DUSP13 MUTATION ANALYSIS
D595V1, survival
                  sevent
clus2               0  1
  DUSP13 MUTATED    2  1
  DUSP13 WILD-TYPE 61 61
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               3              122 
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               1               61 
$`DUSP13 MUTATED`
TCGA-HV-A7OL TCGA-IB-7651 TCGA-IB-AAUV 
        8.28        19.82        13.28 

$`DUSP13 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V 
       36.20        20.35        17.79        22.06        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         7.40         8.05         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DUSP13 MUTATED DUSP13 WILD-TYPE 
            8.28             0.23 
  DUSP13 MUTATED DUSP13 WILD-TYPE 
           19.82            90.12 
  DUSP13 MUTATED DUSP13 WILD-TYPE 
           13.28            15.27 
[1] "8.3 - 19.8 (13.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D595V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DUSP13 MUTATED         0        0        0         1         2         0
  DUSP13 WILD-TYPE       1        3       12        18        80         4
                  vv
clus               STAGE IV
  DUSP13 MUTATED          0
  DUSP13 WILD-TYPE        3
D595V3, multiclass
           clus
vv          DUSP13 MUTATED DUSP13 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  DUSP13 MUTATED    0  0     3
  DUSP13 WILD-TYPE  5 17    99
D595V4, multiclass
       clus
vv      DUSP13 MUTATED DUSP13 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V5, binary
                  cls
clus                0  1
  DUSP13 MUTATED    1  2
  DUSP13 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP13 MUTATED      1    2
  DUSP13 WILD-TYPE   34   87
   clus
vv  DUSP13 MUTATED DUSP13 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D595V6, binary
                  cls
clus                0  1
  DUSP13 MUTATED    2  0
  DUSP13 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP13 MUTATED      2    0
  DUSP13 WILD-TYPE   55    3
   clus
vv  DUSP13 MUTATED DUSP13 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D595V7, binary
                  cls
clus                0  1
  DUSP13 MUTATED    1  2
  DUSP13 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP13 MUTATED      1    2
  DUSP13 WILD-TYPE   50   73
        clus
vv       DUSP13 MUTATED DUSP13 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D595V8, binary
                  cls
clus                0  1
  DUSP13 MUTATED    3  0
  DUSP13 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP13 MUTATED      3    0
  DUSP13 WILD-TYPE   85   30
     clus
vv    DUSP13 MUTATED DUSP13 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DUSP13 MUTATED                                     3
  DUSP13 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DUSP13 MUTATED                                       0
  DUSP13 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DUSP13 MUTATED                                                  0
  DUSP13 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  DUSP13 MUTATED                                     0
  DUSP13 WILD-TYPE                                   1
D595V9, multiclass
                                                  clus
vv                                                 DUSP13 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 DUSP13 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V10, continuous
[1] "Remove cluster labels:" "DUSP13 MUTATED"        
clus
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-YY-A8LH 
"DUSP13 WILD-TYPE" 
D595V11, continuous
[1] "Remove cluster labels:" "DUSP13 MUTATED"        
clus
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-LB-A9Q5       TCGA-OE-A75W 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  DUSP13 MUTATED    2  0  1  0
  DUSP13 WILD-TYPE 78 35  3  2
D595V12, multiclass
    clus
vv   DUSP13 MUTATED DUSP13 WILD-TYPE
  R0              2               78
  R1              0               35
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V13, continuous
[1] "Remove cluster labels:" "DUSP13 MUTATED"        
clus
  DUSP13 MUTATED DUSP13 WILD-TYPE 
               2              122 
      TCGA-2J-AABR       TCGA-2J-AABT       TCGA-3A-A9I5       TCGA-3A-A9IJ 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9IL       TCGA-F2-A44G       TCGA-FB-AAQ6       TCGA-FZ-5924 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-S4-A8RO       TCGA-US-A77E       TCGA-XD-AAUL       TCGA-2J-AAB1 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AAB4       TCGA-2J-AAB6       TCGA-2J-AAB8       TCGA-2J-AAB9 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AABA       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABH 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AABK       TCGA-2J-AABO       TCGA-2J-AABP       TCGA-2J-AABU 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2J-AABV       TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-2L-AAQI 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-2L-AAQJ       TCGA-2L-AAQL       TCGA-2L-AAQM       TCGA-3A-A9I7 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IC       TCGA-3A-A9IH 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9IR       TCGA-3A-A9IS       TCGA-3A-A9IU       TCGA-3A-A9IV 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-3A-A9IZ       TCGA-3A-A9J0       TCGA-3E-AAAY 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-3E-AAAZ       TCGA-F2-7273       TCGA-F2-A7TX       TCGA-F2-A8YN 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPP       TCGA-FB-AAPQ 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-FB-AAPU       TCGA-FB-AAPZ       TCGA-FB-AAQ0 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FB-AAQ1       TCGA-FB-AAQ2       TCGA-FB-AAQ3       TCGA-FZ-5919 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FZ-5920       TCGA-FZ-5921       TCGA-FZ-5922       TCGA-FZ-5923 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-FZ-5926       TCGA-H8-A6C1       TCGA-HV-A7OP       TCGA-HV-AA8V 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-HV-AA8X       TCGA-HZ-7918       TCGA-HZ-7925       TCGA-HZ-8637 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-HZ-A49I       TCGA-HZ-A77O       TCGA-HZ-A77P       TCGA-HZ-A8P1 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-HZ-A9TJ       TCGA-IB-7652       TCGA-IB-7885       TCGA-IB-8126 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-A5SO       TCGA-IB-A5SP       TCGA-IB-A5SQ       TCGA-IB-A5ST 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7LX       TCGA-IB-A7M4 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-AAUM       TCGA-IB-AAUN       TCGA-IB-AAUO       TCGA-IB-AAUP 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUR       TCGA-IB-AAUS       TCGA-IB-AAUU 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-IB-AAUW       TCGA-LB-A8F3       TCGA-LB-A9Q5       TCGA-OE-A75W 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-Q3-A5QY       TCGA-Q3-AA2A       TCGA-RB-A7B8       TCGA-RB-AA9M 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-RL-AAAS       TCGA-US-A776       TCGA-US-A779       TCGA-US-A77G 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-US-A77J       TCGA-XD-AAUG       TCGA-XD-AAUH       TCGA-XD-AAUI 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-XN-A8T3       TCGA-XN-A8T5       TCGA-YB-A89D       TCGA-YH-A8SY 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
      TCGA-YY-A8LH       TCGA-Z5-AAPL 
"DUSP13 WILD-TYPE" "DUSP13 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DUSP13 MUTATED       1                         0     2
  DUSP13 WILD-TYPE     5                         5   112
D595V14, multiclass
                           clus
vv                          DUSP13 MUTATED DUSP13 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V15, binary
                  cls
clus                0  1
  DUSP13 MUTATED    0  2
  DUSP13 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP13 MUTATED      0    2
  DUSP13 WILD-TYPE    5   89
                        clus
vv                       DUSP13 MUTATED DUSP13 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(596) Variable = C1ORF110 MUTATION ANALYSIS
D596V1, survival
                    sevent
clus2                 0  1
  C1ORF110 MUTATED    2  2
  C1ORF110 WILD-TYPE 61 60
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 4                121 
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 2                 60 
$`C1ORF110 MUTATED`
TCGA-FB-AAQ6 TCGA-HV-A7OL TCGA-IB-7651 TCGA-XN-A8T3 
        8.02         8.28        19.82        31.27 

$`C1ORF110 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
              8.02               0.23 
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
             31.27              90.12 
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
             14.05              15.22 
[1] "8.0 - 31.3 (14.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D596V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C1ORF110 MUTATED         0        1        1         1         1         0
  C1ORF110 WILD-TYPE       1        2       11        18        81         4
                    vv
clus                 STAGE IV
  C1ORF110 MUTATED          0
  C1ORF110 WILD-TYPE        3
D596V3, multiclass
           clus
vv          C1ORF110 MUTATED C1ORF110 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 1                  2
  STAGE IB                 1                 11
  STAGE IIA                1                 18
  STAGE IIB                1                 81
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2 T3+T4
  C1ORF110 MUTATED     1   1     2
  C1ORF110 WILD-TYPE   4  16   100
D596V4, multiclass
       clus
vv      C1ORF110 MUTATED C1ORF110 WILD-TYPE
  T1                   1                  4
  T2                   1                 16
  T3+T4                2                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V5, binary
                    cls
clus                  0  1
  C1ORF110 MUTATED    3  1
  C1ORF110 WILD-TYPE 32 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF110 MUTATED      3    1
  C1ORF110 WILD-TYPE   32   88
   clus
vv  C1ORF110 MUTATED C1ORF110 WILD-TYPE
  0                3                 32
  1                1                 88
[1] 2 2
[1] FALSE
D596V6, binary
                    cls
clus                  0  1
  C1ORF110 MUTATED    2  0
  C1ORF110 WILD-TYPE 55  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF110 MUTATED      2    0
  C1ORF110 WILD-TYPE   55    3
   clus
vv  C1ORF110 MUTATED C1ORF110 WILD-TYPE
  0                2                 55
  1                0                  3
[1] 2 2
[1] FALSE
D596V7, binary
                    cls
clus                  0  1
  C1ORF110 MUTATED    1  3
  C1ORF110 WILD-TYPE 50 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF110 MUTATED      1    3
  C1ORF110 WILD-TYPE   50   72
        clus
vv       C1ORF110 MUTATED C1ORF110 WILD-TYPE
  FEMALE                1                 50
  MALE                  3                 72
[1] 2 2
[1] FALSE
D596V8, binary
                    cls
clus                  0  1
  C1ORF110 MUTATED    3  1
  C1ORF110 WILD-TYPE 85 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF110 MUTATED      3    1
  C1ORF110 WILD-TYPE   85   29
     clus
vv    C1ORF110 MUTATED C1ORF110 WILD-TYPE
  NO                 3                 85
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C1ORF110 MUTATED                                     4
  C1ORF110 WILD-TYPE                                 101
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C1ORF110 MUTATED                                       0
  C1ORF110 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C1ORF110 MUTATED                                                  0
  C1ORF110 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C1ORF110 MUTATED                                     0
  C1ORF110 WILD-TYPE                                   1
D596V9, multiclass
                                                  clus
vv                                                 C1ORF110 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C1ORF110 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V10, continuous
[1] "Remove cluster labels:" "C1ORF110 MUTATED"      
clus
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
D596V11, continuous
[1] "Remove cluster labels:" "C1ORF110 MUTATED"      
clus
  C1ORF110 MUTATED C1ORF110 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C1ORF110 WILD-TYPE" "C1ORF110 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C1ORF110 MUTATED    2  1  1  0
  C1ORF110 WILD-TYPE 78 34  3  2
D596V12, multiclass
    clus
vv   C1ORF110 MUTATED C1ORF110 WILD-TYPE
  R0                2                 78
  R1                1                 34
  R2                1                  3
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1ORF110 MUTATED       1                         0     3
  C1ORF110 WILD-TYPE     5                         5   111
D596V14, multiclass
                           clus
vv                          C1ORF110 MUTATED C1ORF110 WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V15, binary
                    cls
clus                  0  1
  C1ORF110 MUTATED    1  2
  C1ORF110 WILD-TYPE  4 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF110 MUTATED      1    2
  C1ORF110 WILD-TYPE    4   89
                        clus
vv                       C1ORF110 MUTATED C1ORF110 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(597) Variable = PCOLCE2 MUTATION ANALYSIS
D597V1, survival
                   sevent
clus2                0  1
  PCOLCE2 MUTATED    2  1
  PCOLCE2 WILD-TYPE 61 61
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                3               122 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                1                61 
$`PCOLCE2 MUTATED`
TCGA-2J-AABE TCGA-FB-AAPZ TCGA-IB-7651 
       22.22        23.54        19.82 

$`PCOLCE2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
            19.82              0.23 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
            23.54             90.12 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
           22.220            15.155 
[1] "19.8 - 23.5 (22.2)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.3"
D597V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PCOLCE2 MUTATED         0        0        0         1         2         0
  PCOLCE2 WILD-TYPE       1        3       12        18        80         4
                   vv
clus                STAGE IV
  PCOLCE2 MUTATED          0
  PCOLCE2 WILD-TYPE        3
D597V3, multiclass
           clus
vv          PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               2                80
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  PCOLCE2 MUTATED     0   1     2
  PCOLCE2 WILD-TYPE   5  16   100
D597V4, multiclass
       clus
vv      PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V5, binary
                   cls
clus                 0  1
  PCOLCE2 MUTATED    1  2
  PCOLCE2 WILD-TYPE 34 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      1    2
  PCOLCE2 WILD-TYPE   34   87
   clus
vv  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  0               1                34
  1               2                87
[1] 2 2
[1] FALSE
D597V6, binary
                   cls
clus                 0  1
  PCOLCE2 MUTATED    2  0
  PCOLCE2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      2    0
  PCOLCE2 WILD-TYPE   55    3
   clus
vv  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D597V7, binary
                   cls
clus                 0  1
  PCOLCE2 MUTATED    1  2
  PCOLCE2 WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      1    2
  PCOLCE2 WILD-TYPE   50   73
        clus
vv       PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  FEMALE               1                50
  MALE                 2                73
[1] 2 2
[1] FALSE
D597V8, binary
                   cls
clus                 0  1
  PCOLCE2 MUTATED    2  1
  PCOLCE2 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      2    1
  PCOLCE2 WILD-TYPE   86   29
     clus
vv    PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PCOLCE2 MUTATED                                     3
  PCOLCE2 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PCOLCE2 MUTATED                                       0
  PCOLCE2 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PCOLCE2 MUTATED                                                  0
  PCOLCE2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PCOLCE2 MUTATED                                     0
  PCOLCE2 WILD-TYPE                                   1
D597V9, multiclass
                                                  clus
vv                                                 PCOLCE2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PCOLCE2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V10, continuous
[1] "Remove cluster labels:" "PCOLCE2 MUTATED"       
clus
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-YY-A8LH 
"PCOLCE2 WILD-TYPE" 
D597V11, continuous
[1] "Remove cluster labels:" "PCOLCE2 MUTATED"       
clus
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABF 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" "PCOLCE2 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  PCOLCE2 MUTATED    3  0  0  0
  PCOLCE2 WILD-TYPE 77 35  4  2
D597V12, multiclass
    clus
vv   PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCOLCE2 MUTATED       0                         0     3
  PCOLCE2 WILD-TYPE     6                         5   111
D597V14, multiclass
                           clus
vv                          PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V15, binary
                   cls
clus                 0  1
  PCOLCE2 MUTATED    0  2
  PCOLCE2 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      0    2
  PCOLCE2 WILD-TYPE    5   89
                        clus
vv                       PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(598) Variable = FLVCR1 MUTATION ANALYSIS
D598V1, survival
                  sevent
clus2               0  1
  FLVCR1 MUTATED    1  2
  FLVCR1 WILD-TYPE 62 60
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              122 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               60 
$`FLVCR1 MUTATED`
TCGA-HZ-A77Q TCGA-3A-A9IU TCGA-IB-7651 
        1.08        15.06        19.82 

$`FLVCR1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        32.81        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
            1.08             0.23 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           19.82            90.12 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           15.06            15.27 
[1] "1.1 - 19.8 (15.1)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D598V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FLVCR1 MUTATED         0        0        0         0         3         0
  FLVCR1 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  FLVCR1 MUTATED          0
  FLVCR1 WILD-TYPE        3
D598V3, multiclass
           clus
vv          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  FLVCR1 MUTATED    0  0     3
  FLVCR1 WILD-TYPE  5 17    99
D598V4, multiclass
       clus
vv      FLVCR1 MUTATED FLVCR1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V5, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    0  3
  FLVCR1 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE   35   86
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D598V6, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    1  0
  FLVCR1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      1    0
  FLVCR1 WILD-TYPE   56    3
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D598V7, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    2  1
  FLVCR1 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      2    1
  FLVCR1 WILD-TYPE   49   74
        clus
vv       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D598V8, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    2  0
  FLVCR1 WILD-TYPE 86 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      2    0
  FLVCR1 WILD-TYPE   86   30
     clus
vv    FLVCR1 MUTATED FLVCR1 WILD-TYPE
  NO               2               86
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FLVCR1 MUTATED                                     2
  FLVCR1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FLVCR1 MUTATED                                       1
  FLVCR1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FLVCR1 MUTATED                                                  0
  FLVCR1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  FLVCR1 MUTATED                                     0
  FLVCR1 WILD-TYPE                                   1
D598V9, multiclass
                                                  clus
vv                                                 FLVCR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 FLVCR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V10, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA       TCGA-2J-AABE 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV       TCGA-2L-AAQA 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" 
D598V11, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A8P0       TCGA-IB-A5SS       TCGA-LB-A7SX 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR       TCGA-3A-A9IX 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  FLVCR1 MUTATED    3  0  0  0
  FLVCR1 WILD-TYPE 77 35  4  2
D598V12, multiclass
    clus
vv   FLVCR1 MUTATED FLVCR1 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLVCR1 MUTATED       0                         0     3
  FLVCR1 WILD-TYPE     6                         5   111
D598V14, multiclass
                           clus
vv                          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V15, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    0  3
  FLVCR1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE    5   88
                        clus
vv                       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(599) Variable = EXOSC5 MUTATION ANALYSIS
D599V1, survival
                  sevent
clus2               0  1
  EXOSC5 MUTATED    0  4
  EXOSC5 WILD-TYPE 63 58
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               4              121 
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               4               58 
$`EXOSC5 MUTATED`
TCGA-2L-AAQL TCGA-IB-7651 TCGA-OE-A75W TCGA-US-A779 
        9.60        19.82         8.78        16.80 

$`EXOSC5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
            8.78             0.23 
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
           19.82            90.12 
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
           13.20            15.22 
[1] "8.8 - 19.8 (13.2)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.7"
D599V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EXOSC5 MUTATED         0        0        0         1         3         0
  EXOSC5 WILD-TYPE       1        3       12        18        79         4
                  vv
clus               STAGE IV
  EXOSC5 MUTATED          0
  EXOSC5 WILD-TYPE        3
D599V3, multiclass
           clus
vv          EXOSC5 MUTATED EXOSC5 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  EXOSC5 MUTATED    0  0     4
  EXOSC5 WILD-TYPE  5 17    98
D599V4, multiclass
       clus
vv      EXOSC5 MUTATED EXOSC5 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V5, binary
                  cls
clus                0  1
  EXOSC5 MUTATED    1  3
  EXOSC5 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC5 MUTATED      1    3
  EXOSC5 WILD-TYPE   34   86
   clus
vv  EXOSC5 MUTATED EXOSC5 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D599V6, binary
                  cls
clus                0  1
  EXOSC5 MUTATED    2  0
  EXOSC5 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC5 MUTATED      2    0
  EXOSC5 WILD-TYPE   55    3
   clus
vv  EXOSC5 MUTATED EXOSC5 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D599V7, binary
                  cls
clus                0  1
  EXOSC5 MUTATED    2  2
  EXOSC5 WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC5 MUTATED      2    2
  EXOSC5 WILD-TYPE   49   73
        clus
vv       EXOSC5 MUTATED EXOSC5 WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D599V8, binary
                  cls
clus                0  1
  EXOSC5 MUTATED    2  1
  EXOSC5 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC5 MUTATED      2    1
  EXOSC5 WILD-TYPE   86   29
     clus
vv    EXOSC5 MUTATED EXOSC5 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EXOSC5 MUTATED                                     4
  EXOSC5 WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EXOSC5 MUTATED                                       0
  EXOSC5 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EXOSC5 MUTATED                                                  0
  EXOSC5 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  EXOSC5 MUTATED                                     0
  EXOSC5 WILD-TYPE                                   1
D599V9, multiclass
                                                  clus
vv                                                 EXOSC5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 EXOSC5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V10, continuous
[1] "Remove cluster labels:" "EXOSC5 MUTATED"        
clus
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-XN-A8T5 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-YY-A8LH 
"EXOSC5 WILD-TYPE" 
D599V11, continuous
[1] "Remove cluster labels:" "EXOSC5 MUTATED"        
clus
  EXOSC5 MUTATED EXOSC5 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" "EXOSC5 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  EXOSC5 MUTATED    3  0  0  1
  EXOSC5 WILD-TYPE 77 35  4  1
D599V12, multiclass
    clus
vv   EXOSC5 MUTATED EXOSC5 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EXOSC5 MUTATED       0                         0     4
  EXOSC5 WILD-TYPE     6                         5   110
D599V14, multiclass
                           clus
vv                          EXOSC5 MUTATED EXOSC5 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V15, binary
                  cls
clus                0  1
  EXOSC5 MUTATED    0  3
  EXOSC5 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EXOSC5 MUTATED      0    3
  EXOSC5 WILD-TYPE    5   88
                        clus
vv                       EXOSC5 MUTATED EXOSC5 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(600) Variable = PDXDC1 MUTATION ANALYSIS
D600V1, survival
                  sevent
clus2               0  1
  PDXDC1 MUTATED    1  2
  PDXDC1 WILD-TYPE 62 60
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              122 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               2               60 
$`PDXDC1 MUTATED`
TCGA-FB-AAPZ TCGA-FB-AAQ3 TCGA-IB-7651 
       23.54         1.02        19.82 

$`PDXDC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15         7.50        12.53        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        5.03        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
            1.02             0.23 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
           23.54            90.12 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
          19.820           15.205 
[1] "1.0 - 23.5 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.4"
D600V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PDXDC1 MUTATED         0        0        0         0         3         0
  PDXDC1 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  PDXDC1 MUTATED          0
  PDXDC1 WILD-TYPE        3
D600V3, multiclass
           clus
vv          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  PDXDC1 MUTATED     0   1     2
  PDXDC1 WILD-TYPE   5  16   100
D600V4, multiclass
       clus
vv      PDXDC1 MUTATED PDXDC1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V5, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    0  3
  PDXDC1 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE   35   86
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D600V6, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    1  0
  PDXDC1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      1    0
  PDXDC1 WILD-TYPE   56    3
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D600V7, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    2  1
  PDXDC1 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      2    1
  PDXDC1 WILD-TYPE   49   74
        clus
vv       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D600V8, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    3  0
  PDXDC1 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      3    0
  PDXDC1 WILD-TYPE   85   30
     clus
vv    PDXDC1 MUTATED PDXDC1 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDXDC1 MUTATED                                     3
  PDXDC1 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDXDC1 MUTATED                                       0
  PDXDC1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDXDC1 MUTATED                                                  0
  PDXDC1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PDXDC1 MUTATED                                     0
  PDXDC1 WILD-TYPE                                   1
D600V9, multiclass
                                                  clus
vv                                                 PDXDC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PDXDC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V10, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
D600V11, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PDXDC1 MUTATED    3  0  0  0
  PDXDC1 WILD-TYPE 77 35  4  2
D600V12, multiclass
    clus
vv   PDXDC1 MUTATED PDXDC1 WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDXDC1 MUTATED       0                         0     3
  PDXDC1 WILD-TYPE     6                         5   111
D600V14, multiclass
                           clus
vv                          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V15, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    0  3
  PDXDC1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE    5   88
                        clus
vv                       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(601) Variable = C11ORF63 MUTATION ANALYSIS
D601V1, survival
                    sevent
clus2                 0  1
  C11ORF63 MUTATED    1  2
  C11ORF63 WILD-TYPE 62 60
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 3                122 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 2                 60 
$`C11ORF63 MUTATED`
TCGA-LB-A7SX TCGA-2L-AAQI TCGA-IB-A6UF 
       12.92         3.39        21.90 

$`C11ORF63 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
              3.39               0.23 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             21.90              90.12 
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
             12.92              15.27 
[1] "3.4 - 21.9 (12.9)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.7"
D601V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C11ORF63 MUTATED         0        0        0         0         3         0
  C11ORF63 WILD-TYPE       1        3       12        19        79         4
                    vv
clus                 STAGE IV
  C11ORF63 MUTATED          0
  C11ORF63 WILD-TYPE        3
D601V3, multiclass
           clus
vv          C11ORF63 MUTATED C11ORF63 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                0                 19
  STAGE IIB                3                 79
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C11ORF63 MUTATED    0  0     3
  C11ORF63 WILD-TYPE  5 17    99
D601V4, multiclass
       clus
vv      C11ORF63 MUTATED C11ORF63 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                3                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V5, binary
                    cls
clus                  0  1
  C11ORF63 MUTATED    0  3
  C11ORF63 WILD-TYPE 35 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0    3
  C11ORF63 WILD-TYPE   35   86
   clus
vv  C11ORF63 MUTATED C11ORF63 WILD-TYPE
  0                0                 35
  1                3                 86
[1] 2 2
[1] FALSE
D601V6, binary
                    cls
clus                  0  1
  C11ORF63 MUTATED    1  0
  C11ORF63 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      1    0
  C11ORF63 WILD-TYPE   56    3
   clus
vv  C11ORF63 MUTATED C11ORF63 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D601V7, binary
                    cls
clus                  0  1
  C11ORF63 MUTATED    1  2
  C11ORF63 WILD-TYPE 50 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      1    2
  C11ORF63 WILD-TYPE   50   73
        clus
vv       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  FEMALE                1                 50
  MALE                  2                 73
[1] 2 2
[1] FALSE
D601V8, binary
                    cls
clus                  0  1
  C11ORF63 MUTATED    3  0
  C11ORF63 WILD-TYPE 85 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      3    0
  C11ORF63 WILD-TYPE   85   30
     clus
vv    C11ORF63 MUTATED C11ORF63 WILD-TYPE
  NO                 3                 85
  YES                0                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C11ORF63 MUTATED                                     3
  C11ORF63 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C11ORF63 MUTATED                                       0
  C11ORF63 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C11ORF63 MUTATED                                                  0
  C11ORF63 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C11ORF63 MUTATED                                     0
  C11ORF63 WILD-TYPE                                   1
D601V9, multiclass
                                                  clus
vv                                                 C11ORF63 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C11ORF63 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V10, continuous
[1] "Remove cluster labels:" "C11ORF63 MUTATED"      
clus
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-2J-AABA         TCGA-2J-AABE         TCGA-2J-AABF 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-2J-AABV         TCGA-2L-AAQA 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-2L-AAQE         TCGA-3A-A9I9         TCGA-3A-A9IB 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-YY-A8LH 
"C11ORF63 WILD-TYPE" 
D601V11, continuous
[1] "Remove cluster labels:" "C11ORF63 MUTATED"      
clus
  C11ORF63 MUTATED C11ORF63 WILD-TYPE 
                 2                 31 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-XD-AAUL         TCGA-2J-AAB1 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-2J-AABE         TCGA-2J-AABF         TCGA-2J-AABO 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IR         TCGA-3A-A9IX 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HZ-A8P1 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-8126 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUV         TCGA-LB-A9Q5 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-OE-A75W         TCGA-XD-AAUI         TCGA-XN-A8T5 
"C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" "C11ORF63 WILD-TYPE" 
        TCGA-YY-A8LH 
"C11ORF63 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C11ORF63 MUTATED    0  3  0  0
  C11ORF63 WILD-TYPE 80 32  4  2
D601V12, multiclass
    clus
vv   C11ORF63 MUTATED C11ORF63 WILD-TYPE
  R0                0                 80
  R1                3                 32
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C11ORF63 MUTATED       0                         1     2
  C11ORF63 WILD-TYPE     6                         4   112
D601V14, multiclass
                           clus
vv                          C11ORF63 MUTATED C11ORF63 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                  4
  WHITE                                    2                112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V15, binary
                    cls
clus                  0  1
  C11ORF63 MUTATED    0  2
  C11ORF63 WILD-TYPE  5 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF63 MUTATED      0    2
  C11ORF63 WILD-TYPE    5   89
                        clus
vv                       C11ORF63 MUTATED C11ORF63 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                2                 89
[1] 2 2
[1] FALSE

Clustering(602) Variable = FAM71F1 MUTATION ANALYSIS
D602V1, survival
                   sevent
clus2                0  1
  FAM71F1 MUTATED    1  2
  FAM71F1 WILD-TYPE 62 60
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
                3               122 
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
                2                60 
$`FAM71F1 MUTATED`
TCGA-2L-AAQJ TCGA-HZ-8637 TCGA-HZ-A77P 
       12.95        17.00        10.85 

$`FAM71F1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       17.49        31.86        20.19        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
            10.85              0.23 
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
            17.00             90.12 
  FAM71F1 MUTATED FAM71F1 WILD-TYPE 
            12.95             15.27 
[1] "10.8 - 17.0 (12.9)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "1.8"
D602V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FAM71F1 MUTATED         0        0        0         0         2         1
  FAM71F1 WILD-TYPE       1        3       12        19        80         3
                   vv
clus                STAGE IV
  FAM71F1 MUTATED          0
  FAM71F1 WILD-TYPE        3
D602V3, multiclass
           clus
vv          FAM71F1 MUTATED FAM71F1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               2                80
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  FAM71F1 MUTATED    0  0     3
  FAM71F1 WILD-TYPE  5 17    99
D602V4, multiclass
       clus
vv      FAM71F1 MUTATED FAM71F1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V5, binary
                   cls
clus                 0  1
  FAM71F1 MUTATED    1  2
  FAM71F1 WILD-TYPE 34 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM71F1 MUTATED      1    2
  FAM71F1 WILD-TYPE   34   87
   clus
vv  FAM71F1 MUTATED FAM71F1 WILD-TYPE
  0               1                34
  1               2                87
[1] 2 2
[1] FALSE
D602V6, binary
                   cls
clus                 0  1
  FAM71F1 MUTATED    0  0
  FAM71F1 WILD-TYPE 57  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM71F1 MUTATED      0    0
  FAM71F1 WILD-TYPE   57    3
D602V7, binary
                   cls
clus                 0  1
  FAM71F1 MUTATED    2  1
  FAM71F1 WILD-TYPE 49 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM71F1 MUTATED      2    1
  FAM71F1 WILD-TYPE   49   74
        clus
vv       FAM71F1 MUTATED FAM71F1 WILD-TYPE
  FEMALE               2                49
  MALE                 1                74
[1] 2 2
[1] FALSE
D602V8, binary
                   cls
clus                 0  1
  FAM71F1 MUTATED    2  1
  FAM71F1 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM71F1 MUTATED      2    1
  FAM71F1 WILD-TYPE   86   29
     clus
vv    FAM71F1 MUTATED FAM71F1 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM71F1 MUTATED                                     2
  FAM71F1 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM71F1 MUTATED                                       1
  FAM71F1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM71F1 MUTATED                                                  0
  FAM71F1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  FAM71F1 MUTATED                                     0
  FAM71F1 WILD-TYPE                                   1
D602V9, multiclass
                                                  clus
vv                                                 FAM71F1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 FAM71F1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V10, continuous
D602V11, continuous
                   vv
clus                R0 R1 R2 RX
  FAM71F1 MUTATED    2  1  0  0
  FAM71F1 WILD-TYPE 78 34  4  2
D602V12, multiclass
    clus
vv   FAM71F1 MUTATED FAM71F1 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM71F1 MUTATED       0                         0     3
  FAM71F1 WILD-TYPE     6                         5   111
D602V14, multiclass
                           clus
vv                          FAM71F1 MUTATED FAM71F1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V15, binary
                   cls
clus                 0  1
  FAM71F1 MUTATED    1  1
  FAM71F1 WILD-TYPE  4 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM71F1 MUTATED      1    1
  FAM71F1 WILD-TYPE    4   90
                        clus
vv                       FAM71F1 MUTATED FAM71F1 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               1                90
[1] 2 2
[1] FALSE

Clustering(603) Variable = UBE2Q1 MUTATION ANALYSIS
D603V1, survival
                  sevent
clus2               0  1
  UBE2Q1 MUTATED    3  0
  UBE2Q1 WILD-TYPE 60 62
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               3              122 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
               0               62 
$`UBE2Q1 MUTATED`
TCGA-2J-AAB4 TCGA-HZ-7918 TCGA-Q3-AA2A 
       23.97        31.86         3.12 

$`UBE2Q1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37         2.17         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
            3.12             0.23 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
           31.86            90.12 
  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE 
          23.970           15.205 
[1] "3.1 - 31.9 (24.0)" "0.2 - 90.1 (15.2)"
[1] "hr="     "2.6e+07"
D603V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UBE2Q1 MUTATED         0        0        1         0         2         0
  UBE2Q1 WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  UBE2Q1 MUTATED          0
  UBE2Q1 WILD-TYPE        3
D603V3, multiclass
           clus
vv          UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  UBE2Q1 MUTATED     0   1     2
  UBE2Q1 WILD-TYPE   5  16   100
D603V4, multiclass
       clus
vv      UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V5, binary
                  cls
clus                0  1
  UBE2Q1 MUTATED    0  3
  UBE2Q1 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      0    3
  UBE2Q1 WILD-TYPE   35   86
   clus
vv  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D603V6, binary
                  cls
clus                0  1
  UBE2Q1 MUTATED    2  0
  UBE2Q1 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      2    0
  UBE2Q1 WILD-TYPE   55    3
   clus
vv  UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D603V7, binary
                  cls
clus                0  1
  UBE2Q1 MUTATED    1  2
  UBE2Q1 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      1    2
  UBE2Q1 WILD-TYPE   50   73
        clus
vv       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D603V8, binary
                  cls
clus                0  1
  UBE2Q1 MUTATED    2  1
  UBE2Q1 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      2    1
  UBE2Q1 WILD-TYPE   86   29
     clus
vv    UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBE2Q1 MUTATED                                     2
  UBE2Q1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBE2Q1 MUTATED                                       1
  UBE2Q1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBE2Q1 MUTATED                                                  0
  UBE2Q1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  UBE2Q1 MUTATED                                     0
  UBE2Q1 WILD-TYPE                                   1
D603V9, multiclass
                                                  clus
vv                                                 UBE2Q1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 UBE2Q1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V10, continuous
D603V11, continuous
                  vv
clus               R0 R1 R2 RX
  UBE2Q1 MUTATED    2  0  0  1
  UBE2Q1 WILD-TYPE 78 35  4  1
D603V12, multiclass
    clus
vv   UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  R0              2               78
  R1              0               35
  R2              0                4
  RX              1                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBE2Q1 MUTATED       0                         0     3
  UBE2Q1 WILD-TYPE     6                         5   111
D603V14, multiclass
                           clus
vv                          UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V15, binary
                  cls
clus                0  1
  UBE2Q1 MUTATED    0  2
  UBE2Q1 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBE2Q1 MUTATED      0    2
  UBE2Q1 WILD-TYPE    5   89
                        clus
vv                       UBE2Q1 MUTATED UBE2Q1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(604) Variable = GALNT10 MUTATION ANALYSIS
D604V1, survival
                   sevent
clus2                0  1
  GALNT10 MUTATED    3  2
  GALNT10 WILD-TYPE 60 60
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                5               120 
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                2                60 
$`GALNT10 MUTATED`
TCGA-IB-7651 TCGA-IB-7652 TCGA-LB-A9Q5 TCGA-Q3-AA2A TCGA-US-A776 
       19.82        36.69        10.29         3.12        39.98 

$`GALNT10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7885 TCGA-IB-8126 
        5.26        10.85         0.23        19.82        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
       12.46         8.78        13.68        15.32         9.40         0.30 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  GALNT10 MUTATED GALNT10 WILD-TYPE 
             3.12              0.23 
  GALNT10 MUTATED GALNT10 WILD-TYPE 
            39.98             90.12 
  GALNT10 MUTATED GALNT10 WILD-TYPE 
           19.820            15.205 
[1] "3.1 - 40.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D604V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GALNT10 MUTATED         0        0        1         1         3         0
  GALNT10 WILD-TYPE       1        3       11        18        79         4
                   vv
clus                STAGE IV
  GALNT10 MUTATED          0
  GALNT10 WILD-TYPE        3
D604V3, multiclass
           clus
vv          GALNT10 MUTATED GALNT10 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  GALNT10 MUTATED    0  0     5
  GALNT10 WILD-TYPE  5 17    97
D604V4, multiclass
       clus
vv      GALNT10 MUTATED GALNT10 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               5                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V5, binary
                   cls
clus                 0  1
  GALNT10 MUTATED    1  4
  GALNT10 WILD-TYPE 34 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT10 MUTATED      1    4
  GALNT10 WILD-TYPE   34   85
   clus
vv  GALNT10 MUTATED GALNT10 WILD-TYPE
  0               1                34
  1               4                85
[1] 2 2
[1] FALSE
D604V6, binary
                   cls
clus                 0  1
  GALNT10 MUTATED    2  0
  GALNT10 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT10 MUTATED      2    0
  GALNT10 WILD-TYPE   55    3
   clus
vv  GALNT10 MUTATED GALNT10 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D604V7, binary
                   cls
clus                 0  1
  GALNT10 MUTATED    4  1
  GALNT10 WILD-TYPE 47 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT10 MUTATED      4    1
  GALNT10 WILD-TYPE   47   74
        clus
vv       GALNT10 MUTATED GALNT10 WILD-TYPE
  FEMALE               4                47
  MALE                 1                74
[1] 2 2
[1] FALSE
D604V8, binary
                   cls
clus                 0  1
  GALNT10 MUTATED    4  1
  GALNT10 WILD-TYPE 84 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT10 MUTATED      4    1
  GALNT10 WILD-TYPE   84   29
     clus
vv    GALNT10 MUTATED GALNT10 WILD-TYPE
  NO                4                84
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GALNT10 MUTATED                                     4
  GALNT10 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GALNT10 MUTATED                                       0
  GALNT10 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GALNT10 MUTATED                                                  1
  GALNT10 WILD-TYPE                                                0
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  GALNT10 MUTATED                                     0
  GALNT10 WILD-TYPE                                   1
D604V9, multiclass
                                                  clus
vv                                                 GALNT10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 GALNT10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V10, continuous
[1] "Remove cluster labels:" "GALNT10 MUTATED"       
clus
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-OE-A75W        TCGA-XN-A8T5 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-YY-A8LH 
"GALNT10 WILD-TYPE" 
D604V11, continuous
[1] "Remove cluster labels:" "GALNT10 MUTATED"       
clus
  GALNT10 MUTATED GALNT10 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-OE-A75W 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" "GALNT10 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  GALNT10 MUTATED    3  1  0  1
  GALNT10 WILD-TYPE 77 34  4  1
D604V12, multiclass
    clus
vv   GALNT10 MUTATED GALNT10 WILD-TYPE
  R0               3                77
  R1               1                34
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GALNT10 MUTATED       1                         0     4
  GALNT10 WILD-TYPE     5                         5   110
D604V14, multiclass
                           clus
vv                          GALNT10 MUTATED GALNT10 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V15, binary
                   cls
clus                 0  1
  GALNT10 MUTATED    0  5
  GALNT10 WILD-TYPE  5 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GALNT10 MUTATED      0    5
  GALNT10 WILD-TYPE    5   86
                        clus
vv                       GALNT10 MUTATED GALNT10 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5                86
[1] 2 2
[1] FALSE

Clustering(605) Variable = PPL MUTATION ANALYSIS
D605V1, survival
               sevent
clus2            0  1
  PPL MUTATED    1  3
  PPL WILD-TYPE 62 59
  PPL MUTATED PPL WILD-TYPE 
            4           121 
  PPL MUTATED PPL WILD-TYPE 
            3            59 
$`PPL MUTATED`
TCGA-2L-AAQA TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-AAUR 
        4.70        19.82        12.00        11.11 

$`PPL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PPL MUTATED PPL WILD-TYPE 
         4.70          0.23 
  PPL MUTATED PPL WILD-TYPE 
        19.82         90.12 
  PPL MUTATED PPL WILD-TYPE 
       11.555        15.320 
[1] "4.7 - 19.8 (11.6)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2.5"
D605V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PPL MUTATED         0        0        0         0         4         0
  PPL WILD-TYPE       1        3       12        19        78         4
               vv
clus            STAGE IV
  PPL MUTATED          0
  PPL WILD-TYPE        3
D605V3, multiclass
           clus
vv          PPL MUTATED PPL WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           0            19
  STAGE IIB           4            78
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  PPL MUTATED    0  0     4
  PPL WILD-TYPE  5 17    98
D605V4, multiclass
       clus
vv      PPL MUTATED PPL WILD-TYPE
  T1              0             5
  T2              0            17
  T3+T4           4            98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V5, binary
               cls
clus             0  1
  PPL MUTATED    0  4
  PPL WILD-TYPE 35 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      0    4
  PPL WILD-TYPE   35   85
   clus
vv  PPL MUTATED PPL WILD-TYPE
  0           0            35
  1           4            85
[1] 2 2
[1] FALSE
D605V6, binary
               cls
clus             0  1
  PPL MUTATED    3  0
  PPL WILD-TYPE 54  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      3    0
  PPL WILD-TYPE   54    3
   clus
vv  PPL MUTATED PPL WILD-TYPE
  0           3            54
  1           0             3
[1] 2 2
[1] FALSE
D605V7, binary
               cls
clus             0  1
  PPL MUTATED    1  3
  PPL WILD-TYPE 50 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      1    3
  PPL WILD-TYPE   50   72
        clus
vv       PPL MUTATED PPL WILD-TYPE
  FEMALE           1            50
  MALE             3            72
[1] 2 2
[1] FALSE
D605V8, binary
               cls
clus             0  1
  PPL MUTATED    4  0
  PPL WILD-TYPE 84 30
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      4    0
  PPL WILD-TYPE   84   30
     clus
vv    PPL MUTATED PPL WILD-TYPE
  NO            4            84
  YES           0            30
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPL MUTATED                                     4
  PPL WILD-TYPE                                 101
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPL MUTATED                                       0
  PPL WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPL MUTATED                                                  0
  PPL WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  PPL MUTATED                                     0
  PPL WILD-TYPE                                   1
D605V9, multiclass
                                                  clus
vv                                                 PPL MUTATED PPL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V10, continuous
[1] "Remove cluster labels:" "PPL MUTATED"           
clus
  PPL MUTATED PPL WILD-TYPE 
            2            37 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQE    TCGA-3A-A9I9    TCGA-3A-A9IB 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-AAPQ 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1    TCGA-IB-7885 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"PPL WILD-TYPE" "PPL WILD-TYPE" 
D605V11, continuous
[1] "Remove cluster labels:" "PPL MUTATED"           
clus
  PPL MUTATED PPL WILD-TYPE 
            1            32 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-7885 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI 
"PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" "PPL WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"PPL WILD-TYPE" "PPL WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  PPL MUTATED    2  2  0  0
  PPL WILD-TYPE 78 33  4  2
D605V12, multiclass
    clus
vv   PPL MUTATED PPL WILD-TYPE
  R0           2            78
  R1           2            33
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPL MUTATED       0                         0     4
  PPL WILD-TYPE     6                         5   110
D605V14, multiclass
                           clus
vv                          PPL MUTATED PPL WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V15, binary
               cls
clus             0  1
  PPL MUTATED    0  2
  PPL WILD-TYPE  5 89
[1] "tbl2"
               cls
clus            [,1] [,2]
  PPL MUTATED      0    2
  PPL WILD-TYPE    5   89
                        clus
vv                       PPL MUTATED PPL WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           2            89
[1] 2 2
[1] FALSE

Clustering(606) Variable = CDC42BPG MUTATION ANALYSIS
D606V1, survival
                    sevent
clus2                 0  1
  CDC42BPG MUTATED    2  3
  CDC42BPG WILD-TYPE 61 59
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 5                120 
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 3                 59 
$`CDC42BPG MUTATED`
TCGA-2L-AAQM TCGA-FZ-5922 TCGA-HV-A7OP TCGA-HZ-A77O TCGA-IB-7651 
       45.47        36.20        32.15         5.26        19.82 

$`CDC42BPG WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39        12.95         9.60        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5923 
        5.03         1.02        24.36         2.01         5.10        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       17.79        22.06         8.28        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       20.19        17.00        10.13        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
              5.26               0.23 
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
             45.47              90.12 
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
            32.150             15.155 
[1] "5.3 - 45.5 (32.1)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D606V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDC42BPG MUTATED         0        0        0         1         4         0
  CDC42BPG WILD-TYPE       1        3       12        18        78         4
                    vv
clus                 STAGE IV
  CDC42BPG MUTATED          0
  CDC42BPG WILD-TYPE        3
D606V3, multiclass
           clus
vv          CDC42BPG MUTATED CDC42BPG WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                4                 78
  STAGE III                0                  4
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  CDC42BPG MUTATED    0  1     4
  CDC42BPG WILD-TYPE  5 16    98
D606V4, multiclass
       clus
vv      CDC42BPG MUTATED CDC42BPG WILD-TYPE
  T1                   0                  5
  T2                   1                 16
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V5, binary
                    cls
clus                  0  1
  CDC42BPG MUTATED    1  4
  CDC42BPG WILD-TYPE 34 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPG MUTATED      1    4
  CDC42BPG WILD-TYPE   34   85
   clus
vv  CDC42BPG MUTATED CDC42BPG WILD-TYPE
  0                1                 34
  1                4                 85
[1] 2 2
[1] FALSE
D606V6, binary
                    cls
clus                  0  1
  CDC42BPG MUTATED    3  0
  CDC42BPG WILD-TYPE 54  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPG MUTATED      3    0
  CDC42BPG WILD-TYPE   54    3
   clus
vv  CDC42BPG MUTATED CDC42BPG WILD-TYPE
  0                3                 54
  1                0                  3
[1] 2 2
[1] FALSE
D606V7, binary
                    cls
clus                  0  1
  CDC42BPG MUTATED    2  3
  CDC42BPG WILD-TYPE 49 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPG MUTATED      2    3
  CDC42BPG WILD-TYPE   49   72
        clus
vv       CDC42BPG MUTATED CDC42BPG WILD-TYPE
  FEMALE                2                 49
  MALE                  3                 72
[1] 2 2
[1] FALSE
D606V8, binary
                    cls
clus                  0  1
  CDC42BPG MUTATED    4  1
  CDC42BPG WILD-TYPE 84 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPG MUTATED      4    1
  CDC42BPG WILD-TYPE   84   29
     clus
vv    CDC42BPG MUTATED CDC42BPG WILD-TYPE
  NO                 4                 84
  YES                1                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC42BPG MUTATED                                     3
  CDC42BPG WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC42BPG MUTATED                                       2
  CDC42BPG WILD-TYPE                                    16
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC42BPG MUTATED                                                  0
  CDC42BPG WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDC42BPG MUTATED                                     0
  CDC42BPG WILD-TYPE                                   1
D606V9, multiclass
                                                  clus
vv                                                 CDC42BPG MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 CDC42BPG WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V10, continuous
[1] "Remove cluster labels:" "CDC42BPG MUTATED"      
clus
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 1                 38 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-AAPQ 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-H8-A6C1         TCGA-HV-AA8V 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUU 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-AAUV         TCGA-LB-A9Q5         TCGA-OE-A75W 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
D606V11, continuous
[1] "Remove cluster labels:" "CDC42BPG MUTATED"      
clus
  CDC42BPG MUTATED CDC42BPG WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"CDC42BPG WILD-TYPE" "CDC42BPG WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  CDC42BPG MUTATED    4  1  0  0
  CDC42BPG WILD-TYPE 76 34  4  2
D606V12, multiclass
    clus
vv   CDC42BPG MUTATED CDC42BPG WILD-TYPE
  R0                4                 76
  R1                1                 34
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC42BPG MUTATED       1                         0     4
  CDC42BPG WILD-TYPE     5                         5   110
D606V14, multiclass
                           clus
vv                          CDC42BPG MUTATED CDC42BPG WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V15, binary
                    cls
clus                  0  1
  CDC42BPG MUTATED    0  3
  CDC42BPG WILD-TYPE  5 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPG MUTATED      0    3
  CDC42BPG WILD-TYPE    5   88
                        clus
vv                       CDC42BPG MUTATED CDC42BPG WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(607) Variable = THBS1 MUTATION ANALYSIS
D607V1, survival
                 sevent
clus2              0  1
  THBS1 MUTATED    4  3
  THBS1 WILD-TYPE 59 59
  THBS1 MUTATED THBS1 WILD-TYPE 
              7             118 
  THBS1 MUTATED THBS1 WILD-TYPE 
              3              59 
$`THBS1 MUTATED`
TCGA-2J-AAB8 TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IX TCGA-HV-A7OP TCGA-HZ-8637 
        2.63        43.50        20.84        34.09        32.15        17.00 
TCGA-IB-7651 
       19.82 

$`THBS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB9 
       14.14        16.37         2.17        23.97         9.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       12.95         9.60        45.47         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IZ 
       63.85        50.70        32.81        15.06        36.26        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       24.43        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I 
        8.28        30.25        17.49        31.86        20.19        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       15.32         9.40         0.30        39.98        16.80         0.39 
TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 
       18.67        13.81        12.99        12.03        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  THBS1 MUTATED THBS1 WILD-TYPE 
           2.63            0.23 
  THBS1 MUTATED THBS1 WILD-TYPE 
          43.50           90.12 
  THBS1 MUTATED THBS1 WILD-TYPE 
          20.84           15.09 
[1] "2.6 - 43.5 (20.8)" "0.2 - 90.1 (15.1)"
[1] "hr=" "1.7"
D607V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  THBS1 MUTATED         0        1        0         1         5         0
  THBS1 WILD-TYPE       1        2       12        18        77         4
                 vv
clus              STAGE IV
  THBS1 MUTATED          0
  THBS1 WILD-TYPE        3
D607V3, multiclass
           clus
vv          THBS1 MUTATED THBS1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  THBS1 MUTATED    1  0     6
  THBS1 WILD-TYPE  4 17    96
D607V4, multiclass
       clus
vv      THBS1 MUTATED THBS1 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V5, binary
                 cls
clus               0  1
  THBS1 MUTATED    2  5
  THBS1 WILD-TYPE 33 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      2    5
  THBS1 WILD-TYPE   33   84
   clus
vv  THBS1 MUTATED THBS1 WILD-TYPE
  0             2              33
  1             5              84
[1] 2 2
[1] FALSE
D607V6, binary
                 cls
clus               0  1
  THBS1 MUTATED    3  0
  THBS1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      3    0
  THBS1 WILD-TYPE   54    3
   clus
vv  THBS1 MUTATED THBS1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D607V7, binary
                 cls
clus               0  1
  THBS1 MUTATED    2  5
  THBS1 WILD-TYPE 49 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      2    5
  THBS1 WILD-TYPE   49   70
        clus
vv       THBS1 MUTATED THBS1 WILD-TYPE
  FEMALE             2              49
  MALE               5              70
[1] 2 2
[1] FALSE
D607V8, binary
                 cls
clus               0  1
  THBS1 MUTATED    1  5
  THBS1 WILD-TYPE 87 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      1    5
  THBS1 WILD-TYPE   87   25
     clus
vv    THBS1 MUTATED THBS1 WILD-TYPE
  NO              1              87
  YES             5              25
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  THBS1 MUTATED                                     6
  THBS1 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  THBS1 MUTATED                                       1
  THBS1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  THBS1 MUTATED                                                  0
  THBS1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  THBS1 MUTATED                                     0
  THBS1 WILD-TYPE                                   1
D607V9, multiclass
                                                  clus
vv                                                 THBS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 THBS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V10, continuous
D607V11, continuous
[1] "Remove cluster labels:" "THBS1 MUTATED"         
clus
  THBS1 MUTATED THBS1 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  THBS1 MUTATED    6  1  0  0
  THBS1 WILD-TYPE 74 34  4  2
D607V12, multiclass
    clus
vv   THBS1 MUTATED THBS1 WILD-TYPE
  R0             6              74
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THBS1 MUTATED       1                         1     5
  THBS1 WILD-TYPE     5                         4   109
D607V14, multiclass
                           clus
vv                          THBS1 MUTATED THBS1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V15, binary
                 cls
clus               0  1
  THBS1 MUTATED    1  4
  THBS1 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      1    4
  THBS1 WILD-TYPE    4   87
                        clus
vv                       THBS1 MUTATED THBS1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(608) Variable = LAMA3 MUTATION ANALYSIS
D608V1, survival
                 sevent
clus2              0  1
  LAMA3 MUTATED    3  1
  LAMA3 WILD-TYPE 60 61
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              4             121 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              1              61 
$`LAMA3 MUTATED`
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-XN-A8T3 TCGA-YY-A8LH 
       19.82        19.82        31.27        66.28 

$`LAMA3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        5.26        10.85         0.23        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  LAMA3 MUTATED LAMA3 WILD-TYPE 
          19.82            0.23 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
          66.28           90.12 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         25.545          15.120 
[1] "19.8 - 66.3 (25.5)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3.4"
D608V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LAMA3 MUTATED         0        0        1         0         2         0
  LAMA3 WILD-TYPE       1        3       11        19        80         4
                 vv
clus              STAGE IV
  LAMA3 MUTATED          1
  LAMA3 WILD-TYPE        2
D608V3, multiclass
           clus
vv          LAMA3 MUTATED LAMA3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              1               2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  LAMA3 MUTATED    0  1     3
  LAMA3 WILD-TYPE  5 16    99
D608V4, multiclass
       clus
vv      LAMA3 MUTATED LAMA3 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V5, binary
                 cls
clus               0  1
  LAMA3 MUTATED    2  2
  LAMA3 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      2    2
  LAMA3 WILD-TYPE   33   87
   clus
vv  LAMA3 MUTATED LAMA3 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D608V6, binary
                 cls
clus               0  1
  LAMA3 MUTATED    2  1
  LAMA3 WILD-TYPE 55  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      2    1
  LAMA3 WILD-TYPE   55    2
   clus
vv  LAMA3 MUTATED LAMA3 WILD-TYPE
  0             2              55
  1             1               2
[1] 2 2
[1] FALSE
D608V7, binary
                 cls
clus               0  1
  LAMA3 MUTATED    2  2
  LAMA3 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      2    2
  LAMA3 WILD-TYPE   49   73
        clus
vv       LAMA3 MUTATED LAMA3 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D608V8, binary
                 cls
clus               0  1
  LAMA3 MUTATED    2  2
  LAMA3 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      2    2
  LAMA3 WILD-TYPE   86   28
     clus
vv    LAMA3 MUTATED LAMA3 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LAMA3 MUTATED                                     3
  LAMA3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LAMA3 MUTATED                                       1
  LAMA3 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LAMA3 MUTATED                                                  0
  LAMA3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LAMA3 MUTATED                                     0
  LAMA3 WILD-TYPE                                   1
D608V9, multiclass
                                                  clus
vv                                                 LAMA3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LAMA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V10, continuous
[1] "Remove cluster labels:" "LAMA3 MUTATED"         
clus
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-XN-A8T5 
"LAMA3 WILD-TYPE" 
D608V11, continuous
[1] "Remove cluster labels:" "LAMA3 MUTATED"         
clus
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  LAMA3 MUTATED    3  1  0  0
  LAMA3 WILD-TYPE 77 34  4  2
D608V12, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LAMA3 MUTATED       0                         0     4
  LAMA3 WILD-TYPE     6                         5   110
D608V14, multiclass
                           clus
vv                          LAMA3 MUTATED LAMA3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V15, binary
                 cls
clus               0  1
  LAMA3 MUTATED    1  3
  LAMA3 WILD-TYPE  4 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      1    3
  LAMA3 WILD-TYPE    4   88
                        clus
vv                       LAMA3 MUTATED LAMA3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(609) Variable = DYRK4 MUTATION ANALYSIS
D609V1, survival
                 sevent
clus2              0  1
  DYRK4 MUTATED    2  1
  DYRK4 WILD-TYPE 61 61
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              3             122 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              1              61 
$`DYRK4 MUTATED`
TCGA-IB-7651 TCGA-US-A776 TCGA-YY-A8LH 
       19.82        39.98        66.28 

$`DYRK4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A 
        7.56        12.46        10.29         8.78        13.68         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
       15.32         9.40         0.30        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  DYRK4 MUTATED DYRK4 WILD-TYPE 
          19.82            0.23 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          66.28           90.12 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
         39.980          15.155 
[1] "19.8 - 66.3 (40.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.8"
D609V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DYRK4 MUTATED         0        0        0         1         2         0
  DYRK4 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  DYRK4 MUTATED          0
  DYRK4 WILD-TYPE        3
D609V3, multiclass
           clus
vv          DYRK4 MUTATED DYRK4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  DYRK4 MUTATED    0  0     3
  DYRK4 WILD-TYPE  5 17    99
D609V4, multiclass
       clus
vv      DYRK4 MUTATED DYRK4 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V5, binary
                 cls
clus               0  1
  DYRK4 MUTATED    1  2
  DYRK4 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      1    2
  DYRK4 WILD-TYPE   34   87
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D609V6, binary
                 cls
clus               0  1
  DYRK4 MUTATED    1  0
  DYRK4 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      1    0
  DYRK4 WILD-TYPE   56    3
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D609V7, binary
                 cls
clus               0  1
  DYRK4 MUTATED    2  1
  DYRK4 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      2    1
  DYRK4 WILD-TYPE   49   74
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D609V8, binary
                 cls
clus               0  1
  DYRK4 MUTATED    2  1
  DYRK4 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      2    1
  DYRK4 WILD-TYPE   86   29
     clus
vv    DYRK4 MUTATED DYRK4 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DYRK4 MUTATED                                     2
  DYRK4 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DYRK4 MUTATED                                       0
  DYRK4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DYRK4 MUTATED                                                  1
  DYRK4 WILD-TYPE                                                0
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  DYRK4 MUTATED                                     0
  DYRK4 WILD-TYPE                                   1
D609V9, multiclass
                                                  clus
vv                                                 DYRK4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 DYRK4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V10, continuous
[1] "Remove cluster labels:" "DYRK4 MUTATED"         
clus
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-XN-A8T5 
"DYRK4 WILD-TYPE" 
D609V11, continuous
[1] "Remove cluster labels:" "DYRK4 MUTATED"         
clus
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" "DYRK4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DYRK4 MUTATED    3  0  0  0
  DYRK4 WILD-TYPE 77 35  4  2
D609V12, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DYRK4 MUTATED       0                         0     3
  DYRK4 WILD-TYPE     6                         5   111
D609V14, multiclass
                           clus
vv                          DYRK4 MUTATED DYRK4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V15, binary
                 cls
clus               0  1
  DYRK4 MUTATED    0  3
  DYRK4 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      0    3
  DYRK4 WILD-TYPE    5   88
                        clus
vv                       DYRK4 MUTATED DYRK4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(610) Variable = HNRNPH1 MUTATION ANALYSIS
D610V1, survival
                   sevent
clus2                0  1
  HNRNPH1 MUTATED    1  3
  HNRNPH1 WILD-TYPE 62 59
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                4               121 
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                3                59 
$`HNRNPH1 MUTATED`
TCGA-FB-AAPP TCGA-HV-A7OL TCGA-IB-7651 TCGA-RB-A7B8 
       15.95         8.28        19.82        15.32 

$`HNRNPH1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS 
       10.29         8.78        13.68         3.12         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
             8.28              0.23 
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
            19.82             90.12 
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
           15.635            15.190 
[1] "8.3 - 19.8 (15.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D610V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HNRNPH1 MUTATED         0        0        0         1         3         0
  HNRNPH1 WILD-TYPE       1        3       12        18        79         4
                   vv
clus                STAGE IV
  HNRNPH1 MUTATED          0
  HNRNPH1 WILD-TYPE        3
D610V3, multiclass
           clus
vv          HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  HNRNPH1 MUTATED    0  0     4
  HNRNPH1 WILD-TYPE  5 17    98
D610V4, multiclass
       clus
vv      HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V5, binary
                   cls
clus                 0  1
  HNRNPH1 MUTATED    1  3
  HNRNPH1 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH1 MUTATED      1    3
  HNRNPH1 WILD-TYPE   34   86
   clus
vv  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D610V6, binary
                   cls
clus                 0  1
  HNRNPH1 MUTATED    1  0
  HNRNPH1 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH1 MUTATED      1    0
  HNRNPH1 WILD-TYPE   56    3
   clus
vv  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D610V7, binary
                   cls
clus                 0  1
  HNRNPH1 MUTATED    2  2
  HNRNPH1 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH1 MUTATED      2    2
  HNRNPH1 WILD-TYPE   49   73
        clus
vv       HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D610V8, binary
                   cls
clus                 0  1
  HNRNPH1 MUTATED    3  1
  HNRNPH1 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH1 MUTATED      3    1
  HNRNPH1 WILD-TYPE   85   29
     clus
vv    HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HNRNPH1 MUTATED                                     3
  HNRNPH1 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HNRNPH1 MUTATED                                       1
  HNRNPH1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HNRNPH1 MUTATED                                                  0
  HNRNPH1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  HNRNPH1 MUTATED                                     0
  HNRNPH1 WILD-TYPE                                   1
D610V9, multiclass
                                                  clus
vv                                                 HNRNPH1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 HNRNPH1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V10, continuous
[1] "Remove cluster labels:" "HNRNPH1 MUTATED"       
clus
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
D610V11, continuous
[1] "Remove cluster labels:" "HNRNPH1 MUTATED"       
clus
  HNRNPH1 MUTATED HNRNPH1 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" "HNRNPH1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  HNRNPH1 MUTATED    3  0  1  0
  HNRNPH1 WILD-TYPE 77 35  3  2
D610V12, multiclass
    clus
vv   HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  R0               3                77
  R1               0                35
  R2               1                 3
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HNRNPH1 MUTATED       1                         0     3
  HNRNPH1 WILD-TYPE     5                         5   111
D610V14, multiclass
                           clus
vv                          HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V15, binary
                   cls
clus                 0  1
  HNRNPH1 MUTATED    0  3
  HNRNPH1 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH1 MUTATED      0    3
  HNRNPH1 WILD-TYPE    5   88
                        clus
vv                       HNRNPH1 MUTATED HNRNPH1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(611) Variable = UGT1A10 MUTATION ANALYSIS
D611V1, survival
                   sevent
clus2                0  1
  UGT1A10 MUTATED    2  2
  UGT1A10 WILD-TYPE 61 60
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
                4               121 
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
                2                60 
$`UGT1A10 MUTATED`
TCGA-2L-AAQI TCGA-FB-AAPU TCGA-Q3-AA2A TCGA-YB-A89D 
        3.39        12.53         3.12        11.51 

$`UGT1A10 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
             3.12              0.23 
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
            12.53             90.12 
  UGT1A10 MUTATED UGT1A10 WILD-TYPE 
             7.45             15.35 
[1] "3.1 - 12.5 (7.5)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "3"  
D611V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  UGT1A10 MUTATED         0        0        1         1         2         0
  UGT1A10 WILD-TYPE       1        3       11        18        80         4
                   vv
clus                STAGE IV
  UGT1A10 MUTATED          0
  UGT1A10 WILD-TYPE        3
D611V3, multiclass
           clus
vv          UGT1A10 MUTATED UGT1A10 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               2                80
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  UGT1A10 MUTATED    0  0     4
  UGT1A10 WILD-TYPE  5 17    98
D611V4, multiclass
       clus
vv      UGT1A10 MUTATED UGT1A10 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V5, binary
                   cls
clus                 0  1
  UGT1A10 MUTATED    1  3
  UGT1A10 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT1A10 MUTATED      1    3
  UGT1A10 WILD-TYPE   34   86
   clus
vv  UGT1A10 MUTATED UGT1A10 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D611V6, binary
                   cls
clus                 0  1
  UGT1A10 MUTATED    0  0
  UGT1A10 WILD-TYPE 57  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT1A10 MUTATED      0    0
  UGT1A10 WILD-TYPE   57    3
D611V7, binary
                   cls
clus                 0  1
  UGT1A10 MUTATED    2  2
  UGT1A10 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT1A10 MUTATED      2    2
  UGT1A10 WILD-TYPE   49   73
        clus
vv       UGT1A10 MUTATED UGT1A10 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D611V8, binary
                   cls
clus                 0  1
  UGT1A10 MUTATED    3  1
  UGT1A10 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT1A10 MUTATED      3    1
  UGT1A10 WILD-TYPE   85   29
     clus
vv    UGT1A10 MUTATED UGT1A10 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UGT1A10 MUTATED                                     4
  UGT1A10 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UGT1A10 MUTATED                                       0
  UGT1A10 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UGT1A10 MUTATED                                                  0
  UGT1A10 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  UGT1A10 MUTATED                                     0
  UGT1A10 WILD-TYPE                                   1
D611V9, multiclass
                                                  clus
vv                                                 UGT1A10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 UGT1A10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V10, continuous
D611V11, continuous
                   vv
clus                R0 R1 R2 RX
  UGT1A10 MUTATED    1  2  0  1
  UGT1A10 WILD-TYPE 79 33  4  1
D611V12, multiclass
    clus
vv   UGT1A10 MUTATED UGT1A10 WILD-TYPE
  R0               1                79
  R1               2                33
  R2               0                 4
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UGT1A10 MUTATED       1                         0     3
  UGT1A10 WILD-TYPE     5                         5   111
D611V14, multiclass
                           clus
vv                          UGT1A10 MUTATED UGT1A10 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V15, binary
                   cls
clus                 0  1
  UGT1A10 MUTATED    0  3
  UGT1A10 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT1A10 MUTATED      0    3
  UGT1A10 WILD-TYPE    5   88
                        clus
vv                       UGT1A10 MUTATED UGT1A10 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(612) Variable = TEKT4 MUTATION ANALYSIS
D612V1, survival
                 sevent
clus2              0  1
  TEKT4 MUTATED    2  4
  TEKT4 WILD-TYPE 61 58
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             119 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              4              58 
$`TEKT4 MUTATED`
TCGA-HZ-A77Q TCGA-2L-AAQI TCGA-3A-A9J0 TCGA-FB-A78T TCGA-IB-7651 TCGA-IB-A5SQ 
        1.08         3.39        24.43        12.33        19.82         7.20 

$`TEKT4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       34.09        10.13        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       17.00        16.37        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST 
       36.69        41.33        15.19        12.00        15.85        20.88 
TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       21.90         1.35         8.22        15.88         0.26         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TEKT4 MUTATED TEKT4 WILD-TYPE 
           1.08            0.23 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
          24.43           90.12 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
          9.765          15.320 
[1] "1.1 - 24.4 (9.8)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D612V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TEKT4 MUTATED         0        0        1         0         5         0
  TEKT4 WILD-TYPE       1        3       11        19        77         4
                 vv
clus              STAGE IV
  TEKT4 MUTATED          0
  TEKT4 WILD-TYPE        3
D612V3, multiclass
           clus
vv          TEKT4 MUTATED TEKT4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              1              11
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  TEKT4 MUTATED    0  1     5
  TEKT4 WILD-TYPE  5 16    97
D612V4, multiclass
       clus
vv      TEKT4 MUTATED TEKT4 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V5, binary
                 cls
clus               0  1
  TEKT4 MUTATED    1  5
  TEKT4 WILD-TYPE 34 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      1    5
  TEKT4 WILD-TYPE   34   84
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             1              34
  1             5              84
[1] 2 2
[1] FALSE
D612V6, binary
                 cls
clus               0  1
  TEKT4 MUTATED    3  0
  TEKT4 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      3    0
  TEKT4 WILD-TYPE   54    3
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D612V7, binary
                 cls
clus               0  1
  TEKT4 MUTATED    4  2
  TEKT4 WILD-TYPE 47 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      4    2
  TEKT4 WILD-TYPE   47   73
        clus
vv       TEKT4 MUTATED TEKT4 WILD-TYPE
  FEMALE             4              47
  MALE               2              73
[1] 2 2
[1] FALSE
D612V8, binary
                 cls
clus               0  1
  TEKT4 MUTATED    5  0
  TEKT4 WILD-TYPE 83 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      5    0
  TEKT4 WILD-TYPE   83   30
     clus
vv    TEKT4 MUTATED TEKT4 WILD-TYPE
  NO              5              83
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEKT4 MUTATED                                     5
  TEKT4 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEKT4 MUTATED                                       1
  TEKT4 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEKT4 MUTATED                                                  0
  TEKT4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  TEKT4 MUTATED                                     0
  TEKT4 WILD-TYPE                                   1
D612V9, multiclass
                                                  clus
vv                                                 TEKT4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 TEKT4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V10, continuous
D612V11, continuous
                 vv
clus              R0 R1 R2 RX
  TEKT4 MUTATED    5  1  0  0
  TEKT4 WILD-TYPE 75 34  4  2
D612V12, multiclass
    clus
vv   TEKT4 MUTATED TEKT4 WILD-TYPE
  R0             5              75
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEKT4 MUTATED       0                         0     6
  TEKT4 WILD-TYPE     6                         5   108
D612V14, multiclass
                           clus
vv                          TEKT4 MUTATED TEKT4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V15, binary
                 cls
clus               0  1
  TEKT4 MUTATED    0  5
  TEKT4 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      0    5
  TEKT4 WILD-TYPE    5   86
                        clus
vv                       TEKT4 MUTATED TEKT4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(613) Variable = PHTF2 MUTATION ANALYSIS
D613V1, survival
                 sevent
clus2              0  1
  PHTF2 MUTATED    2  2
  PHTF2 WILD-TYPE 61 60
  PHTF2 MUTATED PHTF2 WILD-TYPE 
              4             121 
  PHTF2 MUTATED PHTF2 WILD-TYPE 
              2              60 
$`PHTF2 MUTATED`
TCGA-2J-AABE TCGA-3A-A9IO TCGA-IB-7651 TCGA-IB-AAUQ 
       22.22        63.85        19.82         6.02 

$`PHTF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86        14.17        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PHTF2 MUTATED PHTF2 WILD-TYPE 
           6.02            0.23 
  PHTF2 MUTATED PHTF2 WILD-TYPE 
          63.85           90.12 
  PHTF2 MUTATED PHTF2 WILD-TYPE 
          21.02           15.19 
[1] "6.0 - 63.9 (21.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D613V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHTF2 MUTATED         0        0        0         1         2         0
  PHTF2 WILD-TYPE       1        3       12        18        80         4
                 vv
clus              STAGE IV
  PHTF2 MUTATED          0
  PHTF2 WILD-TYPE        3
D613V3, multiclass
           clus
vv          PHTF2 MUTATED PHTF2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             1              18
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PHTF2 MUTATED    0  0     3
  PHTF2 WILD-TYPE  5 17    99
D613V4, multiclass
       clus
vv      PHTF2 MUTATED PHTF2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V5, binary
                 cls
clus               0  1
  PHTF2 MUTATED    1  2
  PHTF2 WILD-TYPE 34 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF2 MUTATED      1    2
  PHTF2 WILD-TYPE   34   87
   clus
vv  PHTF2 MUTATED PHTF2 WILD-TYPE
  0             1              34
  1             2              87
[1] 2 2
[1] FALSE
D613V6, binary
                 cls
clus               0  1
  PHTF2 MUTATED    3  0
  PHTF2 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF2 MUTATED      3    0
  PHTF2 WILD-TYPE   54    3
   clus
vv  PHTF2 MUTATED PHTF2 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D613V7, binary
                 cls
clus               0  1
  PHTF2 MUTATED    1  3
  PHTF2 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF2 MUTATED      1    3
  PHTF2 WILD-TYPE   50   72
        clus
vv       PHTF2 MUTATED PHTF2 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D613V8, binary
                 cls
clus               0  1
  PHTF2 MUTATED    3  1
  PHTF2 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF2 MUTATED      3    1
  PHTF2 WILD-TYPE   85   29
     clus
vv    PHTF2 MUTATED PHTF2 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHTF2 MUTATED                                     3
  PHTF2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHTF2 MUTATED                                       1
  PHTF2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHTF2 MUTATED                                                  0
  PHTF2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHTF2 MUTATED                                     0
  PHTF2 WILD-TYPE                                   1
D613V9, multiclass
                                                  clus
vv                                                 PHTF2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PHTF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V10, continuous
D613V11, continuous
                 vv
clus              R0 R1 R2 RX
  PHTF2 MUTATED    3  1  0  0
  PHTF2 WILD-TYPE 77 34  4  2
D613V12, multiclass
    clus
vv   PHTF2 MUTATED PHTF2 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHTF2 MUTATED       0                         0     4
  PHTF2 WILD-TYPE     6                         5   110
D613V14, multiclass
                           clus
vv                          PHTF2 MUTATED PHTF2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V15, binary
                 cls
clus               0  1
  PHTF2 MUTATED    0  3
  PHTF2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHTF2 MUTATED      0    3
  PHTF2 WILD-TYPE    5   88
                        clus
vv                       PHTF2 MUTATED PHTF2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(614) Variable = CDC6 MUTATION ANALYSIS
D614V1, survival
                sevent
clus2             0  1
  CDC6 MUTATED    1  2
  CDC6 WILD-TYPE 62 60
  CDC6 MUTATED CDC6 WILD-TYPE 
             3            122 
  CDC6 MUTATED CDC6 WILD-TYPE 
             2             60 
$`CDC6 MUTATED`
TCGA-IB-7651 TCGA-IB-A5SP TCGA-RB-A7B8 
       19.82        15.85        15.32 

$`CDC6 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       15.19        12.00         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M 
       12.46        10.29         8.78        13.68         3.12         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CDC6 MUTATED CDC6 WILD-TYPE 
         15.32           0.23 
  CDC6 MUTATED CDC6 WILD-TYPE 
         19.82          90.12 
  CDC6 MUTATED CDC6 WILD-TYPE 
        15.850         15.155 
[1] "15.3 - 19.8 (15.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D614V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CDC6 MUTATED         0        0        0         1         2         0
  CDC6 WILD-TYPE       1        3       12        18        80         4
                vv
clus             STAGE IV
  CDC6 MUTATED          0
  CDC6 WILD-TYPE        3
D614V3, multiclass
           clus
vv          CDC6 MUTATED CDC6 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            1             18
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CDC6 MUTATED    0  0     3
  CDC6 WILD-TYPE  5 17    99
D614V4, multiclass
       clus
vv      CDC6 MUTATED CDC6 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V5, binary
                cls
clus              0  1
  CDC6 MUTATED    1  2
  CDC6 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      1    2
  CDC6 WILD-TYPE   34   87
   clus
vv  CDC6 MUTATED CDC6 WILD-TYPE
  0            1             34
  1            2             87
[1] 2 2
[1] FALSE
D614V6, binary
                cls
clus              0  1
  CDC6 MUTATED    2  0
  CDC6 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      2    0
  CDC6 WILD-TYPE   55    3
   clus
vv  CDC6 MUTATED CDC6 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D614V7, binary
                cls
clus              0  1
  CDC6 MUTATED    2  1
  CDC6 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      2    1
  CDC6 WILD-TYPE   49   74
        clus
vv       CDC6 MUTATED CDC6 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D614V8, binary
                cls
clus              0  1
  CDC6 MUTATED    3  0
  CDC6 WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      3    0
  CDC6 WILD-TYPE   85   30
     clus
vv    CDC6 MUTATED CDC6 WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC6 MUTATED                                     2
  CDC6 WILD-TYPE                                 103
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC6 MUTATED                                       1
  CDC6 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC6 MUTATED                                                  0
  CDC6 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CDC6 MUTATED                                     0
  CDC6 WILD-TYPE                                   1
D614V9, multiclass
                                                  clus
vv                                                 CDC6 MUTATED CDC6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V10, continuous
[1] "Remove cluster labels:" "CDC6 MUTATED"          
clus
  CDC6 MUTATED CDC6 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
D614V11, continuous
[1] "Remove cluster labels:" "CDC6 MUTATED"          
clus
  CDC6 MUTATED CDC6 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" "CDC6 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CDC6 MUTATED    2  1  0  0
  CDC6 WILD-TYPE 78 34  4  2
D614V12, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC6 MUTATED       0                         0     3
  CDC6 WILD-TYPE     6                         5   111
D614V14, multiclass
                           clus
vv                          CDC6 MUTATED CDC6 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V15, binary
                cls
clus              0  1
  CDC6 MUTATED    0  2
  CDC6 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      0    2
  CDC6 WILD-TYPE    5   89
                        clus
vv                       CDC6 MUTATED CDC6 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2             89
[1] 2 2
[1] FALSE

Clustering(615) Variable = PRKDC MUTATION ANALYSIS
D615V1, survival
                 sevent
clus2              0  1
  PRKDC MUTATED    1  2
  PRKDC WILD-TYPE 62 60
  PRKDC MUTATED PRKDC WILD-TYPE 
              3             122 
  PRKDC MUTATED PRKDC WILD-TYPE 
              2              60 
$`PRKDC MUTATED`
TCGA-LB-A7SX TCGA-IB-7651 TCGA-IB-A7M4 
       12.92        19.82        15.88 

$`PRKDC WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        15.12        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
        8.22         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PRKDC MUTATED PRKDC WILD-TYPE 
          12.92            0.23 
  PRKDC MUTATED PRKDC WILD-TYPE 
          19.82           90.12 
  PRKDC MUTATED PRKDC WILD-TYPE 
         15.880          15.205 
[1] "12.9 - 19.8 (15.9)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D615V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PRKDC MUTATED         0        0        0         0         3         0
  PRKDC WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  PRKDC MUTATED          0
  PRKDC WILD-TYPE        3
D615V3, multiclass
           clus
vv          PRKDC MUTATED PRKDC WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PRKDC MUTATED    0  0     3
  PRKDC WILD-TYPE  5 17    99
D615V4, multiclass
       clus
vv      PRKDC MUTATED PRKDC WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V5, binary
                 cls
clus               0  1
  PRKDC MUTATED    0  3
  PRKDC WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      0    3
  PRKDC WILD-TYPE   35   86
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D615V6, binary
                 cls
clus               0  1
  PRKDC MUTATED    1  0
  PRKDC WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      1    0
  PRKDC WILD-TYPE   56    3
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D615V7, binary
                 cls
clus               0  1
  PRKDC MUTATED    2  1
  PRKDC WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      2    1
  PRKDC WILD-TYPE   49   74
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D615V8, binary
                 cls
clus               0  1
  PRKDC MUTATED    3  0
  PRKDC WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      3    0
  PRKDC WILD-TYPE   85   30
     clus
vv    PRKDC MUTATED PRKDC WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRKDC MUTATED                                     3
  PRKDC WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRKDC MUTATED                                       0
  PRKDC WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRKDC MUTATED                                                  0
  PRKDC WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PRKDC MUTATED                                     0
  PRKDC WILD-TYPE                                   1
D615V9, multiclass
                                                  clus
vv                                                 PRKDC MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PRKDC WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V10, continuous
D615V11, continuous
                 vv
clus              R0 R1 R2 RX
  PRKDC MUTATED    2  1  0  0
  PRKDC WILD-TYPE 78 34  4  2
D615V12, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKDC MUTATED       0                         1     2
  PRKDC WILD-TYPE     6                         4   112
D615V14, multiclass
                           clus
vv                          PRKDC MUTATED PRKDC WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V15, binary
                 cls
clus               0  1
  PRKDC MUTATED    0  3
  PRKDC WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      0    3
  PRKDC WILD-TYPE    5   88
                        clus
vv                       PRKDC MUTATED PRKDC WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(616) Variable = KDM6B MUTATION ANALYSIS
D616V1, survival
                 sevent
clus2              0  1
  KDM6B MUTATED    2  4
  KDM6B WILD-TYPE 61 58
  KDM6B MUTATED KDM6B WILD-TYPE 
              6             119 
  KDM6B MUTATED KDM6B WILD-TYPE 
              4              58 
$`KDM6B MUTATED`
TCGA-IB-A5SS TCGA-2J-AABV TCGA-F2-7273 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-AAUM 
       15.12        21.44        19.46        32.15        19.82         0.26 

$`KDM6B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78         1.08        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A7TX 
       34.09        10.13        24.43        75.12        71.74         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
       22.06         8.28        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUN 
       20.88        21.90         1.35         8.22        15.88         4.73 
TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU 
        7.86        14.17         6.02        11.11         7.40         8.05 
TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY 
       13.28         7.56        12.46        10.29         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
        3.12        15.32         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  KDM6B MUTATED KDM6B WILD-TYPE 
           0.26            0.23 
  KDM6B MUTATED KDM6B WILD-TYPE 
          32.15           90.12 
  KDM6B MUTATED KDM6B WILD-TYPE 
          19.64           15.19 
[1] "0.3 - 32.1 (19.6)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D616V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  KDM6B MUTATED         0        0        0         0         6         0
  KDM6B WILD-TYPE       1        3       12        19        76         4
                 vv
clus              STAGE IV
  KDM6B MUTATED          0
  KDM6B WILD-TYPE        3
D616V3, multiclass
           clus
vv          KDM6B MUTATED KDM6B WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  KDM6B MUTATED    0  1     5
  KDM6B WILD-TYPE  5 16    97
D616V4, multiclass
       clus
vv      KDM6B MUTATED KDM6B WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V5, binary
                 cls
clus               0  1
  KDM6B MUTATED    0  6
  KDM6B WILD-TYPE 35 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6B MUTATED      0    6
  KDM6B WILD-TYPE   35   83
   clus
vv  KDM6B MUTATED KDM6B WILD-TYPE
  0             0              35
  1             6              83
[1] 2 2
[1] FALSE
D616V6, binary
                 cls
clus               0  1
  KDM6B MUTATED    6  0
  KDM6B WILD-TYPE 51  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6B MUTATED      6    0
  KDM6B WILD-TYPE   51    3
   clus
vv  KDM6B MUTATED KDM6B WILD-TYPE
  0             6              51
  1             0               3
[1] 2 2
[1] FALSE
D616V7, binary
                 cls
clus               0  1
  KDM6B MUTATED    2  4
  KDM6B WILD-TYPE 49 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6B MUTATED      2    4
  KDM6B WILD-TYPE   49   71
        clus
vv       KDM6B MUTATED KDM6B WILD-TYPE
  FEMALE             2              49
  MALE               4              71
[1] 2 2
[1] FALSE
D616V8, binary
                 cls
clus               0  1
  KDM6B MUTATED    4  2
  KDM6B WILD-TYPE 84 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6B MUTATED      4    2
  KDM6B WILD-TYPE   84   28
     clus
vv    KDM6B MUTATED KDM6B WILD-TYPE
  NO              4              84
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KDM6B MUTATED                                     5
  KDM6B WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KDM6B MUTATED                                       1
  KDM6B WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KDM6B MUTATED                                                  0
  KDM6B WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  KDM6B MUTATED                                     0
  KDM6B WILD-TYPE                                   1
D616V9, multiclass
                                                  clus
vv                                                 KDM6B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 KDM6B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V10, continuous
D616V11, continuous
[1] "Remove cluster labels:" "KDM6B MUTATED"         
clus
  KDM6B MUTATED KDM6B WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-LB-A7SX 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KDM6B WILD-TYPE" "KDM6B WILD-TYPE" "KDM6B WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KDM6B MUTATED    4  2  0  0
  KDM6B WILD-TYPE 76 33  4  2
D616V12, multiclass
    clus
vv   KDM6B MUTATED KDM6B WILD-TYPE
  R0             4              76
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6B MUTATED       1                         1     4
  KDM6B WILD-TYPE     5                         4   110
D616V14, multiclass
                           clus
vv                          KDM6B MUTATED KDM6B WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V15, binary
                 cls
clus               0  1
  KDM6B MUTATED    0  4
  KDM6B WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6B MUTATED      0    4
  KDM6B WILD-TYPE    5   87
                        clus
vv                       KDM6B MUTATED KDM6B WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(617) Variable = LRRCC1 MUTATION ANALYSIS
D617V1, survival
                  sevent
clus2               0  1
  LRRCC1 MUTATED    1  4
  LRRCC1 WILD-TYPE 62 58
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               5              120 
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               4               58 
$`LRRCC1 MUTATED`
TCGA-2J-AABU TCGA-2L-AAQA TCGA-3A-A9IC TCGA-IB-7651 TCGA-Z5-AAPL 
        9.11         4.70        24.26        19.82        15.35 

$`LRRCC1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       14.47        15.22        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 

  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
            4.70             0.23 
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
           24.26            90.12 
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
          15.350           15.205 
[1] "4.7 - 24.3 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.9"
D617V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LRRCC1 MUTATED         0        0        0         1         4         0
  LRRCC1 WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  LRRCC1 MUTATED          0
  LRRCC1 WILD-TYPE        3
D617V3, multiclass
           clus
vv          LRRCC1 MUTATED LRRCC1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  LRRCC1 MUTATED    0  0     5
  LRRCC1 WILD-TYPE  5 17    97
D617V4, multiclass
       clus
vv      LRRCC1 MUTATED LRRCC1 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V5, binary
                  cls
clus                0  1
  LRRCC1 MUTATED    1  4
  LRRCC1 WILD-TYPE 34 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRCC1 MUTATED      1    4
  LRRCC1 WILD-TYPE   34   85
   clus
vv  LRRCC1 MUTATED LRRCC1 WILD-TYPE
  0              1               34
  1              4               85
[1] 2 2
[1] FALSE
D617V6, binary
                  cls
clus                0  1
  LRRCC1 MUTATED    3  0
  LRRCC1 WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRCC1 MUTATED      3    0
  LRRCC1 WILD-TYPE   54    3
   clus
vv  LRRCC1 MUTATED LRRCC1 WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D617V7, binary
                  cls
clus                0  1
  LRRCC1 MUTATED    3  2
  LRRCC1 WILD-TYPE 48 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRCC1 MUTATED      3    2
  LRRCC1 WILD-TYPE   48   73
        clus
vv       LRRCC1 MUTATED LRRCC1 WILD-TYPE
  FEMALE              3               48
  MALE                2               73
[1] 2 2
[1] FALSE
D617V8, binary
                  cls
clus                0  1
  LRRCC1 MUTATED    4  1
  LRRCC1 WILD-TYPE 84 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRCC1 MUTATED      4    1
  LRRCC1 WILD-TYPE   84   29
     clus
vv    LRRCC1 MUTATED LRRCC1 WILD-TYPE
  NO               4               84
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LRRCC1 MUTATED                                     5
  LRRCC1 WILD-TYPE                                 100
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LRRCC1 MUTATED                                       0
  LRRCC1 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LRRCC1 MUTATED                                                  0
  LRRCC1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  LRRCC1 MUTATED                                     0
  LRRCC1 WILD-TYPE                                   1
D617V9, multiclass
                                                  clus
vv                                                 LRRCC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 LRRCC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V10, continuous
[1] "Remove cluster labels:" "LRRCC1 MUTATED"        
clus
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-YY-A8LH 
"LRRCC1 WILD-TYPE" 
D617V11, continuous
[1] "Remove cluster labels:" "LRRCC1 MUTATED"        
clus
  LRRCC1 MUTATED LRRCC1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" "LRRCC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LRRCC1 MUTATED    4  1  0  0
  LRRCC1 WILD-TYPE 76 34  4  2
D617V12, multiclass
    clus
vv   LRRCC1 MUTATED LRRCC1 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LRRCC1 MUTATED       0                         0     5
  LRRCC1 WILD-TYPE     6                         5   109
D617V14, multiclass
                           clus
vv                          LRRCC1 MUTATED LRRCC1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V15, binary
                  cls
clus                0  1
  LRRCC1 MUTATED    0  3
  LRRCC1 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRCC1 MUTATED      0    3
  LRRCC1 WILD-TYPE    5   88
                        clus
vv                       LRRCC1 MUTATED LRRCC1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(618) Variable = ZNF285 MUTATION ANALYSIS
D618V1, survival
                  sevent
clus2               0  1
  ZNF285 MUTATED    2  2
  ZNF285 WILD-TYPE 61 60
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               4              121 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               2               60 
$`ZNF285 MUTATED`
TCGA-HZ-A77O TCGA-LB-A9Q5 TCGA-XN-A8T3 TCGA-YH-A8SY 
        5.26        10.29        31.27        12.76 

$`ZNF285 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
       10.85         0.23        19.82        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
        1.35         8.22        15.88         0.26         4.73         7.86 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV 
       14.17         6.02        11.11         7.40         8.05        13.28 
TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
        7.56        12.46         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        12.03        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF285 MUTATED ZNF285 WILD-TYPE 
            5.26             0.23 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
           31.27            90.12 
  ZNF285 MUTATED ZNF285 WILD-TYPE 
          11.525           15.320 
[1] "5.3 - 31.3 (11.5)" "0.2 - 90.1 (15.3)"
[1] "hr=" "1.2"
D618V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ZNF285 MUTATED         0        0        1         0         2         1
  ZNF285 WILD-TYPE       1        3       11        19        80         3
                  vv
clus               STAGE IV
  ZNF285 MUTATED          0
  ZNF285 WILD-TYPE        3
D618V3, multiclass
           clus
vv          ZNF285 MUTATED ZNF285 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ZNF285 MUTATED     0   2     2
  ZNF285 WILD-TYPE   5  15   100
D618V4, multiclass
       clus
vv      ZNF285 MUTATED ZNF285 WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V5, binary
                  cls
clus                0  1
  ZNF285 MUTATED    1  3
  ZNF285 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      1    3
  ZNF285 WILD-TYPE   34   86
   clus
vv  ZNF285 MUTATED ZNF285 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D618V6, binary
                  cls
clus                0  1
  ZNF285 MUTATED    1  0
  ZNF285 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      1    0
  ZNF285 WILD-TYPE   56    3
   clus
vv  ZNF285 MUTATED ZNF285 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D618V7, binary
                  cls
clus                0  1
  ZNF285 MUTATED    3  1
  ZNF285 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      3    1
  ZNF285 WILD-TYPE   48   74
        clus
vv       ZNF285 MUTATED ZNF285 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D618V8, binary
                  cls
clus                0  1
  ZNF285 MUTATED    1  3
  ZNF285 WILD-TYPE 87 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      1    3
  ZNF285 WILD-TYPE   87   27
     clus
vv    ZNF285 MUTATED ZNF285 WILD-TYPE
  NO               1               87
  YES              3               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF285 MUTATED                                     3
  ZNF285 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF285 MUTATED                                       0
  ZNF285 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF285 MUTATED                                                  0
  ZNF285 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ZNF285 MUTATED                                     0
  ZNF285 WILD-TYPE                                   1
D618V9, multiclass
                                                  clus
vv                                                 ZNF285 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ZNF285 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V10, continuous
[1] "Remove cluster labels:" "ZNF285 MUTATED"        
clus
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-8126 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-OE-A75W 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
D618V11, continuous
[1] "Remove cluster labels:" "ZNF285 MUTATED"        
clus
  ZNF285 MUTATED ZNF285 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7651 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" "ZNF285 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF285 MUTATED    2  1  0  0
  ZNF285 WILD-TYPE 78 34  4  2
D618V12, multiclass
    clus
vv   ZNF285 MUTATED ZNF285 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF285 MUTATED       0                         0     4
  ZNF285 WILD-TYPE     6                         5   110
D618V14, multiclass
                           clus
vv                          ZNF285 MUTATED ZNF285 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V15, binary
                  cls
clus                0  1
  ZNF285 MUTATED    1  3
  ZNF285 WILD-TYPE  4 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF285 MUTATED      1    3
  ZNF285 WILD-TYPE    4   88
                        clus
vv                       ZNF285 MUTATED ZNF285 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(619) Variable = RPS6KA5 MUTATION ANALYSIS
D619V1, survival
                   sevent
clus2                0  1
  RPS6KA5 MUTATED    2  2
  RPS6KA5 WILD-TYPE 61 60
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                4               121 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                2                60 
$`RPS6KA5 MUTATED`
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-IB-7651 TCGA-YY-A8LH 
       43.50        20.84        19.82        66.28 

$`RPS6KA5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9IB TCGA-3A-A9IC 
        3.39        12.95         9.60        45.47         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            19.82              0.23 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            66.28             90.12 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            32.17             15.12 
[1] "19.8 - 66.3 (32.2)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.8"
D619V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  RPS6KA5 MUTATED         0        0        0         1         3         0
  RPS6KA5 WILD-TYPE       1        3       12        18        79         4
                   vv
clus                STAGE IV
  RPS6KA5 MUTATED          0
  RPS6KA5 WILD-TYPE        3
D619V3, multiclass
           clus
vv          RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               1                18
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  RPS6KA5 MUTATED    0  0     4
  RPS6KA5 WILD-TYPE  5 17    98
D619V4, multiclass
       clus
vv      RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V5, binary
                   cls
clus                 0  1
  RPS6KA5 MUTATED    1  3
  RPS6KA5 WILD-TYPE 34 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      1    3
  RPS6KA5 WILD-TYPE   34   86
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               1                34
  1               3                86
[1] 2 2
[1] FALSE
D619V6, binary
                   cls
clus                 0  1
  RPS6KA5 MUTATED    1  0
  RPS6KA5 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      1    0
  RPS6KA5 WILD-TYPE   56    3
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D619V7, binary
                   cls
clus                 0  1
  RPS6KA5 MUTATED    2  2
  RPS6KA5 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      2    2
  RPS6KA5 WILD-TYPE   49   73
        clus
vv       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D619V8, binary
                   cls
clus                 0  1
  RPS6KA5 MUTATED    1  3
  RPS6KA5 WILD-TYPE 87 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      1    3
  RPS6KA5 WILD-TYPE   87   27
     clus
vv    RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  NO                1                87
  YES               3                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RPS6KA5 MUTATED                                     4
  RPS6KA5 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RPS6KA5 MUTATED                                       0
  RPS6KA5 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RPS6KA5 MUTATED                                                  0
  RPS6KA5 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  RPS6KA5 MUTATED                                     0
  RPS6KA5 WILD-TYPE                                   1
D619V9, multiclass
                                                  clus
vv                                                 RPS6KA5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 RPS6KA5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V10, continuous
D619V11, continuous
[1] "Remove cluster labels:" "RPS6KA5 MUTATED"       
clus
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5 
"RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" "RPS6KA5 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  RPS6KA5 MUTATED    4  0  0  0
  RPS6KA5 WILD-TYPE 76 35  4  2
D619V12, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA5 MUTATED       0                         1     3
  RPS6KA5 WILD-TYPE     6                         4   111
D619V14, multiclass
                           clus
vv                          RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V15, binary
                   cls
clus                 0  1
  RPS6KA5 MUTATED    0  4
  RPS6KA5 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      0    4
  RPS6KA5 WILD-TYPE    5   87
                        clus
vv                       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(620) Variable = ASB11 MUTATION ANALYSIS
D620V1, survival
                 sevent
clus2              0  1
  ASB11 MUTATED    2  1
  ASB11 WILD-TYPE 61 61
  ASB11 MUTATED ASB11 WILD-TYPE 
              3             122 
  ASB11 MUTATED ASB11 WILD-TYPE 
              1              61 
$`ASB11 MUTATED`
TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-7885 
        7.50        19.82        41.33 

$`ASB11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ASB11 MUTATED ASB11 WILD-TYPE 
           7.50            0.23 
  ASB11 MUTATED ASB11 WILD-TYPE 
          41.33           90.12 
  ASB11 MUTATED ASB11 WILD-TYPE 
         19.820          15.205 
[1] "7.5 - 41.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D620V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ASB11 MUTATED         0        0        0         0         3         0
  ASB11 WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  ASB11 MUTATED          0
  ASB11 WILD-TYPE        3
D620V3, multiclass
           clus
vv          ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ASB11 MUTATED     0   1     2
  ASB11 WILD-TYPE   5  16   100
D620V4, multiclass
       clus
vv      ASB11 MUTATED ASB11 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V5, binary
                 cls
clus               0  1
  ASB11 MUTATED    0  3
  ASB11 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      0    3
  ASB11 WILD-TYPE   35   86
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D620V6, binary
                 cls
clus               0  1
  ASB11 MUTATED    2  0
  ASB11 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      2    0
  ASB11 WILD-TYPE   55    3
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D620V7, binary
                 cls
clus               0  1
  ASB11 MUTATED    3  0
  ASB11 WILD-TYPE 48 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      3    0
  ASB11 WILD-TYPE   48   75
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             3              48
  MALE               0              75
[1] 2 2
[1] FALSE
D620V8, binary
                 cls
clus               0  1
  ASB11 MUTATED    2  1
  ASB11 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      2    1
  ASB11 WILD-TYPE   86   29
     clus
vv    ASB11 MUTATED ASB11 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASB11 MUTATED                                     3
  ASB11 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASB11 MUTATED                                       0
  ASB11 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASB11 MUTATED                                                  0
  ASB11 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ASB11 MUTATED                                     0
  ASB11 WILD-TYPE                                   1
D620V9, multiclass
                                                  clus
vv                                                 ASB11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ASB11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V10, continuous
D620V11, continuous
                 vv
clus              R0 R1 R2 RX
  ASB11 MUTATED    3  0  0  0
  ASB11 WILD-TYPE 77 35  4  2
D620V12, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASB11 MUTATED       0                         0     3
  ASB11 WILD-TYPE     6                         5   111
D620V14, multiclass
                           clus
vv                          ASB11 MUTATED ASB11 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V15, binary
                 cls
clus               0  1
  ASB11 MUTATED    0  3
  ASB11 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      0    3
  ASB11 WILD-TYPE    5   88
                        clus
vv                       ASB11 MUTATED ASB11 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(621) Variable = CCT8 MUTATION ANALYSIS
D621V1, survival
                sevent
clus2             0  1
  CCT8 MUTATED    1  3
  CCT8 WILD-TYPE 62 59
  CCT8 MUTATED CCT8 WILD-TYPE 
             4            121 
  CCT8 MUTATED CCT8 WILD-TYPE 
             3             59 
$`CCT8 MUTATED`
TCGA-3A-A9IJ TCGA-2L-AAQE TCGA-FZ-5923 TCGA-IB-7651 
       60.95        22.49        20.35        19.82 

$`CCT8 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5926 
        1.02        24.36         2.01         5.10        36.20        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CCT8 MUTATED CCT8 WILD-TYPE 
         19.82           0.23 
  CCT8 MUTATED CCT8 WILD-TYPE 
         60.95          90.12 
  CCT8 MUTATED CCT8 WILD-TYPE 
         21.42          15.12 
[1] "19.8 - 61.0 (21.4)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.1"
D621V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCT8 MUTATED         0        0        1         0         2         0
  CCT8 WILD-TYPE       1        3       11        19        80         4
                vv
clus             STAGE IV
  CCT8 MUTATED          1
  CCT8 WILD-TYPE        2
D621V3, multiclass
           clus
vv          CCT8 MUTATED CCT8 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             1             11
  STAGE IIA            0             19
  STAGE IIB            2             80
  STAGE III            0              4
  STAGE IV             1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  CCT8 MUTATED    0  1     3
  CCT8 WILD-TYPE  5 16    99
D621V4, multiclass
       clus
vv      CCT8 MUTATED CCT8 WILD-TYPE
  T1               0              5
  T2               1             16
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V5, binary
                cls
clus              0  1
  CCT8 MUTATED    1  3
  CCT8 WILD-TYPE 34 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT8 MUTATED      1    3
  CCT8 WILD-TYPE   34   86
   clus
vv  CCT8 MUTATED CCT8 WILD-TYPE
  0            1             34
  1            3             86
[1] 2 2
[1] FALSE
D621V6, binary
                cls
clus              0  1
  CCT8 MUTATED    2  1
  CCT8 WILD-TYPE 55  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT8 MUTATED      2    1
  CCT8 WILD-TYPE   55    2
   clus
vv  CCT8 MUTATED CCT8 WILD-TYPE
  0            2             55
  1            1              2
[1] 2 2
[1] FALSE
D621V7, binary
                cls
clus              0  1
  CCT8 MUTATED    1  3
  CCT8 WILD-TYPE 50 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT8 MUTATED      1    3
  CCT8 WILD-TYPE   50   72
        clus
vv       CCT8 MUTATED CCT8 WILD-TYPE
  FEMALE            1             50
  MALE              3             72
[1] 2 2
[1] FALSE
D621V8, binary
                cls
clus              0  1
  CCT8 MUTATED    4  0
  CCT8 WILD-TYPE 84 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT8 MUTATED      4    0
  CCT8 WILD-TYPE   84   30
     clus
vv    CCT8 MUTATED CCT8 WILD-TYPE
  NO             4             84
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCT8 MUTATED                                     3
  CCT8 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCT8 MUTATED                                       1
  CCT8 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCT8 MUTATED                                                  0
  CCT8 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCT8 MUTATED                                     0
  CCT8 WILD-TYPE                                   1
D621V9, multiclass
                                                  clus
vv                                                 CCT8 MUTATED CCT8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V10, continuous
D621V11, continuous
[1] "Remove cluster labels:" "CCT8 MUTATED"          
clus
  CCT8 MUTATED CCT8 WILD-TYPE 
             2             31 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR     TCGA-3A-A9IX 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ     TCGA-FB-AAPS 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"CCT8 WILD-TYPE" "CCT8 WILD-TYPE" "CCT8 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CCT8 MUTATED    4  0  0  0
  CCT8 WILD-TYPE 76 35  4  2
D621V12, multiclass
    clus
vv   CCT8 MUTATED CCT8 WILD-TYPE
  R0            4             76
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCT8 MUTATED       0                         0     4
  CCT8 WILD-TYPE     6                         5   110
D621V14, multiclass
                           clus
vv                          CCT8 MUTATED CCT8 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V15, binary
                cls
clus              0  1
  CCT8 MUTATED    0  3
  CCT8 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT8 MUTATED      0    3
  CCT8 WILD-TYPE    5   88
                        clus
vv                       CCT8 MUTATED CCT8 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(622) Variable = PSMB4 MUTATION ANALYSIS
D622V1, survival
                 sevent
clus2              0  1
  PSMB4 MUTATED    1  3
  PSMB4 WILD-TYPE 62 59
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              4             121 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              3              59 
$`PSMB4 MUTATED`
TCGA-2J-AABA TCGA-2L-AAQA TCGA-IB-A5SO TCGA-YY-A8LH 
       19.96         4.70        12.00        66.28 

$`PSMB4 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11        21.44        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  PSMB4 MUTATED PSMB4 WILD-TYPE 
           4.70            0.23 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
          66.28           90.12 
  PSMB4 MUTATED PSMB4 WILD-TYPE 
          15.98           15.22 
[1] "4.7 - 66.3 (16.0)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D622V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PSMB4 MUTATED         0        0        0         0         4         0
  PSMB4 WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  PSMB4 MUTATED          0
  PSMB4 WILD-TYPE        3
D622V3, multiclass
           clus
vv          PSMB4 MUTATED PSMB4 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PSMB4 MUTATED    0  0     4
  PSMB4 WILD-TYPE  5 17    98
D622V4, multiclass
       clus
vv      PSMB4 MUTATED PSMB4 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             4              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V5, binary
                 cls
clus               0  1
  PSMB4 MUTATED    0  4
  PSMB4 WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      0    4
  PSMB4 WILD-TYPE   35   85
   clus
vv  PSMB4 MUTATED PSMB4 WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D622V6, binary
                 cls
clus               0  1
  PSMB4 MUTATED    2  0
  PSMB4 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      2    0
  PSMB4 WILD-TYPE   55    3
   clus
vv  PSMB4 MUTATED PSMB4 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D622V7, binary
                 cls
clus               0  1
  PSMB4 MUTATED    1  3
  PSMB4 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      1    3
  PSMB4 WILD-TYPE   50   72
        clus
vv       PSMB4 MUTATED PSMB4 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D622V8, binary
                 cls
clus               0  1
  PSMB4 MUTATED    3  1
  PSMB4 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      3    1
  PSMB4 WILD-TYPE   85   29
     clus
vv    PSMB4 MUTATED PSMB4 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PSMB4 MUTATED                                     4
  PSMB4 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PSMB4 MUTATED                                       0
  PSMB4 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PSMB4 MUTATED                                                  0
  PSMB4 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PSMB4 MUTATED                                     0
  PSMB4 WILD-TYPE                                   1
D622V9, multiclass
                                                  clus
vv                                                 PSMB4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PSMB4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V10, continuous
D622V11, continuous
[1] "Remove cluster labels:" "PSMB4 MUTATED"         
clus
  PSMB4 MUTATED PSMB4 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7651 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5 
"PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" "PSMB4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PSMB4 MUTATED    2  2  0  0
  PSMB4 WILD-TYPE 78 33  4  2
D622V12, multiclass
    clus
vv   PSMB4 MUTATED PSMB4 WILD-TYPE
  R0             2              78
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSMB4 MUTATED       0                         0     4
  PSMB4 WILD-TYPE     6                         5   110
D622V14, multiclass
                           clus
vv                          PSMB4 MUTATED PSMB4 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V15, binary
                 cls
clus               0  1
  PSMB4 MUTATED    0  1
  PSMB4 WILD-TYPE  5 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB4 MUTATED      0    1
  PSMB4 WILD-TYPE    5   90
                        clus
vv                       PSMB4 MUTATED PSMB4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             1              90
[1] 2 2
[1] FALSE

Clustering(623) Variable = SIGLEC7 MUTATION ANALYSIS
D623V1, survival
                   sevent
clus2                0  1
  SIGLEC7 MUTATED    1  2
  SIGLEC7 WILD-TYPE 62 60
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                3               122 
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                2                60 
$`SIGLEC7 MUTATED`
TCGA-HV-AA8X TCGA-IB-7651 TCGA-YH-A8SY 
       17.49        19.82        12.76 

$`SIGLEC7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
            12.76              0.23 
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
            19.82             90.12 
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
           17.490            15.205 
[1] "12.8 - 19.8 (17.5)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D623V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SIGLEC7 MUTATED         0        0        0         0         2         1
  SIGLEC7 WILD-TYPE       1        3       12        19        80         3
                   vv
clus                STAGE IV
  SIGLEC7 MUTATED          0
  SIGLEC7 WILD-TYPE        3
D623V3, multiclass
           clus
vv          SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               2                80
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  SIGLEC7 MUTATED     0   1     2
  SIGLEC7 WILD-TYPE   5  16   100
D623V4, multiclass
       clus
vv      SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V5, binary
                   cls
clus                 0  1
  SIGLEC7 MUTATED    0  3
  SIGLEC7 WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC7 MUTATED      0    3
  SIGLEC7 WILD-TYPE   35   86
   clus
vv  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D623V6, binary
                   cls
clus                 0  1
  SIGLEC7 MUTATED    1  0
  SIGLEC7 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC7 MUTATED      1    0
  SIGLEC7 WILD-TYPE   56    3
   clus
vv  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D623V7, binary
                   cls
clus                 0  1
  SIGLEC7 MUTATED    3  0
  SIGLEC7 WILD-TYPE 48 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC7 MUTATED      3    0
  SIGLEC7 WILD-TYPE   48   75
        clus
vv       SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  FEMALE               3                48
  MALE                 0                75
[1] 2 2
[1] FALSE
D623V8, binary
                   cls
clus                 0  1
  SIGLEC7 MUTATED    2  1
  SIGLEC7 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC7 MUTATED      2    1
  SIGLEC7 WILD-TYPE   86   29
     clus
vv    SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIGLEC7 MUTATED                                     2
  SIGLEC7 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIGLEC7 MUTATED                                       0
  SIGLEC7 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIGLEC7 MUTATED                                                  0
  SIGLEC7 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SIGLEC7 MUTATED                                     0
  SIGLEC7 WILD-TYPE                                   1
D623V9, multiclass
[1] "Remove cluster labels:" "SIGLEC7 MUTATED"       
clus
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                2               123 
       TCGA-2J-AABR        TCGA-2J-AABT        TCGA-3A-A9I5        TCGA-3A-A9IJ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IL        TCGA-F2-A44G        TCGA-FB-AAQ6        TCGA-FZ-5924 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-S4-A8RO        TCGA-US-A77E        TCGA-XD-AAUL        TCGA-2J-AAB1 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AAB4        TCGA-2J-AAB6        TCGA-2J-AAB8        TCGA-2J-AAB9 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABK        TCGA-2J-AABO        TCGA-2J-AABP        TCGA-2J-AABU 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-2L-AAQI 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2L-AAQJ        TCGA-2L-AAQL        TCGA-2L-AAQM        TCGA-3A-A9I7 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IC        TCGA-3A-A9IH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IO        TCGA-3A-A9IR        TCGA-3A-A9IS        TCGA-3A-A9IU 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IV        TCGA-3A-A9IX        TCGA-3A-A9IZ        TCGA-3A-A9J0 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3E-AAAY        TCGA-3E-AAAZ        TCGA-F2-7273        TCGA-F2-A7TX 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPP 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-FB-AAPU        TCGA-FB-AAPZ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAQ0        TCGA-FB-AAQ1        TCGA-FB-AAQ2        TCGA-FB-AAQ3 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FZ-5919        TCGA-FZ-5920        TCGA-FZ-5921        TCGA-FZ-5922 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FZ-5923        TCGA-FZ-5926        TCGA-H8-A6C1        TCGA-HV-A7OL 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HV-A7OP        TCGA-HV-AA8V        TCGA-HZ-7918        TCGA-HZ-7925 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-8637        TCGA-HZ-A49I        TCGA-HZ-A77O        TCGA-HZ-A77P 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-HZ-A9TJ        TCGA-IB-7652        TCGA-IB-7885 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SO        TCGA-IB-A5SP        TCGA-IB-A5SQ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-A5ST        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7LX 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUM        TCGA-IB-AAUN        TCGA-IB-AAUO 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUP        TCGA-IB-AAUQ        TCGA-IB-AAUR        TCGA-IB-AAUS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-IB-AAUW        TCGA-LB-A8F3 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-Q3-A5QY        TCGA-Q3-AA2A 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-RB-A7B8        TCGA-RB-AA9M        TCGA-RL-AAAS        TCGA-US-A776 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-US-A779        TCGA-US-A77G        TCGA-US-A77J        TCGA-XD-AAUG 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-XD-AAUH        TCGA-XD-AAUI        TCGA-XN-A8T3        TCGA-XN-A8T5 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-YB-A89D        TCGA-YY-A8LH        TCGA-Z5-AAPL 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
D623V10, continuous
[1] "Remove cluster labels:" "SIGLEC7 MUTATED"       
clus
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                1                38 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-XN-A8T5        TCGA-YY-A8LH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
D623V11, continuous
[1] "Remove cluster labels:" "SIGLEC7 MUTATED"       
clus
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                1                32 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SIGLEC7 MUTATED    1  0  1  0
  SIGLEC7 WILD-TYPE 79 35  3  2
D623V12, multiclass
[1] "Remove cluster labels:" "SIGLEC7 MUTATED"       
clus
  SIGLEC7 MUTATED SIGLEC7 WILD-TYPE 
                2               119 
       TCGA-2J-AABR        TCGA-2J-AABT        TCGA-3A-A9I5        TCGA-3A-A9IJ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IL        TCGA-F2-A44G        TCGA-FB-AAQ6        TCGA-FZ-5924 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS        TCGA-LB-A7SX 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-S4-A8RO        TCGA-US-A77E        TCGA-XD-AAUL        TCGA-2J-AAB1 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AAB4        TCGA-2J-AAB6        TCGA-2J-AAB8        TCGA-2J-AAB9 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABK        TCGA-2J-AABO        TCGA-2J-AABP        TCGA-2J-AABU 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-2L-AAQI 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-2L-AAQJ        TCGA-2L-AAQL        TCGA-2L-AAQM        TCGA-3A-A9I7 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IC        TCGA-3A-A9IH 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IO        TCGA-3A-A9IR        TCGA-3A-A9IS        TCGA-3A-A9IU 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-3A-A9IV        TCGA-3A-A9IX        TCGA-3A-A9IZ        TCGA-3A-A9J0 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-F2-7273        TCGA-F2-A7TX        TCGA-F2-A8YN        TCGA-FB-A5VM 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-A78T        TCGA-FB-AAPP        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAPU        TCGA-FB-AAPZ        TCGA-FB-AAQ0        TCGA-FB-AAQ1 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FB-AAQ2        TCGA-FB-AAQ3        TCGA-FZ-5920        TCGA-FZ-5922 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-FZ-5923        TCGA-FZ-5926        TCGA-H8-A6C1        TCGA-HV-A7OL 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HV-A7OP        TCGA-HV-AA8V        TCGA-HZ-7918        TCGA-HZ-7925 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-8637        TCGA-HZ-A49I        TCGA-HZ-A77O        TCGA-HZ-A77P 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-HZ-A9TJ        TCGA-IB-7652        TCGA-IB-7885 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SO        TCGA-IB-A5SP        TCGA-IB-A5SQ 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-A5ST        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7LX 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUM        TCGA-IB-AAUN        TCGA-IB-AAUO 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUP        TCGA-IB-AAUQ        TCGA-IB-AAUR        TCGA-IB-AAUS 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-IB-AAUU        TCGA-IB-AAUV        TCGA-IB-AAUW        TCGA-LB-A8F3 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-Q3-A5QY        TCGA-Q3-AA2A 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-RB-A7B8        TCGA-RB-AA9M        TCGA-RL-AAAS        TCGA-US-A776 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-US-A779        TCGA-US-A77G        TCGA-US-A77J        TCGA-XD-AAUG 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-XD-AAUH        TCGA-XD-AAUI        TCGA-XN-A8T3        TCGA-XN-A8T5 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
       TCGA-YB-A89D        TCGA-YY-A8LH        TCGA-Z5-AAPL 
"SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" "SIGLEC7 WILD-TYPE" 
D623V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC7 MUTATED       1                         0     2
  SIGLEC7 WILD-TYPE     5                         5   112
D623V14, multiclass
                           clus
vv                          SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   2               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V15, binary
                   cls
clus                 0  1
  SIGLEC7 MUTATED    0  2
  SIGLEC7 WILD-TYPE  5 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SIGLEC7 MUTATED      0    2
  SIGLEC7 WILD-TYPE    5   89
                        clus
vv                       SIGLEC7 MUTATED SIGLEC7 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2                89
[1] 2 2
[1] FALSE

Clustering(624) Variable = ATP2B3 MUTATION ANALYSIS
D624V1, survival
                  sevent
clus2               0  1
  ATP2B3 MUTATED    2  1
  ATP2B3 WILD-TYPE 61 61
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
               3              122 
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
               1               61 
$`ATP2B3 MUTATED`
TCGA-FB-AAPS TCGA-IB-7651 TCGA-IB-AAUS 
        7.50        19.82         7.40 

$`ATP2B3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       15.95        37.15        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
        6.02        11.11         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
            7.40             0.23 
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
           19.82            90.12 
  ATP2B3 MUTATED ATP2B3 WILD-TYPE 
            7.50            15.27 
[1] "7.4 - 19.8 (7.5)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "1.1"
D624V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ATP2B3 MUTATED         0        0        0         0         3         0
  ATP2B3 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  ATP2B3 MUTATED          0
  ATP2B3 WILD-TYPE        3
D624V3, multiclass
           clus
vv          ATP2B3 MUTATED ATP2B3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  ATP2B3 MUTATED     0   1     2
  ATP2B3 WILD-TYPE   5  16   100
D624V4, multiclass
       clus
vv      ATP2B3 MUTATED ATP2B3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V5, binary
                  cls
clus                0  1
  ATP2B3 MUTATED    0  3
  ATP2B3 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B3 MUTATED      0    3
  ATP2B3 WILD-TYPE   35   86
   clus
vv  ATP2B3 MUTATED ATP2B3 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D624V6, binary
                  cls
clus                0  1
  ATP2B3 MUTATED    2  0
  ATP2B3 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B3 MUTATED      2    0
  ATP2B3 WILD-TYPE   55    3
   clus
vv  ATP2B3 MUTATED ATP2B3 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D624V7, binary
                  cls
clus                0  1
  ATP2B3 MUTATED    3  0
  ATP2B3 WILD-TYPE 48 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B3 MUTATED      3    0
  ATP2B3 WILD-TYPE   48   75
        clus
vv       ATP2B3 MUTATED ATP2B3 WILD-TYPE
  FEMALE              3               48
  MALE                0               75
[1] 2 2
[1] FALSE
D624V8, binary
                  cls
clus                0  1
  ATP2B3 MUTATED    2  1
  ATP2B3 WILD-TYPE 86 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B3 MUTATED      2    1
  ATP2B3 WILD-TYPE   86   29
     clus
vv    ATP2B3 MUTATED ATP2B3 WILD-TYPE
  NO               2               86
  YES              1               29
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2B3 MUTATED                                     3
  ATP2B3 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2B3 MUTATED                                       0
  ATP2B3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2B3 MUTATED                                                  0
  ATP2B3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ATP2B3 MUTATED                                     0
  ATP2B3 WILD-TYPE                                   1
D624V9, multiclass
                                                  clus
vv                                                 ATP2B3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ATP2B3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V10, continuous
D624V11, continuous
                  vv
clus               R0 R1 R2 RX
  ATP2B3 MUTATED    2  1  0  0
  ATP2B3 WILD-TYPE 78 34  4  2
D624V12, multiclass
    clus
vv   ATP2B3 MUTATED ATP2B3 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2B3 MUTATED       0                         0     3
  ATP2B3 WILD-TYPE     6                         5   111
D624V14, multiclass
                           clus
vv                          ATP2B3 MUTATED ATP2B3 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V15, binary
                  cls
clus                0  1
  ATP2B3 MUTATED    0  3
  ATP2B3 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B3 MUTATED      0    3
  ATP2B3 WILD-TYPE    5   88
                        clus
vv                       ATP2B3 MUTATED ATP2B3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(625) Variable = CCDC130 MUTATION ANALYSIS
D625V1, survival
                   sevent
clus2                0  1
  CCDC130 MUTATED    3  1
  CCDC130 WILD-TYPE 60 61
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                4               121 
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                1                61 
$`CCDC130 MUTATED`
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-IB-7651 TCGA-Z5-AAPL 
       36.26        34.09        19.82        15.35 

$`CCDC130 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       15.06        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  CCDC130 MUTATED CCDC130 WILD-TYPE 
            15.35              0.23 
  CCDC130 MUTATED CCDC130 WILD-TYPE 
            36.26             90.12 
  CCDC130 MUTATED CCDC130 WILD-TYPE 
           26.955            15.120 
[1] "15.3 - 36.3 (27.0)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "3"  
D625V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC130 MUTATED         0        1        1         1         1         0
  CCDC130 WILD-TYPE       1        2       11        18        81         4
                   vv
clus                STAGE IV
  CCDC130 MUTATED          0
  CCDC130 WILD-TYPE        3
D625V3, multiclass
           clus
vv          CCDC130 MUTATED CCDC130 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                1                11
  STAGE IIA               1                18
  STAGE IIB               1                81
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  CCDC130 MUTATED     1   1     2
  CCDC130 WILD-TYPE   4  16   100
D625V4, multiclass
       clus
vv      CCDC130 MUTATED CCDC130 WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V5, binary
                   cls
clus                 0  1
  CCDC130 MUTATED    3  1
  CCDC130 WILD-TYPE 32 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC130 MUTATED      3    1
  CCDC130 WILD-TYPE   32   88
   clus
vv  CCDC130 MUTATED CCDC130 WILD-TYPE
  0               3                32
  1               1                88
[1] 2 2
[1] FALSE
D625V6, binary
                   cls
clus                 0  1
  CCDC130 MUTATED    2  0
  CCDC130 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC130 MUTATED      2    0
  CCDC130 WILD-TYPE   55    3
   clus
vv  CCDC130 MUTATED CCDC130 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D625V7, binary
                   cls
clus                 0  1
  CCDC130 MUTATED    3  1
  CCDC130 WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC130 MUTATED      3    1
  CCDC130 WILD-TYPE   48   74
        clus
vv       CCDC130 MUTATED CCDC130 WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D625V8, binary
                   cls
clus                 0  1
  CCDC130 MUTATED    3  1
  CCDC130 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC130 MUTATED      3    1
  CCDC130 WILD-TYPE   85   29
     clus
vv    CCDC130 MUTATED CCDC130 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC130 MUTATED                                     3
  CCDC130 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC130 MUTATED                                       1
  CCDC130 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC130 MUTATED                                                  0
  CCDC130 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC130 MUTATED                                     0
  CCDC130 WILD-TYPE                                   1
D625V9, multiclass
                                                  clus
vv                                                 CCDC130 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC130 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V10, continuous
[1] "Remove cluster labels:" "CCDC130 MUTATED"       
clus
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-YY-A8LH 
"CCDC130 WILD-TYPE" 
D625V11, continuous
[1] "Remove cluster labels:" "CCDC130 MUTATED"       
clus
  CCDC130 MUTATED CCDC130 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" "CCDC130 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC130 MUTATED    4  0  0  0
  CCDC130 WILD-TYPE 76 35  4  2
D625V12, multiclass
    clus
vv   CCDC130 MUTATED CCDC130 WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC130 MUTATED       0                         0     4
  CCDC130 WILD-TYPE     6                         5   110
D625V14, multiclass
                           clus
vv                          CCDC130 MUTATED CCDC130 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V15, binary
                   cls
clus                 0  1
  CCDC130 MUTATED    0  4
  CCDC130 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC130 MUTATED      0    4
  CCDC130 WILD-TYPE    5   87
                        clus
vv                       CCDC130 MUTATED CCDC130 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(626) Variable = BAT2 MUTATION ANALYSIS
D626V1, survival
                sevent
clus2             0  1
  BAT2 MUTATED    2  4
  BAT2 WILD-TYPE 61 58
  BAT2 MUTATED BAT2 WILD-TYPE 
             6            119 
  BAT2 MUTATED BAT2 WILD-TYPE 
             4             58 
$`BAT2 MUTATED`
TCGA-2J-AABR TCGA-F2-A8YN TCGA-FB-AAPQ TCGA-FZ-5926 TCGA-IB-7651 TCGA-RB-A7B8 
       14.40        17.00        37.15        17.79        19.82        15.32 

$`BAT2 WILD-TYPE`
TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       10.49        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPS 
       19.46         3.12        16.37        12.33        15.95         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 
       24.36         2.01         5.10        36.20        20.35        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 
       13.68         3.12         9.40         0.30        39.98        16.80 
TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 
        0.39        18.67        13.81        12.99        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  BAT2 MUTATED BAT2 WILD-TYPE 
         14.40           0.23 
  BAT2 MUTATED BAT2 WILD-TYPE 
         37.15          90.12 
  BAT2 MUTATED BAT2 WILD-TYPE 
        17.395         15.120 
[1] "14.4 - 37.1 (17.4)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.1"
D626V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  BAT2 MUTATED         0        0        0         2         3         1
  BAT2 WILD-TYPE       1        3       12        17        79         3
                vv
clus             STAGE IV
  BAT2 MUTATED          0
  BAT2 WILD-TYPE        3
D626V3, multiclass
           clus
vv          BAT2 MUTATED BAT2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            2             17
  STAGE IIB            3             79
  STAGE III            1              3
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  BAT2 MUTATED    0  0     6
  BAT2 WILD-TYPE  5 17    96
D626V4, multiclass
       clus
vv      BAT2 MUTATED BAT2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            6             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V5, binary
                cls
clus              0  1
  BAT2 MUTATED    2  4
  BAT2 WILD-TYPE 33 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT2 MUTATED      2    4
  BAT2 WILD-TYPE   33   85
   clus
vv  BAT2 MUTATED BAT2 WILD-TYPE
  0            2             33
  1            4             85
[1] 2 2
[1] FALSE
D626V6, binary
                cls
clus              0  1
  BAT2 MUTATED    4  0
  BAT2 WILD-TYPE 53  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT2 MUTATED      4    0
  BAT2 WILD-TYPE   53    3
   clus
vv  BAT2 MUTATED BAT2 WILD-TYPE
  0            4             53
  1            0              3
[1] 2 2
[1] FALSE
D626V7, binary
                cls
clus              0  1
  BAT2 MUTATED    4  2
  BAT2 WILD-TYPE 47 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT2 MUTATED      4    2
  BAT2 WILD-TYPE   47   73
        clus
vv       BAT2 MUTATED BAT2 WILD-TYPE
  FEMALE            4             47
  MALE              2             73
[1] 2 2
[1] FALSE
D626V8, binary
                cls
clus              0  1
  BAT2 MUTATED    6  0
  BAT2 WILD-TYPE 82 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT2 MUTATED      6    0
  BAT2 WILD-TYPE   82   30
     clus
vv    BAT2 MUTATED BAT2 WILD-TYPE
  NO             6             82
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BAT2 MUTATED                                     5
  BAT2 WILD-TYPE                                 100
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BAT2 MUTATED                                       1
  BAT2 WILD-TYPE                                    17
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BAT2 MUTATED                                                  0
  BAT2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  BAT2 MUTATED                                     0
  BAT2 WILD-TYPE                                   1
D626V9, multiclass
                                                  clus
vv                                                 BAT2 MUTATED BAT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V10, continuous
D626V11, continuous
[1] "Remove cluster labels:" "BAT2 MUTATED"          
clus
  BAT2 MUTATED BAT2 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"BAT2 WILD-TYPE" "BAT2 WILD-TYPE" "BAT2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BAT2 MUTATED    5  1  0  0
  BAT2 WILD-TYPE 75 34  4  2
D626V12, multiclass
    clus
vv   BAT2 MUTATED BAT2 WILD-TYPE
  R0            5             75
  R1            1             34
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAT2 MUTATED       0                         0     6
  BAT2 WILD-TYPE     6                         5   108
D626V14, multiclass
                           clus
vv                          BAT2 MUTATED BAT2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V15, binary
                cls
clus              0  1
  BAT2 MUTATED    0  5
  BAT2 WILD-TYPE  5 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAT2 MUTATED      0    5
  BAT2 WILD-TYPE    5   86
                        clus
vv                       BAT2 MUTATED BAT2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5             86
[1] 2 2
[1] FALSE

Clustering(627) Variable = STARD3 MUTATION ANALYSIS
D627V1, survival
                  sevent
clus2               0  1
  STARD3 MUTATED    1  2
  STARD3 WILD-TYPE 62 60
  STARD3 MUTATED STARD3 WILD-TYPE 
               3              122 
  STARD3 MUTATED STARD3 WILD-TYPE 
               2               60 
$`STARD3 MUTATED`
TCGA-3A-A9IZ TCGA-HV-AA8X TCGA-IB-A5ST 
       10.13        17.49        20.88 

$`STARD3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        36.26        34.09        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
        0.23        19.82        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  STARD3 MUTATED STARD3 WILD-TYPE 
           10.13             0.23 
  STARD3 MUTATED STARD3 WILD-TYPE 
           20.88            90.12 
  STARD3 MUTATED STARD3 WILD-TYPE 
          17.490           15.205 
[1] "10.1 - 20.9 (17.5)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.3"
D627V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  STARD3 MUTATED         0        0        0         0         3         0
  STARD3 WILD-TYPE       1        3       12        19        79         4
                  vv
clus               STAGE IV
  STARD3 MUTATED          0
  STARD3 WILD-TYPE        3
D627V3, multiclass
           clus
vv          STARD3 MUTATED STARD3 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  STARD3 MUTATED     0   1     2
  STARD3 WILD-TYPE   5  16   100
D627V4, multiclass
       clus
vv      STARD3 MUTATED STARD3 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V5, binary
                  cls
clus                0  1
  STARD3 MUTATED    0  3
  STARD3 WILD-TYPE 35 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STARD3 MUTATED      0    3
  STARD3 WILD-TYPE   35   86
   clus
vv  STARD3 MUTATED STARD3 WILD-TYPE
  0              0               35
  1              3               86
[1] 2 2
[1] FALSE
D627V6, binary
                  cls
clus                0  1
  STARD3 MUTATED    1  0
  STARD3 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STARD3 MUTATED      1    0
  STARD3 WILD-TYPE   56    3
   clus
vv  STARD3 MUTATED STARD3 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D627V7, binary
                  cls
clus                0  1
  STARD3 MUTATED    2  1
  STARD3 WILD-TYPE 49 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STARD3 MUTATED      2    1
  STARD3 WILD-TYPE   49   74
        clus
vv       STARD3 MUTATED STARD3 WILD-TYPE
  FEMALE              2               49
  MALE                1               74
[1] 2 2
[1] FALSE
D627V8, binary
                  cls
clus                0  1
  STARD3 MUTATED    3  0
  STARD3 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STARD3 MUTATED      3    0
  STARD3 WILD-TYPE   85   30
     clus
vv    STARD3 MUTATED STARD3 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STARD3 MUTATED                                     3
  STARD3 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STARD3 MUTATED                                       0
  STARD3 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STARD3 MUTATED                                                  0
  STARD3 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  STARD3 MUTATED                                     0
  STARD3 WILD-TYPE                                   1
D627V9, multiclass
                                                  clus
vv                                                 STARD3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 STARD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V10, continuous
D627V11, continuous
                  vv
clus               R0 R1 R2 RX
  STARD3 MUTATED    1  1  1  0
  STARD3 WILD-TYPE 79 34  3  2
D627V12, multiclass
    clus
vv   STARD3 MUTATED STARD3 WILD-TYPE
  R0              1               79
  R1              1               34
  R2              1                3
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STARD3 MUTATED       1                         0     2
  STARD3 WILD-TYPE     5                         5   112
D627V14, multiclass
                           clus
vv                          STARD3 MUTATED STARD3 WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V15, binary
                  cls
clus                0  1
  STARD3 MUTATED    1  1
  STARD3 WILD-TYPE  4 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STARD3 MUTATED      1    1
  STARD3 WILD-TYPE    4   90
                        clus
vv                       STARD3 MUTATED STARD3 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              1               90
[1] 2 2
[1] FALSE

Clustering(628) Variable = C16ORF70 MUTATION ANALYSIS
D628V1, survival
                    sevent
clus2                 0  1
  C16ORF70 MUTATED    1  3
  C16ORF70 WILD-TYPE 62 59
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 4                121 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 3                 59 
$`C16ORF70 MUTATED`
TCGA-3A-A9I9 TCGA-HZ-8637 TCGA-IB-7651 TCGA-YH-A8SY 
       20.84        17.00        19.82        12.76 

$`C16ORF70 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9IB 
        3.39        12.95         9.60        45.47        43.50         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       17.49        31.86        20.19        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             12.76               0.23 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             20.84              90.12 
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
             18.41              15.19 
[1] "12.8 - 20.8 (18.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D628V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  C16ORF70 MUTATED         0        0        0         1         2         1
  C16ORF70 WILD-TYPE       1        3       12        18        80         3
                    vv
clus                 STAGE IV
  C16ORF70 MUTATED          0
  C16ORF70 WILD-TYPE        3
D628V3, multiclass
           clus
vv          C16ORF70 MUTATED C16ORF70 WILD-TYPE
  STAGE I                  0                  1
  STAGE IA                 0                  3
  STAGE IB                 0                 12
  STAGE IIA                1                 18
  STAGE IIB                2                 80
  STAGE III                1                  3
  STAGE IV                 0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3+T4
  C16ORF70 MUTATED    0  0     4
  C16ORF70 WILD-TYPE  5 17    98
D628V4, multiclass
       clus
vv      C16ORF70 MUTATED C16ORF70 WILD-TYPE
  T1                   0                  5
  T2                   0                 17
  T3+T4                4                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V5, binary
                    cls
clus                  0  1
  C16ORF70 MUTATED    1  3
  C16ORF70 WILD-TYPE 34 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    3
  C16ORF70 WILD-TYPE   34   86
   clus
vv  C16ORF70 MUTATED C16ORF70 WILD-TYPE
  0                1                 34
  1                3                 86
[1] 2 2
[1] FALSE
D628V6, binary
                    cls
clus                  0  1
  C16ORF70 MUTATED    1  0
  C16ORF70 WILD-TYPE 56  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    0
  C16ORF70 WILD-TYPE   56    3
   clus
vv  C16ORF70 MUTATED C16ORF70 WILD-TYPE
  0                1                 56
  1                0                  3
[1] 2 2
[1] FALSE
D628V7, binary
                    cls
clus                  0  1
  C16ORF70 MUTATED    3  1
  C16ORF70 WILD-TYPE 48 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      3    1
  C16ORF70 WILD-TYPE   48   74
        clus
vv       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  FEMALE                3                 48
  MALE                  1                 74
[1] 2 2
[1] FALSE
D628V8, binary
                    cls
clus                  0  1
  C16ORF70 MUTATED    1  3
  C16ORF70 WILD-TYPE 87 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    3
  C16ORF70 WILD-TYPE   87   27
     clus
vv    C16ORF70 MUTATED C16ORF70 WILD-TYPE
  NO                 1                 87
  YES                3                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C16ORF70 MUTATED                                     3
  C16ORF70 WILD-TYPE                                 102
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C16ORF70 MUTATED                                       0
  C16ORF70 WILD-TYPE                                    18
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C16ORF70 MUTATED                                                  0
  C16ORF70 WILD-TYPE                                                1
                    vv
clus                 PANCREAS-UNDIFFERENTIATED CARCINOMA
  C16ORF70 MUTATED                                     0
  C16ORF70 WILD-TYPE                                   1
D628V9, multiclass
                                                  clus
vv                                                 C16ORF70 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             0
                                                  clus
vv                                                 C16ORF70 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V10, continuous
[1] "Remove cluster labels:" "C16ORF70 MUTATED"      
clus
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 2                 37 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9IB 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-F2-A8YN         TCGA-FB-A5VM 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPQ         TCGA-FB-AAPS 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HV-AA8V         TCGA-HZ-A8P1 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A6UF 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUU         TCGA-IB-AAUV 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XN-A8T5 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-YY-A8LH 
"C16ORF70 WILD-TYPE" 
D628V11, continuous
[1] "Remove cluster labels:" "C16ORF70 MUTATED"      
clus
  C16ORF70 MUTATED C16ORF70 WILD-TYPE 
                 1                 32 
        TCGA-3A-A9IJ         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-LB-A7SX         TCGA-XD-AAUL 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IR 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-3A-A9IX         TCGA-FB-A5VM         TCGA-FB-A78T 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-FB-AAPQ         TCGA-FB-AAPS         TCGA-H8-A6C1 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7885         TCGA-IB-8126 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-A6UF         TCGA-IB-A6UG         TCGA-IB-A7M4 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-IB-AAUQ         TCGA-IB-AAUS         TCGA-IB-AAUV 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-XD-AAUI 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C16ORF70 WILD-TYPE" "C16ORF70 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C16ORF70 MUTATED    3  0  0  0
  C16ORF70 WILD-TYPE 77 35  4  2
D628V12, multiclass
    clus
vv   C16ORF70 MUTATED C16ORF70 WILD-TYPE
  R0                3                 77
  R1                0                 35
  R2                0                  4
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C16ORF70 MUTATED       0                         0     4
  C16ORF70 WILD-TYPE     6                         5   110
D628V14, multiclass
                           clus
vv                          C16ORF70 MUTATED C16ORF70 WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V15, binary
                    cls
clus                  0  1
  C16ORF70 MUTATED    1  3
  C16ORF70 WILD-TYPE  4 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF70 MUTATED      1    3
  C16ORF70 WILD-TYPE    4   88
                        clus
vv                       C16ORF70 MUTATED C16ORF70 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                3                 88
[1] 2 2
[1] FALSE

Clustering(629) Variable = FBXW7 MUTATION ANALYSIS
D629V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    2  3
  FBXW7 WILD-TYPE 61 59
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              5             120 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              3              59 
$`FBXW7 MUTATED`
TCGA-2J-AABT TCGA-LB-A7SX TCGA-2J-AABA TCGA-HZ-7918 TCGA-IB-7651 
       10.49        12.92        19.96        31.86        19.82 

$`FBXW7 WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        58.98        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78         1.08        15.12        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABE 
        2.17        23.97         9.63         2.63        20.61        22.22 
TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.72        42.31        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 
       22.06         8.28        32.15        30.25        17.49        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
          10.49            0.23 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          31.86           90.12 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         19.820          15.205 
[1] "10.5 - 31.9 (19.8)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.1"
D629V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  FBXW7 MUTATED         0        0        0         0         5         0
  FBXW7 WILD-TYPE       1        3       12        19        77         4
                 vv
clus              STAGE IV
  FBXW7 MUTATED          0
  FBXW7 WILD-TYPE        3
D629V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             5              77
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  FBXW7 MUTATED    0  0     5
  FBXW7 WILD-TYPE  5 17    97
D629V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             5              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V5, binary
                 cls
clus               0  1
  FBXW7 MUTATED    0  5
  FBXW7 WILD-TYPE 35 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0    5
  FBXW7 WILD-TYPE   35   84
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             0              35
  1             5              84
[1] 2 2
[1] FALSE
D629V6, binary
                 cls
clus               0  1
  FBXW7 MUTATED    4  0
  FBXW7 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      4    0
  FBXW7 WILD-TYPE   53    3
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D629V7, binary
                 cls
clus               0  1
  FBXW7 MUTATED    3  2
  FBXW7 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      3    2
  FBXW7 WILD-TYPE   48   73
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D629V8, binary
                 cls
clus               0  1
  FBXW7 MUTATED    3  1
  FBXW7 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      3    1
  FBXW7 WILD-TYPE   85   29
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FBXW7 MUTATED                                     5
  FBXW7 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FBXW7 MUTATED                                       0
  FBXW7 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FBXW7 MUTATED                                                  0
  FBXW7 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  FBXW7 MUTATED                                     0
  FBXW7 WILD-TYPE                                   1
D629V9, multiclass
                                                  clus
vv                                                 FBXW7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 FBXW7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V10, continuous
D629V11, continuous
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR      TCGA-3A-A9IX 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  FBXW7 MUTATED    3  2  0  0
  FBXW7 WILD-TYPE 77 33  4  2
D629V12, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0             3              77
  R1             2              33
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       0                         1     4
  FBXW7 WILD-TYPE     6                         4   110
D629V14, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V15, binary
                 cls
clus               0  1
  FBXW7 MUTATED    0  3
  FBXW7 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0    3
  FBXW7 WILD-TYPE    5   88
                        clus
vv                       FBXW7 MUTATED FBXW7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(630) Variable = LATS1 MUTATION ANALYSIS
D630V1, survival
                 sevent
clus2              0  1
  LATS1 MUTATED    2  3
  LATS1 WILD-TYPE 61 59
  LATS1 MUTATED LATS1 WILD-TYPE 
              5             120 
  LATS1 MUTATED LATS1 WILD-TYPE 
              3              59 
$`LATS1 MUTATED`
TCGA-3A-A9I5 TCGA-FB-A5VM TCGA-FB-AAQ3 TCGA-IB-7651 TCGA-XN-A8T5 
       58.98        16.37         1.02        19.82        23.67 

$`LATS1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        11.51        12.76        66.28        15.35 

  LATS1 MUTATED LATS1 WILD-TYPE 
           1.02            0.23 
  LATS1 MUTATED LATS1 WILD-TYPE 
          58.98           90.12 
  LATS1 MUTATED LATS1 WILD-TYPE 
         19.820          15.155 
[1] "1.0 - 59.0 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D630V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LATS1 MUTATED         0        0        2         0         2         0
  LATS1 WILD-TYPE       1        3       10        19        80         4
                 vv
clus              STAGE IV
  LATS1 MUTATED          0
  LATS1 WILD-TYPE        3
D630V3, multiclass
           clus
vv          LATS1 MUTATED LATS1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  LATS1 MUTATED     0   2     2
  LATS1 WILD-TYPE   5  15   100
D630V4, multiclass
       clus
vv      LATS1 MUTATED LATS1 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V5, binary
                 cls
clus               0  1
  LATS1 MUTATED    3  2
  LATS1 WILD-TYPE 32 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      3    2
  LATS1 WILD-TYPE   32   87
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0             3              32
  1             2              87
[1] 2 2
[1] FALSE
D630V6, binary
                 cls
clus               0  1
  LATS1 MUTATED    3  0
  LATS1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      3    0
  LATS1 WILD-TYPE   54    3
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D630V7, binary
                 cls
clus               0  1
  LATS1 MUTATED    3  2
  LATS1 WILD-TYPE 48 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      3    2
  LATS1 WILD-TYPE   48   73
        clus
vv       LATS1 MUTATED LATS1 WILD-TYPE
  FEMALE             3              48
  MALE               2              73
[1] 2 2
[1] FALSE
D630V8, binary
                 cls
clus               0  1
  LATS1 MUTATED    3  2
  LATS1 WILD-TYPE 85 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      3    2
  LATS1 WILD-TYPE   85   28
     clus
vv    LATS1 MUTATED LATS1 WILD-TYPE
  NO              3              85
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LATS1 MUTATED                                     4
  LATS1 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LATS1 MUTATED                                       1
  LATS1 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LATS1 MUTATED                                                  0
  LATS1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  LATS1 MUTATED                                     0
  LATS1 WILD-TYPE                                   1
D630V9, multiclass
                                                  clus
vv                                                 LATS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 LATS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V10, continuous
D630V11, continuous
                 vv
clus              R0 R1 R2 RX
  LATS1 MUTATED    4  1  0  0
  LATS1 WILD-TYPE 76 34  4  2
D630V12, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LATS1 MUTATED       0                         0     5
  LATS1 WILD-TYPE     6                         5   109
D630V14, multiclass
                           clus
vv                          LATS1 MUTATED LATS1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V15, binary
                 cls
clus               0  1
  LATS1 MUTATED    1  4
  LATS1 WILD-TYPE  4 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      1    4
  LATS1 WILD-TYPE    4   87
                        clus
vv                       LATS1 MUTATED LATS1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(631) Variable = LARP1B MUTATION ANALYSIS
D631V1, survival
                  sevent
clus2               0  1
  LARP1B MUTATED    1  2
  LARP1B WILD-TYPE 62 60
  LARP1B MUTATED LARP1B WILD-TYPE 
               3              122 
  LARP1B MUTATED LARP1B WILD-TYPE 
               2               60 
$`LARP1B MUTATED`
TCGA-3A-A9IV TCGA-IB-7651 TCGA-IB-A5SQ 
       36.26        19.82         7.20 

$`LARP1B WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LARP1B MUTATED LARP1B WILD-TYPE 
            7.20             0.23 
  LARP1B MUTATED LARP1B WILD-TYPE 
           36.26            90.12 
  LARP1B MUTATED LARP1B WILD-TYPE 
          19.820           15.205 
[1] "7.2 - 36.3 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D631V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LARP1B MUTATED         0        0        2         0         1         0
  LARP1B WILD-TYPE       1        3       10        19        81         4
                  vv
clus               STAGE IV
  LARP1B MUTATED          0
  LARP1B WILD-TYPE        3
D631V3, multiclass
           clus
vv          LARP1B MUTATED LARP1B WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               2               10
  STAGE IIA              0               19
  STAGE IIB              1               81
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  LARP1B MUTATED     0   2     1
  LARP1B WILD-TYPE   5  15   101
D631V4, multiclass
       clus
vv      LARP1B MUTATED LARP1B WILD-TYPE
  T1                 0                5
  T2                 2               15
  T3+T4              1              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V5, binary
                  cls
clus                0  1
  LARP1B MUTATED    2  1
  LARP1B WILD-TYPE 33 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      2    1
  LARP1B WILD-TYPE   33   88
   clus
vv  LARP1B MUTATED LARP1B WILD-TYPE
  0              2               33
  1              1               88
[1] 2 2
[1] FALSE
D631V6, binary
                  cls
clus                0  1
  LARP1B MUTATED    2  0
  LARP1B WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      2    0
  LARP1B WILD-TYPE   55    3
   clus
vv  LARP1B MUTATED LARP1B WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D631V7, binary
                  cls
clus                0  1
  LARP1B MUTATED    3  0
  LARP1B WILD-TYPE 48 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      3    0
  LARP1B WILD-TYPE   48   75
        clus
vv       LARP1B MUTATED LARP1B WILD-TYPE
  FEMALE              3               48
  MALE                0               75
[1] 2 2
[1] FALSE
D631V8, binary
                  cls
clus                0  1
  LARP1B MUTATED    3  0
  LARP1B WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      3    0
  LARP1B WILD-TYPE   85   30
     clus
vv    LARP1B MUTATED LARP1B WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LARP1B MUTATED                                     2
  LARP1B WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LARP1B MUTATED                                       1
  LARP1B WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LARP1B MUTATED                                                  0
  LARP1B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  LARP1B MUTATED                                     0
  LARP1B WILD-TYPE                                   1
D631V9, multiclass
                                                  clus
vv                                                 LARP1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 LARP1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V10, continuous
[1] "Remove cluster labels:" "LARP1B MUTATED"        
clus
  LARP1B MUTATED LARP1B WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
D631V11, continuous
[1] "Remove cluster labels:" "LARP1B MUTATED"        
clus
  LARP1B MUTATED LARP1B WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" "LARP1B WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LARP1B MUTATED    3  0  0  0
  LARP1B WILD-TYPE 77 35  4  2
D631V12, multiclass
    clus
vv   LARP1B MUTATED LARP1B WILD-TYPE
  R0              3               77
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP1B MUTATED       0                         0     3
  LARP1B WILD-TYPE     6                         5   111
D631V14, multiclass
                           clus
vv                          LARP1B MUTATED LARP1B WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V15, binary
                  cls
clus                0  1
  LARP1B MUTATED    0  3
  LARP1B WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP1B MUTATED      0    3
  LARP1B WILD-TYPE    5   88
                        clus
vv                       LARP1B MUTATED LARP1B WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(632) Variable = PTPN14 MUTATION ANALYSIS
D632V1, survival
                  sevent
clus2               0  1
  PTPN14 MUTATED    4  2
  PTPN14 WILD-TYPE 59 60
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               6              119 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               2               60 
$`PTPN14 MUTATED`
TCGA-3A-A9I5 TCGA-XD-AAUL TCGA-2L-AAQI TCGA-3E-AAAY TCGA-IB-7651 TCGA-YY-A8LH 
       58.98        16.37         3.39        75.12        19.82        66.28 

$`PTPN14 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ TCGA-2L-AAQL 
        9.11        21.44         4.70        22.49        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        24.43        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 
        8.28        32.15        30.25        17.49        31.86        20.19 
TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       17.00        10.13         5.26        10.85         0.23        19.82 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
       36.69        41.33        15.19        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM 
       20.88        21.90         1.35         8.22        15.88         0.26 
TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        4.73         7.86        14.17         6.02        11.11         7.40 
TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W 
        8.05        13.28         7.56        12.46        10.29         8.78 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 
       13.68         3.12        15.32         9.40         0.30        39.98 
TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       16.80         0.39        18.67        13.81        12.99        12.03 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
            3.39             0.23 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           75.12            90.12 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           39.40            15.12 
[1] "3.4 - 75.1 (39.4)" "0.2 - 90.1 (15.1)"
[1] "hr=" "2.5"
D632V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PTPN14 MUTATED         0        0        0         1         4         0
  PTPN14 WILD-TYPE       1        3       12        18        78         4
                  vv
clus               STAGE IV
  PTPN14 MUTATED          0
  PTPN14 WILD-TYPE        3
D632V3, multiclass
           clus
vv          PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              4               78
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PTPN14 MUTATED    0  0     5
  PTPN14 WILD-TYPE  5 17    97
D632V4, multiclass
       clus
vv      PTPN14 MUTATED PTPN14 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              5               97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V5, binary
                  cls
clus                0  1
  PTPN14 MUTATED    2  4
  PTPN14 WILD-TYPE 33 85
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      2    4
  PTPN14 WILD-TYPE   33   85
   clus
vv  PTPN14 MUTATED PTPN14 WILD-TYPE
  0              2               33
  1              4               85
[1] 2 2
[1] FALSE
D632V6, binary
                  cls
clus                0  1
  PTPN14 MUTATED    1  0
  PTPN14 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      1    0
  PTPN14 WILD-TYPE   56    3
   clus
vv  PTPN14 MUTATED PTPN14 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D632V7, binary
                  cls
clus                0  1
  PTPN14 MUTATED    2  4
  PTPN14 WILD-TYPE 49 71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      2    4
  PTPN14 WILD-TYPE   49   71
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              2               49
  MALE                4               71
[1] 2 2
[1] FALSE
D632V8, binary
                  cls
clus                0  1
  PTPN14 MUTATED    4  2
  PTPN14 WILD-TYPE 84 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      4    2
  PTPN14 WILD-TYPE   84   28
     clus
vv    PTPN14 MUTATED PTPN14 WILD-TYPE
  NO               4               84
  YES              2               28
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPN14 MUTATED                                     6
  PTPN14 WILD-TYPE                                  99
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPN14 MUTATED                                       0
  PTPN14 WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPN14 MUTATED                                                  0
  PTPN14 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PTPN14 MUTATED                                     0
  PTPN14 WILD-TYPE                                   1
D632V9, multiclass
                                                  clus
vv                                                 PTPN14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PTPN14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V10, continuous
D632V11, continuous
                  vv
clus               R0 R1 R2 RX
  PTPN14 MUTATED    4  1  0  0
  PTPN14 WILD-TYPE 76 34  4  2
D632V12, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  R0              4               76
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN14 MUTATED       0                         0     6
  PTPN14 WILD-TYPE     6                         5   108
D632V14, multiclass
                           clus
vv                          PTPN14 MUTATED PTPN14 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  6              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V15, binary
                  cls
clus                0  1
  PTPN14 MUTATED    0  5
  PTPN14 WILD-TYPE  5 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      0    5
  PTPN14 WILD-TYPE    5   86
                        clus
vv                       PTPN14 MUTATED PTPN14 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5               86
[1] 2 2
[1] FALSE

Clustering(633) Variable = PHKA2 MUTATION ANALYSIS
D633V1, survival
                 sevent
clus2              0  1
  PHKA2 MUTATED    2  4
  PHKA2 WILD-TYPE 61 58
  PHKA2 MUTATED PHKA2 WILD-TYPE 
              6             119 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
              4              58 
$`PHKA2 MUTATED`
TCGA-HZ-A77Q TCGA-2J-AABF TCGA-FB-A78T TCGA-IB-7651 TCGA-US-A77J TCGA-XD-AAUH 
        1.08        22.72        12.33        19.82        18.67        12.99 

$`PHKA2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
        8.02        15.78        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       19.96        22.22        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
        3.12        17.00        16.37        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XN-A8T3 
       39.98        16.80         0.39        13.81        12.03        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PHKA2 MUTATED PHKA2 WILD-TYPE 
           1.08            0.23 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
          22.72           90.12 
  PHKA2 MUTATED PHKA2 WILD-TYPE 
          15.83           15.22 
[1] "1.1 - 22.7 (15.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.5"
D633V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PHKA2 MUTATED         0        0        0         0         6         0
  PHKA2 WILD-TYPE       1        3       12        19        76         4
                 vv
clus              STAGE IV
  PHKA2 MUTATED          0
  PHKA2 WILD-TYPE        3
D633V3, multiclass
           clus
vv          PHKA2 MUTATED PHKA2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             6              76
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  PHKA2 MUTATED    0  0     6
  PHKA2 WILD-TYPE  5 17    96
D633V4, multiclass
       clus
vv      PHKA2 MUTATED PHKA2 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             6              96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V5, binary
                 cls
clus               0  1
  PHKA2 MUTATED    0  6
  PHKA2 WILD-TYPE 35 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      0    6
  PHKA2 WILD-TYPE   35   83
   clus
vv  PHKA2 MUTATED PHKA2 WILD-TYPE
  0             0              35
  1             6              83
[1] 2 2
[1] FALSE
D633V6, binary
                 cls
clus               0  1
  PHKA2 MUTATED    4  0
  PHKA2 WILD-TYPE 53  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      4    0
  PHKA2 WILD-TYPE   53    3
   clus
vv  PHKA2 MUTATED PHKA2 WILD-TYPE
  0             4              53
  1             0               3
[1] 2 2
[1] FALSE
D633V7, binary
                 cls
clus               0  1
  PHKA2 MUTATED    5  1
  PHKA2 WILD-TYPE 46 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      5    1
  PHKA2 WILD-TYPE   46   74
        clus
vv       PHKA2 MUTATED PHKA2 WILD-TYPE
  FEMALE             5              46
  MALE               1              74
[1] 2 2
[1] FALSE
D633V8, binary
                 cls
clus               0  1
  PHKA2 MUTATED    2  2
  PHKA2 WILD-TYPE 86 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      2    2
  PHKA2 WILD-TYPE   86   28
     clus
vv    PHKA2 MUTATED PHKA2 WILD-TYPE
  NO              2              86
  YES             2              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHKA2 MUTATED                                     5
  PHKA2 WILD-TYPE                                 100
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHKA2 MUTATED                                       1
  PHKA2 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHKA2 MUTATED                                                  0
  PHKA2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  PHKA2 MUTATED                                     0
  PHKA2 WILD-TYPE                                   1
D633V9, multiclass
                                                  clus
vv                                                 PHKA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 PHKA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          100
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V10, continuous
D633V11, continuous
                 vv
clus              R0 R1 R2 RX
  PHKA2 MUTATED    4  1  1  0
  PHKA2 WILD-TYPE 76 34  3  2
D633V12, multiclass
    clus
vv   PHKA2 MUTATED PHKA2 WILD-TYPE
  R0             4              76
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHKA2 MUTATED       0                         0     6
  PHKA2 WILD-TYPE     6                         5   108
D633V14, multiclass
                           clus
vv                          PHKA2 MUTATED PHKA2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V15, binary
                 cls
clus               0  1
  PHKA2 MUTATED    0  5
  PHKA2 WILD-TYPE  5 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA2 MUTATED      0    5
  PHKA2 WILD-TYPE    5   86
                        clus
vv                       PHKA2 MUTATED PHKA2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5              86
[1] 2 2
[1] FALSE

Clustering(634) Variable = ABCC3 MUTATION ANALYSIS
D634V1, survival
                 sevent
clus2              0  1
  ABCC3 MUTATED    1  2
  ABCC3 WILD-TYPE 62 60
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              3             122 
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              2              60 
$`ABCC3 MUTATED`
TCGA-FB-A5VM TCGA-IB-7651 TCGA-RL-AAAS 
       16.37        19.82         0.30 

$`ABCC3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ABCC3 MUTATED ABCC3 WILD-TYPE 
           0.30            0.23 
  ABCC3 MUTATED ABCC3 WILD-TYPE 
          19.82           90.12 
  ABCC3 MUTATED ABCC3 WILD-TYPE 
         16.370          15.205 
[1] "0.3 - 19.8 (16.4)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.8"
D634V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ABCC3 MUTATED         0        0        2         0         1         0
  ABCC3 WILD-TYPE       1        3       10        19        81         4
                 vv
clus              STAGE IV
  ABCC3 MUTATED          0
  ABCC3 WILD-TYPE        3
D634V3, multiclass
           clus
vv          ABCC3 MUTATED ABCC3 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             1              81
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  ABCC3 MUTATED     0   2     1
  ABCC3 WILD-TYPE   5  15   101
D634V4, multiclass
       clus
vv      ABCC3 MUTATED ABCC3 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             1             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V5, binary
                 cls
clus               0  1
  ABCC3 MUTATED    2  1
  ABCC3 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC3 MUTATED      2    1
  ABCC3 WILD-TYPE   33   88
   clus
vv  ABCC3 MUTATED ABCC3 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D634V6, binary
                 cls
clus               0  1
  ABCC3 MUTATED    3  0
  ABCC3 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC3 MUTATED      3    0
  ABCC3 WILD-TYPE   54    3
   clus
vv  ABCC3 MUTATED ABCC3 WILD-TYPE
  0             3              54
  1             0               3
[1] 2 2
[1] FALSE
D634V7, binary
                 cls
clus               0  1
  ABCC3 MUTATED    2  1
  ABCC3 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC3 MUTATED      2    1
  ABCC3 WILD-TYPE   49   74
        clus
vv       ABCC3 MUTATED ABCC3 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D634V8, binary
                 cls
clus               0  1
  ABCC3 MUTATED    3  0
  ABCC3 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC3 MUTATED      3    0
  ABCC3 WILD-TYPE   85   30
     clus
vv    ABCC3 MUTATED ABCC3 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ABCC3 MUTATED                                     3
  ABCC3 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ABCC3 MUTATED                                       0
  ABCC3 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ABCC3 MUTATED                                                  0
  ABCC3 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  ABCC3 MUTATED                                     0
  ABCC3 WILD-TYPE                                   1
D634V9, multiclass
                                                  clus
vv                                                 ABCC3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 ABCC3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V10, continuous
[1] "Remove cluster labels:" "ABCC3 MUTATED"         
clus
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A78T      TCGA-FB-AAPQ 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-YY-A8LH 
"ABCC3 WILD-TYPE" 
D634V11, continuous
[1] "Remove cluster labels:" "ABCC3 MUTATED"         
clus
  ABCC3 MUTATED ABCC3 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A78T      TCGA-FB-AAPQ      TCGA-FB-AAPS 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" "ABCC3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ABCC3 MUTATED    3  0  0  0
  ABCC3 WILD-TYPE 77 35  4  2
D634V12, multiclass
    clus
vv   ABCC3 MUTATED ABCC3 WILD-TYPE
  R0             3              77
  R1             0              35
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCC3 MUTATED       0                         0     3
  ABCC3 WILD-TYPE     6                         5   111
D634V14, multiclass
                           clus
vv                          ABCC3 MUTATED ABCC3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V15, binary
                 cls
clus               0  1
  ABCC3 MUTATED    0  3
  ABCC3 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC3 MUTATED      0    3
  ABCC3 WILD-TYPE    5   88
                        clus
vv                       ABCC3 MUTATED ABCC3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(635) Variable = CPNE2 MUTATION ANALYSIS
D635V1, survival
                 sevent
clus2              0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 62 60
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             122 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2              60 
$`CPNE2 MUTATED`
TCGA-3A-A9I5 TCGA-3E-AAAZ TCGA-IB-7651 
       58.98        71.74        19.82 

$`CPNE2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        60.95        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-7273 
       36.26        34.09        10.13        24.43        75.12        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CPNE2 MUTATED CPNE2 WILD-TYPE 
          19.82            0.23 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
          71.74           90.12 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
         58.980          15.155 
[1] "19.8 - 71.7 (59.0)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.6"
D635V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CPNE2 MUTATED         0        0        0         1         1         0
  CPNE2 WILD-TYPE       1        3       12        18        81         4
                 vv
clus              STAGE IV
  CPNE2 MUTATED          0
  CPNE2 WILD-TYPE        3
D635V3, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9IJ      TCGA-3A-A9IL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924      TCGA-HZ-A77Q 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX      TCGA-S4-A8RO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AAB4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9      TCGA-2J-AABA 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH      TCGA-2J-AABK 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU      TCGA-2J-AABV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IR 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV      TCGA-3A-A9IX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-F2-7273 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-FZ-5919      TCGA-FZ-5920      TCGA-FZ-5921 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FZ-5922      TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-A7OL      TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU      TCGA-IB-AAUV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77G 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D      TCGA-YH-A8SY 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
                 vv
clus               T1  T2 T3+T4
  CPNE2 MUTATED     0   0     2
  CPNE2 WILD-TYPE   5  17   100
D635V4, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             122 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9IJ      TCGA-3A-A9IL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924      TCGA-HZ-A77Q 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX      TCGA-S4-A8RO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AAB4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9      TCGA-2J-AABA 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH      TCGA-2J-AABK 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU      TCGA-2J-AABV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IR 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV      TCGA-3A-A9IX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY      TCGA-F2-7273 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-FZ-5919      TCGA-FZ-5920      TCGA-FZ-5921 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FZ-5922      TCGA-FZ-5923      TCGA-FZ-5926      TCGA-H8-A6C1 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-A7OL      TCGA-HV-A7OP      TCGA-HV-AA8V      TCGA-HV-AA8X 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-7918      TCGA-HZ-7925      TCGA-HZ-8637      TCGA-HZ-A49I 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A8P1      TCGA-HZ-A9TJ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7652      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5SP      TCGA-IB-A5SQ      TCGA-IB-A5ST      TCGA-IB-A6UF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUU      TCGA-IB-AAUV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUW      TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8      TCGA-RB-AA9M 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RL-AAAS      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77G 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77J      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D      TCGA-YH-A8SY 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D635V5, binary
                 cls
clus               0  1
  CPNE2 MUTATED    2  1
  CPNE2 WILD-TYPE 33 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      2    1
  CPNE2 WILD-TYPE   33   88
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             2              33
  1             1              88
[1] 2 2
[1] FALSE
D635V6, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  0
  CPNE2 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    0
  CPNE2 WILD-TYPE   56    3
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D635V7, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 50 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE   50   73
        clus
vv       CPNE2 MUTATED CPNE2 WILD-TYPE
  FEMALE             1              50
  MALE               2              73
[1] 2 2
[1] FALSE
D635V8, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  1
  CPNE2 WILD-TYPE 87 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    1
  CPNE2 WILD-TYPE   87   29
     clus
vv    CPNE2 MUTATED CPNE2 WILD-TYPE
  NO              1              87
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CPNE2 MUTATED                                     3
  CPNE2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CPNE2 MUTATED                                       0
  CPNE2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CPNE2 MUTATED                                                  0
  CPNE2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  CPNE2 MUTATED                                     0
  CPNE2 WILD-TYPE                                   1
D635V9, multiclass
                                                  clus
vv                                                 CPNE2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 CPNE2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V10, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D635V11, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CPNE2 MUTATED    2  0  0  0
  CPNE2 WILD-TYPE 78 35  4  2
D635V12, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             119 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9IJ      TCGA-3A-A9IL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924      TCGA-HZ-A77Q 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX      TCGA-S4-A8RO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AAB4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9      TCGA-2J-AABA 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH      TCGA-2J-AABK 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU      TCGA-2J-AABV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-F2-7273 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922      TCGA-FZ-5923 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7652      TCGA-IB-7885 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D635V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPNE2 MUTATED       0                         0     3
  CPNE2 WILD-TYPE     6                         5   111
D635V14, multiclass
                           clus
vv                          CPNE2 MUTATED CPNE2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V15, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE  4 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE    4   89
                        clus
vv                       CPNE2 MUTATED CPNE2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(636) Variable = MICALCL MUTATION ANALYSIS
D636V1, survival
                   sevent
clus2                0  1
  MICALCL MUTATED    2  2
  MICALCL WILD-TYPE 61 60
  MICALCL MUTATED MICALCL WILD-TYPE 
                4               121 
  MICALCL MUTATED MICALCL WILD-TYPE 
                2                60 
$`MICALCL MUTATED`
TCGA-FB-AAQ2 TCGA-HV-A7OP TCGA-IB-7651 TCGA-IB-8126 
        5.03        32.15        19.82        15.19 

$`MICALCL WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        4.04         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
       20.35        17.79        22.06         8.28        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
        0.23        19.82        36.69        41.33        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MICALCL MUTATED MICALCL WILD-TYPE 
             5.03              0.23 
  MICALCL MUTATED MICALCL WILD-TYPE 
            32.15             90.12 
  MICALCL MUTATED MICALCL WILD-TYPE 
           17.505            15.220 
[1] "5.0 - 32.1 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D636V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  MICALCL MUTATED         0        0        0         0         3         1
  MICALCL WILD-TYPE       1        3       12        19        79         3
                   vv
clus                STAGE IV
  MICALCL MUTATED          0
  MICALCL WILD-TYPE        3
D636V3, multiclass
           clus
vv          MICALCL MUTATED MICALCL WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  MICALCL MUTATED    0  0     4
  MICALCL WILD-TYPE  5 17    98
D636V4, multiclass
       clus
vv      MICALCL MUTATED MICALCL WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V5, binary
                   cls
clus                 0  1
  MICALCL MUTATED    0  4
  MICALCL WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      0    4
  MICALCL WILD-TYPE   35   85
   clus
vv  MICALCL MUTATED MICALCL WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D636V6, binary
                   cls
clus                 0  1
  MICALCL MUTATED    3  0
  MICALCL WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      3    0
  MICALCL WILD-TYPE   54    3
   clus
vv  MICALCL MUTATED MICALCL WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D636V7, binary
                   cls
clus                 0  1
  MICALCL MUTATED    3  1
  MICALCL WILD-TYPE 48 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      3    1
  MICALCL WILD-TYPE   48   74
        clus
vv       MICALCL MUTATED MICALCL WILD-TYPE
  FEMALE               3                48
  MALE                 1                74
[1] 2 2
[1] FALSE
D636V8, binary
                   cls
clus                 0  1
  MICALCL MUTATED    3  1
  MICALCL WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      3    1
  MICALCL WILD-TYPE   85   29
     clus
vv    MICALCL MUTATED MICALCL WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MICALCL MUTATED                                     3
  MICALCL WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MICALCL MUTATED                                       1
  MICALCL WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MICALCL MUTATED                                                  0
  MICALCL WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  MICALCL MUTATED                                     0
  MICALCL WILD-TYPE                                   1
D636V9, multiclass
                                                  clus
vv                                                 MICALCL MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 MICALCL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V10, continuous
[1] "Remove cluster labels:" "MICALCL MUTATED"       
clus
  MICALCL MUTATED MICALCL WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-A6UF        TCGA-IB-A6UG 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-YY-A8LH 
"MICALCL WILD-TYPE" 
D636V11, continuous
[1] "Remove cluster labels:" "MICALCL MUTATED"       
clus
  MICALCL MUTATED MICALCL WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"MICALCL WILD-TYPE" "MICALCL WILD-TYPE" "MICALCL WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  MICALCL MUTATED    2  2  0  0
  MICALCL WILD-TYPE 78 33  4  2
D636V12, multiclass
    clus
vv   MICALCL MUTATED MICALCL WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MICALCL MUTATED       1                         0     3
  MICALCL WILD-TYPE     5                         5   111
D636V14, multiclass
                           clus
vv                          MICALCL MUTATED MICALCL WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V15, binary
                   cls
clus                 0  1
  MICALCL MUTATED    0  3
  MICALCL WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MICALCL MUTATED      0    3
  MICALCL WILD-TYPE    5   88
                        clus
vv                       MICALCL MUTATED MICALCL WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(637) Variable = SPAG9 MUTATION ANALYSIS
D637V1, survival
                 sevent
clus2              0  1
  SPAG9 MUTATED    1  3
  SPAG9 WILD-TYPE 62 59
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              4             121 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              3              59 
$`SPAG9 MUTATED`
TCGA-3A-A9IJ TCGA-FB-A5VM TCGA-HZ-A49I TCGA-IB-7651 
       60.95        16.37        10.13        19.82 

$`SPAG9 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IL TCGA-F2-A44G TCGA-FB-AAQ6 
       14.40        10.49        58.98        90.12         7.66         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       31.86        20.19        17.00         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SPAG9 MUTATED SPAG9 WILD-TYPE 
          10.13            0.23 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
          60.95           90.12 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
         18.095          15.190 
[1] "10.1 - 61.0 (18.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.3"
D637V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SPAG9 MUTATED         0        0        2         0         2         0
  SPAG9 WILD-TYPE       1        3       10        19        80         4
                 vv
clus              STAGE IV
  SPAG9 MUTATED          0
  SPAG9 WILD-TYPE        3
D637V3, multiclass
           clus
vv          SPAG9 MUTATED SPAG9 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              2              10
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  SPAG9 MUTATED     0   2     2
  SPAG9 WILD-TYPE   5  15   100
D637V4, multiclass
       clus
vv      SPAG9 MUTATED SPAG9 WILD-TYPE
  T1                0               5
  T2                2              15
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V5, binary
                 cls
clus               0  1
  SPAG9 MUTATED    2  2
  SPAG9 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      2    2
  SPAG9 WILD-TYPE   33   87
   clus
vv  SPAG9 MUTATED SPAG9 WILD-TYPE
  0             2              33
  1             2              87
[1] 2 2
[1] FALSE
D637V6, binary
                 cls
clus               0  1
  SPAG9 MUTATED    2  0
  SPAG9 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      2    0
  SPAG9 WILD-TYPE   55    3
   clus
vv  SPAG9 MUTATED SPAG9 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D637V7, binary
                 cls
clus               0  1
  SPAG9 MUTATED    1  3
  SPAG9 WILD-TYPE 50 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      1    3
  SPAG9 WILD-TYPE   50   72
        clus
vv       SPAG9 MUTATED SPAG9 WILD-TYPE
  FEMALE             1              50
  MALE               3              72
[1] 2 2
[1] FALSE
D637V8, binary
                 cls
clus               0  1
  SPAG9 MUTATED    3  1
  SPAG9 WILD-TYPE 85 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      3    1
  SPAG9 WILD-TYPE   85   29
     clus
vv    SPAG9 MUTATED SPAG9 WILD-TYPE
  NO              3              85
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPAG9 MUTATED                                     3
  SPAG9 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPAG9 MUTATED                                       1
  SPAG9 WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPAG9 MUTATED                                                  0
  SPAG9 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  SPAG9 MUTATED                                     0
  SPAG9 WILD-TYPE                                   1
D637V9, multiclass
                                                  clus
vv                                                 SPAG9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 SPAG9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V10, continuous
D637V11, continuous
                 vv
clus              R0 R1 R2 RX
  SPAG9 MUTATED    3  1  0  0
  SPAG9 WILD-TYPE 77 34  4  2
D637V12, multiclass
    clus
vv   SPAG9 MUTATED SPAG9 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPAG9 MUTATED       0                         0     4
  SPAG9 WILD-TYPE     6                         5   110
D637V14, multiclass
                           clus
vv                          SPAG9 MUTATED SPAG9 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V15, binary
                 cls
clus               0  1
  SPAG9 MUTATED    0  4
  SPAG9 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      0    4
  SPAG9 WILD-TYPE    5   87
                        clus
vv                       SPAG9 MUTATED SPAG9 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(638) Variable = SLITRK3 MUTATION ANALYSIS
D638V1, survival
                   sevent
clus2                0  1
  SLITRK3 MUTATED    2  2
  SLITRK3 WILD-TYPE 61 60
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
                4               121 
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
                2                60 
$`SLITRK3 MUTATED`
TCGA-HZ-7918 TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A6UG 
       31.86        19.82        15.19         1.35 

$`SLITRK3 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       30.25        17.49        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
       10.85         0.23        19.82        36.69        41.33        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88        21.90         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
             1.35              0.23 
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
            31.86             90.12 
  SLITRK3 MUTATED SLITRK3 WILD-TYPE 
           17.505            15.220 
[1] "1.4 - 31.9 (17.5)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D638V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SLITRK3 MUTATED         0        0        0         0         3         1
  SLITRK3 WILD-TYPE       1        3       12        19        79         3
                   vv
clus                STAGE IV
  SLITRK3 MUTATED          0
  SLITRK3 WILD-TYPE        3
D638V3, multiclass
           clus
vv          SLITRK3 MUTATED SLITRK3 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  SLITRK3 MUTATED    0  0     4
  SLITRK3 WILD-TYPE  5 17    98
D638V4, multiclass
       clus
vv      SLITRK3 MUTATED SLITRK3 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               4                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V5, binary
                   cls
clus                 0  1
  SLITRK3 MUTATED    0  4
  SLITRK3 WILD-TYPE 35 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK3 MUTATED      0    4
  SLITRK3 WILD-TYPE   35   85
   clus
vv  SLITRK3 MUTATED SLITRK3 WILD-TYPE
  0               0                35
  1               4                85
[1] 2 2
[1] FALSE
D638V6, binary
                   cls
clus                 0  1
  SLITRK3 MUTATED    4  0
  SLITRK3 WILD-TYPE 53  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK3 MUTATED      4    0
  SLITRK3 WILD-TYPE   53    3
   clus
vv  SLITRK3 MUTATED SLITRK3 WILD-TYPE
  0               4                53
  1               0                 3
[1] 2 2
[1] FALSE
D638V7, binary
                   cls
clus                 0  1
  SLITRK3 MUTATED    2  2
  SLITRK3 WILD-TYPE 49 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK3 MUTATED      2    2
  SLITRK3 WILD-TYPE   49   73
        clus
vv       SLITRK3 MUTATED SLITRK3 WILD-TYPE
  FEMALE               2                49
  MALE                 2                73
[1] 2 2
[1] FALSE
D638V8, binary
                   cls
clus                 0  1
  SLITRK3 MUTATED    3  1
  SLITRK3 WILD-TYPE 85 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK3 MUTATED      3    1
  SLITRK3 WILD-TYPE   85   29
     clus
vv    SLITRK3 MUTATED SLITRK3 WILD-TYPE
  NO                3                85
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLITRK3 MUTATED                                     4
  SLITRK3 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLITRK3 MUTATED                                       0
  SLITRK3 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLITRK3 MUTATED                                                  0
  SLITRK3 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  SLITRK3 MUTATED                                     0
  SLITRK3 WILD-TYPE                                   1
D638V9, multiclass
                                                  clus
vv                                                 SLITRK3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 SLITRK3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V10, continuous
D638V11, continuous
                   vv
clus                R0 R1 R2 RX
  SLITRK3 MUTATED    2  2  0  0
  SLITRK3 WILD-TYPE 78 33  4  2
D638V12, multiclass
    clus
vv   SLITRK3 MUTATED SLITRK3 WILD-TYPE
  R0               2                78
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLITRK3 MUTATED       0                         0     4
  SLITRK3 WILD-TYPE     6                         5   110
D638V14, multiclass
                           clus
vv                          SLITRK3 MUTATED SLITRK3 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V15, binary
                   cls
clus                 0  1
  SLITRK3 MUTATED    0  4
  SLITRK3 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK3 MUTATED      0    4
  SLITRK3 WILD-TYPE    5   87
                        clus
vv                       SLITRK3 MUTATED SLITRK3 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE

Clustering(639) Variable = HIST1H2BE MUTATION ANALYSIS
D639V1, survival
                     sevent
clus2                  0  1
  HIST1H2BE MUTATED    1  2
  HIST1H2BE WILD-TYPE 62 60
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
                  3                 122 
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
                  2                  60 
$`HIST1H2BE MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABV TCGA-3A-A9IH 
       20.61        21.44        33.57 

$`HIST1H2BE WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
       15.22         9.11         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       19.82        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
              20.61                0.23 
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
              33.57               90.12 
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
             21.440              15.155 
[1] "20.6 - 33.6 (21.4)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.2"
D639V2, continuous
                     vv
clus                  STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  HIST1H2BE MUTATED         0        1        0         0         2         0
  HIST1H2BE WILD-TYPE       1        2       12        19        80         4
                     vv
clus                  STAGE IV
  HIST1H2BE MUTATED          0
  HIST1H2BE WILD-TYPE        3
D639V3, multiclass
           clus
vv          HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  STAGE I                   0                   1
  STAGE IA                  1                   2
  STAGE IB                  0                  12
  STAGE IIA                 0                  19
  STAGE IIB                 2                  80
  STAGE III                 0                   4
  STAGE IV                  0                   3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2 T3+T4
  HIST1H2BE MUTATED     1   0     2
  HIST1H2BE WILD-TYPE   4  17   100
D639V4, multiclass
       clus
vv      HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  T1                    1                   4
  T2                    0                  17
  T3+T4                 2                 100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V5, binary
                     cls
clus                   0  1
  HIST1H2BE MUTATED    1  2
  HIST1H2BE WILD-TYPE 34 87
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BE MUTATED      1    2
  HIST1H2BE WILD-TYPE   34   87
   clus
vv  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  0                 1                  34
  1                 2                  87
[1] 2 2
[1] FALSE
D639V6, binary
                     cls
clus                   0  1
  HIST1H2BE MUTATED    2  0
  HIST1H2BE WILD-TYPE 55  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BE MUTATED      2    0
  HIST1H2BE WILD-TYPE   55    3
   clus
vv  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  0                 2                  55
  1                 0                   3
[1] 2 2
[1] FALSE
D639V7, binary
                     cls
clus                   0  1
  HIST1H2BE MUTATED    2  1
  HIST1H2BE WILD-TYPE 49 74
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BE MUTATED      2    1
  HIST1H2BE WILD-TYPE   49   74
        clus
vv       HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  FEMALE                 2                  49
  MALE                   1                  74
[1] 2 2
[1] FALSE
D639V8, binary
                     cls
clus                   0  1
  HIST1H2BE MUTATED    2  1
  HIST1H2BE WILD-TYPE 86 29
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BE MUTATED      2    1
  HIST1H2BE WILD-TYPE   86   29
     clus
vv    HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  NO                  2                  86
  YES                 1                  29
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H2BE MUTATED                                     3
  HIST1H2BE WILD-TYPE                                 102
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H2BE MUTATED                                       0
  HIST1H2BE WILD-TYPE                                    18
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H2BE MUTATED                                                  0
  HIST1H2BE WILD-TYPE                                                1
                     vv
clus                  PANCREAS-UNDIFFERENTIATED CARCINOMA
  HIST1H2BE MUTATED                                     0
  HIST1H2BE WILD-TYPE                                   1
D639V9, multiclass
                                                  clus
vv                                                 HIST1H2BE MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              0
                                                  clus
vv                                                 HIST1H2BE WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                                1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V10, continuous
[1] "Remove cluster labels:" "HIST1H2BE MUTATED"     
clus
  HIST1H2BE MUTATED HIST1H2BE WILD-TYPE 
                  1                  38 
         TCGA-3A-A9IJ          TCGA-HZ-A77Q          TCGA-HZ-A8P0 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-IB-A5SS          TCGA-LB-A7SX          TCGA-XD-AAUL 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-2J-AAB1          TCGA-2J-AABA          TCGA-2J-AABE 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-2J-AABF          TCGA-2J-AABO          TCGA-2L-AAQA 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-2L-AAQE          TCGA-3A-A9I9          TCGA-3A-A9IB 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-3A-A9IX          TCGA-F2-A8YN          TCGA-FB-A5VM 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-FB-A78T          TCGA-FB-AAPQ          TCGA-FB-AAPS 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-H8-A6C1          TCGA-HV-AA8V          TCGA-HZ-A8P1 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-IB-7651          TCGA-IB-7885          TCGA-IB-8126 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-IB-A6UF          TCGA-IB-A6UG          TCGA-IB-A7M4 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-IB-AAUQ          TCGA-IB-AAUS          TCGA-IB-AAUU 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-IB-AAUV          TCGA-LB-A9Q5          TCGA-OE-A75W 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
         TCGA-XN-A8T5          TCGA-YY-A8LH 
"HIST1H2BE WILD-TYPE" "HIST1H2BE WILD-TYPE" 
D639V11, continuous
                     vv
clus                  R0 R1 R2 RX
  HIST1H2BE MUTATED    2  1  0  0
  HIST1H2BE WILD-TYPE 78 34  4  2
D639V12, multiclass
    clus
vv   HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  R0                 2                  78
  R1                 1                  34
  R2                 0                   4
  RX                 0                   2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V13, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BE MUTATED       0                         0     3
  HIST1H2BE WILD-TYPE     6                         5   111
D639V14, multiclass
                           clus
vv                          HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  ASIAN                                     0                   6
  BLACK OR AFRICAN AMERICAN                 0                   5
  WHITE                                     3                 111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V15, binary
                     cls
clus                   0  1
  HIST1H2BE MUTATED    0  1
  HIST1H2BE WILD-TYPE  5 90
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BE MUTATED      0    1
  HIST1H2BE WILD-TYPE    5   90
                        clus
vv                       HIST1H2BE MUTATED HIST1H2BE WILD-TYPE
  HISPANIC OR LATINO                     0                   5
  NOT HISPANIC OR LATINO                 1                  90
[1] 2 2
[1] FALSE

Clustering(640) Variable = NGF MUTATION ANALYSIS
D640V1, survival
               sevent
clus2            0  1
  NGF MUTATED    3  1
  NGF WILD-TYPE 60 61
  NGF MUTATED NGF WILD-TYPE 
            4           121 
  NGF MUTATED NGF WILD-TYPE 
            1            61 
$`NGF MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-YB-A89D TCGA-YH-A8SY 
       19.82        41.33        11.51        12.76 

$`NGF WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-8126 
        5.26        10.85         0.23        19.82        36.69        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YY-A8LH 
       13.81        12.99        12.03        31.27        23.67        66.28 
TCGA-Z5-AAPL 
       15.35 

  NGF MUTATED NGF WILD-TYPE 
        11.51          0.23 
  NGF MUTATED NGF WILD-TYPE 
        41.33         90.12 
  NGF MUTATED NGF WILD-TYPE 
        16.29         15.22 
[1] "11.5 - 41.3 (16.3)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2.3"
D640V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NGF MUTATED         0        0        0         0         3         1
  NGF WILD-TYPE       1        3       12        19        79         3
               vv
clus            STAGE IV
  NGF MUTATED          0
  NGF WILD-TYPE        3
D640V3, multiclass
           clus
vv          NGF MUTATED NGF WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           0            19
  STAGE IIB           3            79
  STAGE III           1             3
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  NGF MUTATED    0  0     4
  NGF WILD-TYPE  5 17    98
D640V4, multiclass
       clus
vv      NGF MUTATED NGF WILD-TYPE
  T1              0             5
  T2              0            17
  T3+T4           4            98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V5, binary
               cls
clus             0  1
  NGF MUTATED    0  4
  NGF WILD-TYPE 35 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      0    4
  NGF WILD-TYPE   35   85
   clus
vv  NGF MUTATED NGF WILD-TYPE
  0           0            35
  1           4            85
[1] 2 2
[1] FALSE
D640V6, binary
               cls
clus             0  1
  NGF MUTATED    2  0
  NGF WILD-TYPE 55  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    0
  NGF WILD-TYPE   55    3
   clus
vv  NGF MUTATED NGF WILD-TYPE
  0           2            55
  1           0             3
[1] 2 2
[1] FALSE
D640V7, binary
               cls
clus             0  1
  NGF MUTATED    3  1
  NGF WILD-TYPE 48 74
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      3    1
  NGF WILD-TYPE   48   74
        clus
vv       NGF MUTATED NGF WILD-TYPE
  FEMALE           3            48
  MALE             1            74
[1] 2 2
[1] FALSE
D640V8, binary
               cls
clus             0  1
  NGF MUTATED    2  2
  NGF WILD-TYPE 86 28
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      2    2
  NGF WILD-TYPE   86   28
     clus
vv    NGF MUTATED NGF WILD-TYPE
  NO            2            86
  YES           2            28
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NGF MUTATED                                     3
  NGF WILD-TYPE                                 102
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NGF MUTATED                                       0
  NGF WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NGF MUTATED                                                  0
  NGF WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  NGF MUTATED                                     0
  NGF WILD-TYPE                                   1
D640V9, multiclass
                                                  clus
vv                                                 NGF MUTATED NGF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        3           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V10, continuous
[1] "Remove cluster labels:" "NGF MUTATED"           
clus
  NGF MUTATED NGF WILD-TYPE 
            2            37 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABA    TCGA-2J-AABE    TCGA-2J-AABF 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-2J-AABO    TCGA-2J-AABV    TCGA-2L-AAQA    TCGA-2L-AAQE    TCGA-3A-A9I9 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IX    TCGA-F2-A8YN    TCGA-FB-A5VM    TCGA-FB-A78T 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HV-AA8V    TCGA-HZ-A8P1 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-AAUS    TCGA-IB-AAUU    TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-XN-A8T5    TCGA-YY-A8LH 
"NGF WILD-TYPE" "NGF WILD-TYPE" 
D640V11, continuous
[1] "Remove cluster labels:" "NGF MUTATED"           
clus
  NGF MUTATED NGF WILD-TYPE 
            2            31 
   TCGA-3A-A9IJ    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-A5SS    TCGA-LB-A7SX 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-2J-AAB1    TCGA-2J-AABE    TCGA-2J-AABF    TCGA-2J-AABO 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-3A-A9IB    TCGA-3A-A9IR    TCGA-3A-A9IX    TCGA-FB-A5VM    TCGA-FB-A78T 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-FB-AAPQ    TCGA-FB-AAPS    TCGA-H8-A6C1    TCGA-HZ-A8P1    TCGA-IB-8126 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-IB-AAUV    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-XD-AAUI    TCGA-XN-A8T5 
"NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" "NGF WILD-TYPE" 
   TCGA-YY-A8LH 
"NGF WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  NGF MUTATED    3  0  0  0
  NGF WILD-TYPE 77 35  4  2
D640V12, multiclass
    clus
vv   NGF MUTATED NGF WILD-TYPE
  R0           3            77
  R1           0            35
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NGF MUTATED       0                         0     4
  NGF WILD-TYPE     6                         5   110
D640V14, multiclass
                           clus
vv                          NGF MUTATED NGF WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V15, binary
               cls
clus             0  1
  NGF MUTATED    0  4
  NGF WILD-TYPE  5 87
[1] "tbl2"
               cls
clus            [,1] [,2]
  NGF MUTATED      0    4
  NGF WILD-TYPE    5   87
                        clus
vv                       NGF MUTATED NGF WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           4            87
[1] 2 2
[1] FALSE

Clustering(641) Variable = EHMT2 MUTATION ANALYSIS
D641V1, survival
                 sevent
clus2              0  1
  EHMT2 MUTATED    0  3
  EHMT2 WILD-TYPE 63 59
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              3             122 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              3              59 
$`EHMT2 MUTATED`
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-A6UG 
        5.26        19.82         1.35 

$`EHMT2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  EHMT2 MUTATED EHMT2 WILD-TYPE 
           1.35            0.23 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
          19.82           90.12 
  EHMT2 MUTATED EHMT2 WILD-TYPE 
           5.26           15.27 
[1] "1.4 - 19.8 (5.3)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.1"
D641V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EHMT2 MUTATED         0        0        0         0         3         0
  EHMT2 WILD-TYPE       1        3       12        19        79         4
                 vv
clus              STAGE IV
  EHMT2 MUTATED          0
  EHMT2 WILD-TYPE        3
D641V3, multiclass
           clus
vv          EHMT2 MUTATED EHMT2 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2 T3+T4
  EHMT2 MUTATED     0   1     2
  EHMT2 WILD-TYPE   5  16   100
D641V4, multiclass
       clus
vv      EHMT2 MUTATED EHMT2 WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             2             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V5, binary
                 cls
clus               0  1
  EHMT2 MUTATED    0  3
  EHMT2 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      0    3
  EHMT2 WILD-TYPE   35   86
   clus
vv  EHMT2 MUTATED EHMT2 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D641V6, binary
                 cls
clus               0  1
  EHMT2 MUTATED    2  0
  EHMT2 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      2    0
  EHMT2 WILD-TYPE   55    3
   clus
vv  EHMT2 MUTATED EHMT2 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D641V7, binary
                 cls
clus               0  1
  EHMT2 MUTATED    2  1
  EHMT2 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      2    1
  EHMT2 WILD-TYPE   49   74
        clus
vv       EHMT2 MUTATED EHMT2 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D641V8, binary
                 cls
clus               0  1
  EHMT2 MUTATED    3  0
  EHMT2 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      3    0
  EHMT2 WILD-TYPE   85   30
     clus
vv    EHMT2 MUTATED EHMT2 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EHMT2 MUTATED                                     3
  EHMT2 WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EHMT2 MUTATED                                       0
  EHMT2 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EHMT2 MUTATED                                                  0
  EHMT2 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  EHMT2 MUTATED                                     0
  EHMT2 WILD-TYPE                                   1
D641V9, multiclass
                                                  clus
vv                                                 EHMT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 EHMT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V10, continuous
[1] "Remove cluster labels:" "EHMT2 MUTATED"         
clus
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-YY-A8LH 
"EHMT2 WILD-TYPE" 
D641V11, continuous
[1] "Remove cluster labels:" "EHMT2 MUTATED"         
clus
  EHMT2 MUTATED EHMT2 WILD-TYPE 
              2              31 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" "EHMT2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  EHMT2 MUTATED    2  1  0  0
  EHMT2 WILD-TYPE 78 34  4  2
D641V12, multiclass
    clus
vv   EHMT2 MUTATED EHMT2 WILD-TYPE
  R0             2              78
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EHMT2 MUTATED       0                         0     3
  EHMT2 WILD-TYPE     6                         5   111
D641V14, multiclass
                           clus
vv                          EHMT2 MUTATED EHMT2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V15, binary
                 cls
clus               0  1
  EHMT2 MUTATED    0  3
  EHMT2 WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHMT2 MUTATED      0    3
  EHMT2 WILD-TYPE    5   88
                        clus
vv                       EHMT2 MUTATED EHMT2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(642) Variable = PLEKHG2 MUTATION ANALYSIS
D642V1, survival
                   sevent
clus2                0  1
  PLEKHG2 MUTATED    2  2
  PLEKHG2 WILD-TYPE 61 60
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
                4               121 
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
                2                60 
$`PLEKHG2 MUTATED`
TCGA-2L-AAQJ TCGA-3A-A9IX TCGA-IB-7651 TCGA-XN-A8T5 
       12.95        34.09        19.82        23.67 

$`PLEKHG2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       36.26        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
            12.95              0.23 
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
            34.09             90.12 
  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE 
           21.745            15.190 
[1] "12.9 - 34.1 (21.7)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "1.4"
D642V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PLEKHG2 MUTATED         0        1        1         0         2         1
  PLEKHG2 WILD-TYPE       1        2       11        19        80         3
                   vv
clus                STAGE IV
  PLEKHG2 MUTATED          0
  PLEKHG2 WILD-TYPE        3
D642V3, multiclass
           clus
vv          PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                1                 2
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               2                80
  STAGE III               1                 3
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  PLEKHG2 MUTATED    1  1     3
  PLEKHG2 WILD-TYPE  4 16    99
D642V4, multiclass
       clus
vv      PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  T1                  1                 4
  T2                  1                16
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V5, binary
                   cls
clus                 0  1
  PLEKHG2 MUTATED    3  2
  PLEKHG2 WILD-TYPE 32 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG2 MUTATED      3    2
  PLEKHG2 WILD-TYPE   32   87
   clus
vv  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  0               3                32
  1               2                87
[1] 2 2
[1] FALSE
D642V6, binary
                   cls
clus                 0  1
  PLEKHG2 MUTATED    2  0
  PLEKHG2 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG2 MUTATED      2    0
  PLEKHG2 WILD-TYPE   55    3
   clus
vv  PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D642V7, binary
                   cls
clus                 0  1
  PLEKHG2 MUTATED    3  2
  PLEKHG2 WILD-TYPE 48 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG2 MUTATED      3    2
  PLEKHG2 WILD-TYPE   48   73
        clus
vv       PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  FEMALE               3                48
  MALE                 2                73
[1] 2 2
[1] FALSE
D642V8, binary
                   cls
clus                 0  1
  PLEKHG2 MUTATED    2  2
  PLEKHG2 WILD-TYPE 86 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG2 MUTATED      2    2
  PLEKHG2 WILD-TYPE   86   28
     clus
vv    PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  NO                2                86
  YES               2                28
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLEKHG2 MUTATED                                     4
  PLEKHG2 WILD-TYPE                                 101
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLEKHG2 MUTATED                                       1
  PLEKHG2 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLEKHG2 MUTATED                                                  0
  PLEKHG2 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  PLEKHG2 MUTATED                                     0
  PLEKHG2 WILD-TYPE                                   1
D642V9, multiclass
                                                  clus
vv                                                 PLEKHG2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 PLEKHG2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V10, continuous
D642V11, continuous
                   vv
clus                R0 R1 R2 RX
  PLEKHG2 MUTATED    3  2  0  0
  PLEKHG2 WILD-TYPE 77 33  4  2
D642V12, multiclass
    clus
vv   PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  R0               3                77
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLEKHG2 MUTATED       0                         0     5
  PLEKHG2 WILD-TYPE     6                         5   109
D642V14, multiclass
                           clus
vv                          PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V15, binary
                   cls
clus                 0  1
  PLEKHG2 MUTATED    1  3
  PLEKHG2 WILD-TYPE  4 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHG2 MUTATED      1    3
  PLEKHG2 WILD-TYPE    4   88
                        clus
vv                       PLEKHG2 MUTATED PLEKHG2 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(643) Variable = SRFBP1 MUTATION ANALYSIS
D643V1, survival
                  sevent
clus2               0  1
  SRFBP1 MUTATED    1  2
  SRFBP1 WILD-TYPE 62 60
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              122 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               2               60 
$`SRFBP1 MUTATED`
TCGA-2L-AAQA TCGA-3A-A9IS TCGA-IB-7651 
        4.70        32.81        19.82 

$`SRFBP1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IU TCGA-3A-A9IV 
       24.26        33.57        63.85        50.70        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
            4.70             0.23 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
           32.81            90.12 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
          19.820           15.205 
[1] "4.7 - 32.8 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.2"
D643V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  SRFBP1 MUTATED         0        0        1         0         2         0
  SRFBP1 WILD-TYPE       1        3       11        19        80         4
                  vv
clus               STAGE IV
  SRFBP1 MUTATED          0
  SRFBP1 WILD-TYPE        3
D643V3, multiclass
           clus
vv          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               1               11
  STAGE IIA              0               19
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2 T3+T4
  SRFBP1 MUTATED     0   1     2
  SRFBP1 WILD-TYPE   5  16   100
D643V4, multiclass
       clus
vv      SRFBP1 MUTATED SRFBP1 WILD-TYPE
  T1                 0                5
  T2                 1               16
  T3+T4              2              100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V5, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    1  2
  SRFBP1 WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      1    2
  SRFBP1 WILD-TYPE   34   87
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D643V6, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    1  0
  SRFBP1 WILD-TYPE 56  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      1    0
  SRFBP1 WILD-TYPE   56    3
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              1               56
  1              0                3
[1] 2 2
[1] FALSE
D643V7, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    1  2
  SRFBP1 WILD-TYPE 50 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      1    2
  SRFBP1 WILD-TYPE   50   73
        clus
vv       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  FEMALE              1               50
  MALE                2               73
[1] 2 2
[1] FALSE
D643V8, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    3  0
  SRFBP1 WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      3    0
  SRFBP1 WILD-TYPE   85   30
     clus
vv    SRFBP1 MUTATED SRFBP1 WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SRFBP1 MUTATED                                     2
  SRFBP1 WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SRFBP1 MUTATED                                       1
  SRFBP1 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SRFBP1 MUTATED                                                  0
  SRFBP1 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  SRFBP1 MUTATED                                     0
  SRFBP1 WILD-TYPE                                   1
D643V9, multiclass
                                                  clus
vv                                                 SRFBP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 SRFBP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V10, continuous
[1] "Remove cluster labels:" "SRFBP1 MUTATED"        
clus
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB       TCGA-3A-A9IX 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-YY-A8LH 
"SRFBP1 WILD-TYPE" 
D643V11, continuous
[1] "Remove cluster labels:" "SRFBP1 MUTATED"        
clus
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SRFBP1 MUTATED    2  1  0  0
  SRFBP1 WILD-TYPE 78 34  4  2
D643V12, multiclass
    clus
vv   SRFBP1 MUTATED SRFBP1 WILD-TYPE
  R0              2               78
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRFBP1 MUTATED       0                         0     3
  SRFBP1 WILD-TYPE     6                         5   111
D643V14, multiclass
                           clus
vv                          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V15, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    0  2
  SRFBP1 WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      0    2
  SRFBP1 WILD-TYPE    5   89
                        clus
vv                       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(644) Variable = TSC22D1 MUTATION ANALYSIS
D644V1, survival
                   sevent
clus2                0  1
  TSC22D1 MUTATED    0  3
  TSC22D1 WILD-TYPE 63 59
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3               122 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3                59 
$`TSC22D1 MUTATED`
TCGA-2J-AAB1 TCGA-2L-AAQI TCGA-IB-7651 
        2.17         3.39        19.82 

$`TSC22D1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       14.14        16.37        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQJ 
       15.22         9.11        21.44         4.70        22.49        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
        9.60        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
             2.17              0.23 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
            19.82             90.12 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
             3.39             15.27 
[1] "2.2 - 19.8 (3.4)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.4"
D644V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TSC22D1 MUTATED         0        0        0         0         3         0
  TSC22D1 WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  TSC22D1 MUTATED          0
  TSC22D1 WILD-TYPE        3
D644V3, multiclass
           clus
vv          TSC22D1 MUTATED TSC22D1 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TSC22D1 MUTATED    0  0     3
  TSC22D1 WILD-TYPE  5 17    99
D644V4, multiclass
       clus
vv      TSC22D1 MUTATED TSC22D1 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V5, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    0  3
  TSC22D1 WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      0    3
  TSC22D1 WILD-TYPE   35   86
   clus
vv  TSC22D1 MUTATED TSC22D1 WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D644V6, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    2  0
  TSC22D1 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      2    0
  TSC22D1 WILD-TYPE   55    3
   clus
vv  TSC22D1 MUTATED TSC22D1 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D644V7, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    1  2
  TSC22D1 WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      1    2
  TSC22D1 WILD-TYPE   50   73
        clus
vv       TSC22D1 MUTATED TSC22D1 WILD-TYPE
  FEMALE               1                50
  MALE                 2                73
[1] 2 2
[1] FALSE
D644V8, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    3  0
  TSC22D1 WILD-TYPE 85 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      3    0
  TSC22D1 WILD-TYPE   85   30
     clus
vv    TSC22D1 MUTATED TSC22D1 WILD-TYPE
  NO                3                85
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TSC22D1 MUTATED                                     2
  TSC22D1 WILD-TYPE                                 103
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TSC22D1 MUTATED                                       1
  TSC22D1 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TSC22D1 MUTATED                                                  0
  TSC22D1 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TSC22D1 MUTATED                                     0
  TSC22D1 WILD-TYPE                                   1
D644V9, multiclass
                                                  clus
vv                                                 TSC22D1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TSC22D1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V10, continuous
[1] "Remove cluster labels:" "TSC22D1 MUTATED"       
clus
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AABA        TCGA-2J-AABE 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V        TCGA-HZ-A8P1 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-YY-A8LH 
"TSC22D1 WILD-TYPE" 
D644V11, continuous
[1] "Remove cluster labels:" "TSC22D1 MUTATED"       
clus
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AABE        TCGA-2J-AABF 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR        TCGA-3A-A9IX 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ        TCGA-FB-AAPS 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TSC22D1 MUTATED    2  1  0  0
  TSC22D1 WILD-TYPE 78 34  4  2
D644V12, multiclass
    clus
vv   TSC22D1 MUTATED TSC22D1 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSC22D1 MUTATED       0                         0     3
  TSC22D1 WILD-TYPE     6                         5   111
D644V14, multiclass
                           clus
vv                          TSC22D1 MUTATED TSC22D1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V15, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    0  1
  TSC22D1 WILD-TYPE  5 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      0    1
  TSC22D1 WILD-TYPE    5   90
                        clus
vv                       TSC22D1 MUTATED TSC22D1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               1                90
[1] 2 2
[1] FALSE

Clustering(645) Variable = EEF2 MUTATION ANALYSIS
D645V1, survival
                sevent
clus2             0  1
  EEF2 MUTATED    0  4
  EEF2 WILD-TYPE 63 58
  EEF2 MUTATED EEF2 WILD-TYPE 
             4            121 
  EEF2 MUTATED EEF2 WILD-TYPE 
             4             58 
$`EEF2 MUTATED`
TCGA-F2-A44G TCGA-2L-AAQL TCGA-FB-AAQ3 TCGA-IB-7651 
        7.66         9.60         1.02        19.82 

$`EEF2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95        45.47        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV 
       33.57        63.85        50.70        32.81        15.06        36.26 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 
       34.09        10.13        24.43        75.12        71.74        19.46 
TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ 
        3.12        17.00        16.37        12.33        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  EEF2 MUTATED EEF2 WILD-TYPE 
          1.02           0.23 
  EEF2 MUTATED EEF2 WILD-TYPE 
         19.82          90.12 
  EEF2 MUTATED EEF2 WILD-TYPE 
          8.63          15.32 
[1] "1.0 - 19.8 (8.6)"  "0.2 - 90.1 (15.3)"
[1] "hr=" "4.2"
D645V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  EEF2 MUTATED         0        0        0         0         4         0
  EEF2 WILD-TYPE       1        3       12        19        78         4
                vv
clus             STAGE IV
  EEF2 MUTATED          0
  EEF2 WILD-TYPE        3
D645V3, multiclass
           clus
vv          EEF2 MUTATED EEF2 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            4             78
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  EEF2 MUTATED    0  0     4
  EEF2 WILD-TYPE  5 17    98
D645V4, multiclass
       clus
vv      EEF2 MUTATED EEF2 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            4             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V5, binary
                cls
clus              0  1
  EEF2 MUTATED    0  4
  EEF2 WILD-TYPE 35 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      0    4
  EEF2 WILD-TYPE   35   85
   clus
vv  EEF2 MUTATED EEF2 WILD-TYPE
  0            0             35
  1            4             85
[1] 2 2
[1] FALSE
D645V6, binary
                cls
clus              0  1
  EEF2 MUTATED    2  0
  EEF2 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      2    0
  EEF2 WILD-TYPE   55    3
   clus
vv  EEF2 MUTATED EEF2 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D645V7, binary
                cls
clus              0  1
  EEF2 MUTATED    3  1
  EEF2 WILD-TYPE 48 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      3    1
  EEF2 WILD-TYPE   48   74
        clus
vv       EEF2 MUTATED EEF2 WILD-TYPE
  FEMALE            3             48
  MALE              1             74
[1] 2 2
[1] FALSE
D645V8, binary
                cls
clus              0  1
  EEF2 MUTATED    3  1
  EEF2 WILD-TYPE 85 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      3    1
  EEF2 WILD-TYPE   85   29
     clus
vv    EEF2 MUTATED EEF2 WILD-TYPE
  NO             3             85
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EEF2 MUTATED                                     4
  EEF2 WILD-TYPE                                 101
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EEF2 MUTATED                                       0
  EEF2 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EEF2 MUTATED                                                  0
  EEF2 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  EEF2 MUTATED                                     0
  EEF2 WILD-TYPE                                   1
D645V9, multiclass
                                                  clus
vv                                                 EEF2 MUTATED EEF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V10, continuous
[1] "Remove cluster labels:" "EEF2 MUTATED"          
clus
  EEF2 MUTATED EEF2 WILD-TYPE 
             1             38 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
D645V11, continuous
[1] "Remove cluster labels:" "EEF2 MUTATED"          
clus
  EEF2 MUTATED EEF2 WILD-TYPE 
             1             32 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" "EEF2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  EEF2 MUTATED    2  1  0  1
  EEF2 WILD-TYPE 78 34  4  1
D645V12, multiclass
    clus
vv   EEF2 MUTATED EEF2 WILD-TYPE
  R0            2             78
  R1            1             34
  R2            0              4
  RX            1              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EEF2 MUTATED       0                         0     4
  EEF2 WILD-TYPE     6                         5   110
D645V14, multiclass
                           clus
vv                          EEF2 MUTATED EEF2 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V15, binary
                cls
clus              0  1
  EEF2 MUTATED    0  3
  EEF2 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEF2 MUTATED      0    3
  EEF2 WILD-TYPE    5   88
                        clus
vv                       EEF2 MUTATED EEF2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(646) Variable = E2F7 MUTATION ANALYSIS
D646V1, survival
                sevent
clus2             0  1
  E2F7 MUTATED    0  3
  E2F7 WILD-TYPE 63 59
  E2F7 MUTATED E2F7 WILD-TYPE 
             3            122 
  E2F7 MUTATED E2F7 WILD-TYPE 
             3             59 
$`E2F7 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-LB-A9Q5 
       12.33        19.82        10.29 

$`E2F7 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP 
       71.74        19.46         3.12        17.00        16.37        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       12.46         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  E2F7 MUTATED E2F7 WILD-TYPE 
         10.29           0.23 
  E2F7 MUTATED E2F7 WILD-TYPE 
         19.82          90.12 
  E2F7 MUTATED E2F7 WILD-TYPE 
         12.33          15.27 
[1] "10.3 - 19.8 (12.3)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "2.6"
D646V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  E2F7 MUTATED         0        0        0         0         3         0
  E2F7 WILD-TYPE       1        3       12        19        79         4
                vv
clus             STAGE IV
  E2F7 MUTATED          0
  E2F7 WILD-TYPE        3
D646V3, multiclass
           clus
vv          E2F7 MUTATED E2F7 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  E2F7 MUTATED    0  0     3
  E2F7 WILD-TYPE  5 17    99
D646V4, multiclass
       clus
vv      E2F7 MUTATED E2F7 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V5, binary
                cls
clus              0  1
  E2F7 MUTATED    0  3
  E2F7 WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      0    3
  E2F7 WILD-TYPE   35   86
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D646V6, binary
                cls
clus              0  1
  E2F7 MUTATED    2  0
  E2F7 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      2    0
  E2F7 WILD-TYPE   55    3
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D646V7, binary
                cls
clus              0  1
  E2F7 MUTATED    3  0
  E2F7 WILD-TYPE 48 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      3    0
  E2F7 WILD-TYPE   48   75
        clus
vv       E2F7 MUTATED E2F7 WILD-TYPE
  FEMALE            3             48
  MALE              0             75
[1] 2 2
[1] FALSE
D646V8, binary
                cls
clus              0  1
  E2F7 MUTATED    2  1
  E2F7 WILD-TYPE 86 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      2    1
  E2F7 WILD-TYPE   86   29
     clus
vv    E2F7 MUTATED E2F7 WILD-TYPE
  NO             2             86
  YES            1             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  E2F7 MUTATED                                     3
  E2F7 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  E2F7 MUTATED                                       0
  E2F7 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  E2F7 MUTATED                                                  0
  E2F7 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  E2F7 MUTATED                                     0
  E2F7 WILD-TYPE                                   1
D646V9, multiclass
                                                  clus
vv                                                 E2F7 MUTATED E2F7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V10, continuous
D646V11, continuous
                vv
clus             R0 R1 R2 RX
  E2F7 MUTATED    3  0  0  0
  E2F7 WILD-TYPE 77 35  4  2
D646V12, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  E2F7 MUTATED       0                         0     3
  E2F7 WILD-TYPE     6                         5   111
D646V14, multiclass
                           clus
vv                          E2F7 MUTATED E2F7 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V15, binary
                cls
clus              0  1
  E2F7 MUTATED    0  3
  E2F7 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED      0    3
  E2F7 WILD-TYPE    5   88
                        clus
vv                       E2F7 MUTATED E2F7 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(647) Variable = NR2C1 MUTATION ANALYSIS
D647V1, survival
                 sevent
clus2              0  1
  NR2C1 MUTATED    1  2
  NR2C1 WILD-TYPE 62 60
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              3             122 
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              2              60 
$`NR2C1 MUTATED`
TCGA-2L-AAQA TCGA-IB-7651 TCGA-YH-A8SY 
        4.70        19.82        12.76 

$`NR2C1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQE TCGA-2L-AAQI 
       14.47        15.22         9.11        21.44        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  NR2C1 MUTATED NR2C1 WILD-TYPE 
           4.70            0.23 
  NR2C1 MUTATED NR2C1 WILD-TYPE 
          19.82           90.12 
  NR2C1 MUTATED NR2C1 WILD-TYPE 
          12.76           15.27 
[1] "4.7 - 19.8 (12.8)" "0.2 - 90.1 (15.3)"
[1] "hr=" "2"  
D647V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  NR2C1 MUTATED         0        0        0         0         2         1
  NR2C1 WILD-TYPE       1        3       12        19        80         3
                 vv
clus              STAGE IV
  NR2C1 MUTATED          0
  NR2C1 WILD-TYPE        3
D647V3, multiclass
           clus
vv          NR2C1 MUTATED NR2C1 WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             2              80
  STAGE III             1               3
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  NR2C1 MUTATED    0  0     3
  NR2C1 WILD-TYPE  5 17    99
D647V4, multiclass
       clus
vv      NR2C1 MUTATED NR2C1 WILD-TYPE
  T1                0               5
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V5, binary
                 cls
clus               0  1
  NR2C1 MUTATED    0  3
  NR2C1 WILD-TYPE 35 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR2C1 MUTATED      0    3
  NR2C1 WILD-TYPE   35   86
   clus
vv  NR2C1 MUTATED NR2C1 WILD-TYPE
  0             0              35
  1             3              86
[1] 2 2
[1] FALSE
D647V6, binary
                 cls
clus               0  1
  NR2C1 MUTATED    1  0
  NR2C1 WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR2C1 MUTATED      1    0
  NR2C1 WILD-TYPE   56    3
   clus
vv  NR2C1 MUTATED NR2C1 WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D647V7, binary
                 cls
clus               0  1
  NR2C1 MUTATED    2  1
  NR2C1 WILD-TYPE 49 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR2C1 MUTATED      2    1
  NR2C1 WILD-TYPE   49   74
        clus
vv       NR2C1 MUTATED NR2C1 WILD-TYPE
  FEMALE             2              49
  MALE               1              74
[1] 2 2
[1] FALSE
D647V8, binary
                 cls
clus               0  1
  NR2C1 MUTATED    2  1
  NR2C1 WILD-TYPE 86 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR2C1 MUTATED      2    1
  NR2C1 WILD-TYPE   86   29
     clus
vv    NR2C1 MUTATED NR2C1 WILD-TYPE
  NO              2              86
  YES             1              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NR2C1 MUTATED                                     2
  NR2C1 WILD-TYPE                                 103
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NR2C1 MUTATED                                       0
  NR2C1 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NR2C1 MUTATED                                                  0
  NR2C1 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  NR2C1 MUTATED                                     0
  NR2C1 WILD-TYPE                                   1
D647V9, multiclass
[1] "Remove cluster labels:" "NR2C1 MUTATED"         
clus
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              2             123 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IO 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-3E-AAAY 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3E-AAAZ      TCGA-F2-7273      TCGA-F2-A7TX      TCGA-F2-A8YN 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPP      TCGA-FB-AAPQ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPU      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-FZ-5919 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FZ-5920      TCGA-FZ-5921      TCGA-FZ-5922      TCGA-FZ-5923 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7652      TCGA-IB-7885 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
D647V10, continuous
[1] "Remove cluster labels:" "NR2C1 MUTATED"         
clus
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              2              37 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V      TCGA-HZ-A8P1 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUU 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-XN-A8T5 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-YY-A8LH 
"NR2C1 WILD-TYPE" 
D647V11, continuous
[1] "Remove cluster labels:" "NR2C1 MUTATED"         
clus
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NR2C1 MUTATED    1  1  0  0
  NR2C1 WILD-TYPE 79 34  4  2
D647V12, multiclass
[1] "Remove cluster labels:" "NR2C1 MUTATED"         
clus
  NR2C1 MUTATED NR2C1 WILD-TYPE 
              2             119 
     TCGA-2J-AABR      TCGA-2J-AABT      TCGA-3A-A9I5      TCGA-3A-A9IJ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IL      TCGA-F2-A44G      TCGA-FB-AAQ6      TCGA-FZ-5924 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS      TCGA-LB-A7SX 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-S4-A8RO      TCGA-US-A77E      TCGA-XD-AAUL      TCGA-2J-AAB1 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AAB4      TCGA-2J-AAB6      TCGA-2J-AAB8      TCGA-2J-AAB9 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABH 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABK      TCGA-2J-AABO      TCGA-2J-AABP      TCGA-2J-AABU 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2J-AABV      TCGA-2L-AAQE      TCGA-2L-AAQI      TCGA-2L-AAQJ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-2L-AAQL      TCGA-2L-AAQM      TCGA-3A-A9I7      TCGA-3A-A9I9 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IC      TCGA-3A-A9IH      TCGA-3A-A9IO 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IR      TCGA-3A-A9IS      TCGA-3A-A9IU      TCGA-3A-A9IV 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-3A-A9IZ      TCGA-3A-A9J0      TCGA-F2-7273 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAPP      TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-FB-AAPU 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAPZ      TCGA-FB-AAQ0      TCGA-FB-AAQ1      TCGA-FB-AAQ2 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FB-AAQ3      TCGA-FZ-5920      TCGA-FZ-5922      TCGA-FZ-5923 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-FZ-5926      TCGA-H8-A6C1      TCGA-HV-A7OL      TCGA-HV-A7OP 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7918      TCGA-HZ-7925 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49I      TCGA-HZ-A77O      TCGA-HZ-A77P 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-HZ-A9TJ      TCGA-IB-7652      TCGA-IB-7885 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SO      TCGA-IB-A5SP      TCGA-IB-A5SQ 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-A5ST      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7LX 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUM      TCGA-IB-AAUN      TCGA-IB-AAUO 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUP      TCGA-IB-AAUQ      TCGA-IB-AAUR      TCGA-IB-AAUS 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-IB-AAUW      TCGA-LB-A8F3 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-RB-A7B8      TCGA-RB-AA9M      TCGA-RL-AAAS      TCGA-US-A776 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-US-A779      TCGA-US-A77G      TCGA-US-A77J      TCGA-XD-AAUG 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-XD-AAUH      TCGA-XD-AAUI      TCGA-XN-A8T3      TCGA-XN-A8T5 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" "NR2C1 WILD-TYPE" 
D647V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NR2C1 MUTATED       0                         0     3
  NR2C1 WILD-TYPE     6                         5   111
D647V14, multiclass
                           clus
vv                          NR2C1 MUTATED NR2C1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V15, binary
                 cls
clus               0  1
  NR2C1 MUTATED    0  2
  NR2C1 WILD-TYPE  5 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR2C1 MUTATED      0    2
  NR2C1 WILD-TYPE    5   89
                        clus
vv                       NR2C1 MUTATED NR2C1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2              89
[1] 2 2
[1] FALSE

Clustering(648) Variable = ASPM MUTATION ANALYSIS
D648V1, survival
                sevent
clus2             0  1
  ASPM MUTATED    4  4
  ASPM WILD-TYPE 59 58
  ASPM MUTATED ASPM WILD-TYPE 
             8            117 
  ASPM MUTATED ASPM WILD-TYPE 
             4             58 
$`ASPM MUTATED`
TCGA-FB-AAQ6 TCGA-HZ-A77Q TCGA-3A-A9IC TCGA-3A-A9J0 TCGA-HV-A7OP TCGA-HZ-A77O 
        8.02         1.08        24.26        24.43        32.15         5.26 
TCGA-HZ-A77P TCGA-IB-7651 
       10.85        19.82 

$`ASPM WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
       15.78        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP 
       22.22        22.72        42.31        15.91        14.47        15.22 
TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ 
        9.11        21.44         4.70        22.49         3.39        12.95 
TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH 
        9.60        45.47        43.50        20.84         7.36        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN 
       10.13        75.12        71.74        19.46         3.12        17.00 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU 
       16.37        12.33        15.95        37.15         7.50        12.53 
TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 
       23.54        15.55         4.04         5.03         1.02        24.36 
TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 
        2.01         5.10        36.20        20.35        17.79        22.06 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
        8.28        30.25        17.49        31.86        20.19        17.00 
TCGA-HZ-A49I TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.13         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        20.88        21.90         1.35 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J 
        9.40         0.30        39.98        16.80         0.39        18.67 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       13.81        12.99        12.03        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ASPM MUTATED ASPM WILD-TYPE 
          1.08           0.23 
  ASPM MUTATED ASPM WILD-TYPE 
         32.15          90.12 
  ASPM MUTATED ASPM WILD-TYPE 
        15.335         15.220 
[1] "1.1 - 32.1 (15.3)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1"  
D648V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ASPM MUTATED         0        1        0         0         8         0
  ASPM WILD-TYPE       1        2       12        19        74         4
                vv
clus             STAGE IV
  ASPM MUTATED          0
  ASPM WILD-TYPE        3
D648V3, multiclass
           clus
vv          ASPM MUTATED ASPM WILD-TYPE
  STAGE I              0              1
  STAGE IA             1              2
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            8             74
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  ASPM MUTATED    1  1     7
  ASPM WILD-TYPE  4 16    95
D648V4, multiclass
       clus
vv      ASPM MUTATED ASPM WILD-TYPE
  T1               1              4
  T2               1             16
  T3+T4            7             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V5, binary
                cls
clus              0  1
  ASPM MUTATED    1  8
  ASPM WILD-TYPE 34 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED      1    8
  ASPM WILD-TYPE   34   81
   clus
vv  ASPM MUTATED ASPM WILD-TYPE
  0            1             34
  1            8             81
[1] 2 2
[1] FALSE
D648V6, binary
                cls
clus              0  1
  ASPM MUTATED    2  0
  ASPM WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED      2    0
  ASPM WILD-TYPE   55    3
   clus
vv  ASPM MUTATED ASPM WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D648V7, binary
                cls
clus              0  1
  ASPM MUTATED    4  5
  ASPM WILD-TYPE 47 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED      4    5
  ASPM WILD-TYPE   47   70
        clus
vv       ASPM MUTATED ASPM WILD-TYPE
  FEMALE            4             47
  MALE              5             70
[1] 2 2
[1] FALSE
D648V8, binary
                cls
clus              0  1
  ASPM MUTATED    5  2
  ASPM WILD-TYPE 83 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED      5    2
  ASPM WILD-TYPE   83   28
     clus
vv    ASPM MUTATED ASPM WILD-TYPE
  NO             5             83
  YES            2             28
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASPM MUTATED                                     6
  ASPM WILD-TYPE                                  99
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASPM MUTATED                                       3
  ASPM WILD-TYPE                                    15
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASPM MUTATED                                                  0
  ASPM WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  ASPM MUTATED                                     0
  ASPM WILD-TYPE                                   1
D648V9, multiclass
                                                  clus
vv                                                 ASPM MUTATED ASPM WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6             99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             15
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V10, continuous
D648V11, continuous
                vv
clus             R0 R1 R2 RX
  ASPM MUTATED    9  0  0  0
  ASPM WILD-TYPE 71 35  4  2
D648V12, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  R0            9             71
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASPM MUTATED       1                         0     8
  ASPM WILD-TYPE     5                         5   106
D648V14, multiclass
                           clus
vv                          ASPM MUTATED ASPM WILD-TYPE
  ASIAN                                1              5
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V15, binary
                cls
clus              0  1
  ASPM MUTATED    0  8
  ASPM WILD-TYPE  5 83
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED      0    8
  ASPM WILD-TYPE    5   83
                        clus
vv                       ASPM MUTATED ASPM WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             83
[1] 2 2
[1] FALSE

Clustering(649) Variable = CCDC108 MUTATION ANALYSIS
D649V1, survival
                   sevent
clus2                0  1
  CCDC108 MUTATED    0  3
  CCDC108 WILD-TYPE 63 59
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                3               122 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                3                59 
$`CCDC108 MUTATED`
TCGA-IB-7651 TCGA-IB-A6UG TCGA-US-A779 
       19.82         1.35        16.80 

$`CCDC108 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        8.22        15.88         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW 
        6.02        11.11         7.40         8.05        13.28         7.56 
TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.46        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        9.40         0.30        39.98         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CCDC108 MUTATED CCDC108 WILD-TYPE 
             1.35              0.23 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
            19.82             90.12 
  CCDC108 MUTATED CCDC108 WILD-TYPE 
           16.800            15.205 
[1] "1.4 - 19.8 (16.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "2.7"
D649V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CCDC108 MUTATED         0        0        0         0         3         0
  CCDC108 WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  CCDC108 MUTATED          0
  CCDC108 WILD-TYPE        3
D649V3, multiclass
           clus
vv          CCDC108 MUTATED CCDC108 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  CCDC108 MUTATED    0  0     3
  CCDC108 WILD-TYPE  5 17    99
D649V4, multiclass
       clus
vv      CCDC108 MUTATED CCDC108 WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V5, binary
                   cls
clus                 0  1
  CCDC108 MUTATED    0  3
  CCDC108 WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      0    3
  CCDC108 WILD-TYPE   35   86
   clus
vv  CCDC108 MUTATED CCDC108 WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D649V6, binary
                   cls
clus                 0  1
  CCDC108 MUTATED    2  0
  CCDC108 WILD-TYPE 55  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      2    0
  CCDC108 WILD-TYPE   55    3
   clus
vv  CCDC108 MUTATED CCDC108 WILD-TYPE
  0               2                55
  1               0                 3
[1] 2 2
[1] FALSE
D649V7, binary
                   cls
clus                 0  1
  CCDC108 MUTATED    2  1
  CCDC108 WILD-TYPE 49 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      2    1
  CCDC108 WILD-TYPE   49   74
        clus
vv       CCDC108 MUTATED CCDC108 WILD-TYPE
  FEMALE               2                49
  MALE                 1                74
[1] 2 2
[1] FALSE
D649V8, binary
                   cls
clus                 0  1
  CCDC108 MUTATED    2  0
  CCDC108 WILD-TYPE 86 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      2    0
  CCDC108 WILD-TYPE   86   30
     clus
vv    CCDC108 MUTATED CCDC108 WILD-TYPE
  NO                2                86
  YES               0                30
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC108 MUTATED                                     3
  CCDC108 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC108 MUTATED                                       0
  CCDC108 WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC108 MUTATED                                                  0
  CCDC108 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CCDC108 MUTATED                                     0
  CCDC108 WILD-TYPE                                   1
D649V9, multiclass
                                                  clus
vv                                                 CCDC108 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CCDC108 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V10, continuous
[1] "Remove cluster labels:" "CCDC108 MUTATED"       
clus
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-YY-A8LH 
"CCDC108 WILD-TYPE" 
D649V11, continuous
[1] "Remove cluster labels:" "CCDC108 MUTATED"       
clus
  CCDC108 MUTATED CCDC108 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" "CCDC108 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CCDC108 MUTATED    2  1  0  0
  CCDC108 WILD-TYPE 78 34  4  2
D649V12, multiclass
    clus
vv   CCDC108 MUTATED CCDC108 WILD-TYPE
  R0               2                78
  R1               1                34
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC108 MUTATED       0                         0     3
  CCDC108 WILD-TYPE     6                         5   111
D649V14, multiclass
                           clus
vv                          CCDC108 MUTATED CCDC108 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V15, binary
                   cls
clus                 0  1
  CCDC108 MUTATED    0  3
  CCDC108 WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC108 MUTATED      0    3
  CCDC108 WILD-TYPE    5   88
                        clus
vv                       CCDC108 MUTATED CCDC108 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(650) Variable = PDGFRB MUTATION ANALYSIS
D650V1, survival
                  sevent
clus2               0  1
  PDGFRB MUTATED    0  4
  PDGFRB WILD-TYPE 63 58
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               4              121 
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               4               58 
$`PDGFRB MUTATED`
TCGA-FB-AAQ6 TCGA-FB-AAPU TCGA-FZ-5920 TCGA-IB-7651 
        8.02        12.53         2.01        19.82 

$`PDGFRB WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
        1.02        24.36         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  PDGFRB MUTATED PDGFRB WILD-TYPE 
            2.01             0.23 
  PDGFRB MUTATED PDGFRB WILD-TYPE 
           19.82            90.12 
  PDGFRB MUTATED PDGFRB WILD-TYPE 
          10.275           15.320 
[1] "2.0 - 19.8 (10.3)" "0.2 - 90.1 (15.3)"
[1] "hr=" "3.7"
D650V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  PDGFRB MUTATED         0        1        0         1         2         0
  PDGFRB WILD-TYPE       1        2       12        18        80         4
                  vv
clus               STAGE IV
  PDGFRB MUTATED          0
  PDGFRB WILD-TYPE        3
D650V3, multiclass
           clus
vv          PDGFRB MUTATED PDGFRB WILD-TYPE
  STAGE I                0                1
  STAGE IA               1                2
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PDGFRB MUTATED    1  0     3
  PDGFRB WILD-TYPE  4 17    99
D650V4, multiclass
       clus
vv      PDGFRB MUTATED PDGFRB WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V5, binary
                  cls
clus                0  1
  PDGFRB MUTATED    2  2
  PDGFRB WILD-TYPE 33 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRB MUTATED      2    2
  PDGFRB WILD-TYPE   33   87
   clus
vv  PDGFRB MUTATED PDGFRB WILD-TYPE
  0              2               33
  1              2               87
[1] 2 2
[1] FALSE
D650V6, binary
                  cls
clus                0  1
  PDGFRB MUTATED    2  0
  PDGFRB WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRB MUTATED      2    0
  PDGFRB WILD-TYPE   55    3
   clus
vv  PDGFRB MUTATED PDGFRB WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D650V7, binary
                  cls
clus                0  1
  PDGFRB MUTATED    2  2
  PDGFRB WILD-TYPE 49 73
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRB MUTATED      2    2
  PDGFRB WILD-TYPE   49   73
        clus
vv       PDGFRB MUTATED PDGFRB WILD-TYPE
  FEMALE              2               49
  MALE                2               73
[1] 2 2
[1] FALSE
D650V8, binary
                  cls
clus                0  1
  PDGFRB MUTATED    4  0
  PDGFRB WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRB MUTATED      4    0
  PDGFRB WILD-TYPE   84   30
     clus
vv    PDGFRB MUTATED PDGFRB WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDGFRB MUTATED                                     4
  PDGFRB WILD-TYPE                                 101
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDGFRB MUTATED                                       0
  PDGFRB WILD-TYPE                                    18
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDGFRB MUTATED                                                  0
  PDGFRB WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  PDGFRB MUTATED                                     0
  PDGFRB WILD-TYPE                                   1
D650V9, multiclass
                                                  clus
vv                                                 PDGFRB MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 PDGFRB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V10, continuous
[1] "Remove cluster labels:" "PDGFRB MUTATED"        
clus
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
D650V11, continuous
[1] "Remove cluster labels:" "PDGFRB MUTATED"        
clus
  PDGFRB MUTATED PDGFRB WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" "PDGFRB WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PDGFRB MUTATED    3  1  0  0
  PDGFRB WILD-TYPE 77 34  4  2
D650V12, multiclass
    clus
vv   PDGFRB MUTATED PDGFRB WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDGFRB MUTATED       1                         1     2
  PDGFRB WILD-TYPE     5                         4   112
D650V14, multiclass
                           clus
vv                          PDGFRB MUTATED PDGFRB WILD-TYPE
  ASIAN                                  1                5
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  2              112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V15, binary
                  cls
clus                0  1
  PDGFRB MUTATED    0  4
  PDGFRB WILD-TYPE  5 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRB MUTATED      0    4
  PDGFRB WILD-TYPE    5   87
                        clus
vv                       PDGFRB MUTATED PDGFRB WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4               87
[1] 2 2
[1] FALSE

Clustering(651) Variable = TWISTNB MUTATION ANALYSIS
D651V1, survival
                   sevent
clus2                0  1
  TWISTNB MUTATED    1  2
  TWISTNB WILD-TYPE 62 60
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3               122 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                60 
$`TWISTNB MUTATED`
TCGA-F2-A44G TCGA-IB-7651 TCGA-IB-A6UF 
        7.66        19.82        21.90 

$`TWISTNB WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-FB-AAQ6 
       14.40        10.49        58.98        60.95        90.12         8.02 
TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E 
       15.78         1.08        15.12        12.92        17.26        14.14 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TWISTNB MUTATED TWISTNB WILD-TYPE 
             7.66              0.23 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
            21.90             90.12 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
           19.820            15.205 
[1] "7.7 - 21.9 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D651V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  TWISTNB MUTATED         0        0        0         0         3         0
  TWISTNB WILD-TYPE       1        3       12        19        79         4
                   vv
clus                STAGE IV
  TWISTNB MUTATED          0
  TWISTNB WILD-TYPE        3
D651V3, multiclass
           clus
vv          TWISTNB MUTATED TWISTNB WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                0                12
  STAGE IIA               0                19
  STAGE IIB               3                79
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3+T4
  TWISTNB MUTATED    0  0     3
  TWISTNB WILD-TYPE  5 17    99
D651V4, multiclass
       clus
vv      TWISTNB MUTATED TWISTNB WILD-TYPE
  T1                  0                 5
  T2                  0                17
  T3+T4               3                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V5, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    0  3
  TWISTNB WILD-TYPE 35 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      0    3
  TWISTNB WILD-TYPE   35   86
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               0                35
  1               3                86
[1] 2 2
[1] FALSE
D651V6, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    3  0
  TWISTNB WILD-TYPE 54  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      3    0
  TWISTNB WILD-TYPE   54    3
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               3                54
  1               0                 3
[1] 2 2
[1] FALSE
D651V7, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    2  1
  TWISTNB WILD-TYPE 49 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      2    1
  TWISTNB WILD-TYPE   49   74
        clus
vv       TWISTNB MUTATED TWISTNB WILD-TYPE
  FEMALE               2                49
  MALE                 1                74
[1] 2 2
[1] FALSE
D651V8, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    2  1
  TWISTNB WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      2    1
  TWISTNB WILD-TYPE   86   29
     clus
vv    TWISTNB MUTATED TWISTNB WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TWISTNB MUTATED                                     3
  TWISTNB WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TWISTNB MUTATED                                       0
  TWISTNB WILD-TYPE                                    18
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TWISTNB MUTATED                                                  0
  TWISTNB WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  TWISTNB MUTATED                                     0
  TWISTNB WILD-TYPE                                   1
D651V9, multiclass
                                                  clus
vv                                                 TWISTNB MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 TWISTNB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V10, continuous
[1] "Remove cluster labels:" "TWISTNB MUTATED"       
clus
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-HZ-A8P1        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UG 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-YY-A8LH 
"TWISTNB WILD-TYPE" 
D651V11, continuous
[1] "Remove cluster labels:" "TWISTNB MUTATED"       
clus
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HZ-A8P1        TCGA-IB-7885 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TWISTNB MUTATED    1  2  0  0
  TWISTNB WILD-TYPE 79 33  4  2
D651V12, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  R0               1                79
  R1               2                33
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TWISTNB MUTATED       0                         0     3
  TWISTNB WILD-TYPE     6                         5   111
D651V14, multiclass
                           clus
vv                          TWISTNB MUTATED TWISTNB WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V15, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    0  3
  TWISTNB WILD-TYPE  5 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      0    3
  TWISTNB WILD-TYPE    5   88
                        clus
vv                       TWISTNB MUTATED TWISTNB WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3                88
[1] 2 2
[1] FALSE

Clustering(652) Variable = GRIN3B MUTATION ANALYSIS
D652V1, survival
                  sevent
clus2               0  1
  GRIN3B MUTATED    3  1
  GRIN3B WILD-TYPE 60 61
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               4              121 
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               1               61 
$`GRIN3B MUTATED`
TCGA-2J-AABT TCGA-3A-A9IL TCGA-2J-AABH TCGA-IB-7651 
       10.49        90.12        42.31        19.82 

$`GRIN3B WILD-TYPE`
TCGA-2J-AABR TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-F2-A44G TCGA-FB-AAQ6 TCGA-FZ-5924 
       14.40        58.98        60.95         7.66         8.02        15.78 
TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO TCGA-US-A77E TCGA-XD-AAUL 
        1.08        15.12        12.92        17.26        14.14        16.37 
TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 TCGA-2J-AABA 
        2.17        23.97         9.63         2.63        20.61        19.96 
TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU 
       22.22        22.72        15.91        14.47        15.22         9.11 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL 
       21.44         4.70        22.49         3.39        12.95         9.60 
TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH 
       45.47        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX 
       63.85        50.70        32.81        15.06        36.26        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX 
       10.13        24.43        75.12        71.74        19.46         3.12 
TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS 
       17.00        16.37        12.33        15.95        37.15         7.50 
TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
       12.53        23.54        15.55         4.04         5.03         1.02 
TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 
       24.36         2.01         5.10        36.20        20.35        17.79 
TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 
       22.06         8.28        32.15        30.25        17.49        31.86 
TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       20.19        17.00        10.13         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GRIN3B MUTATED GRIN3B WILD-TYPE 
           10.49             0.23 
  GRIN3B MUTATED GRIN3B WILD-TYPE 
           90.12            75.12 
  GRIN3B MUTATED GRIN3B WILD-TYPE 
          31.065           15.190 
[1] "10.5 - 90.1 (31.1)" "0.2 - 75.1 (15.2)" 
[1] "hr=" "3.6"
D652V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GRIN3B MUTATED         1        0        0         1         2         0
  GRIN3B WILD-TYPE       0        3       12        18        80         4
                  vv
clus               STAGE IV
  GRIN3B MUTATED          0
  GRIN3B WILD-TYPE        3
D652V3, multiclass
           clus
vv          GRIN3B MUTATED GRIN3B WILD-TYPE
  STAGE I                1                0
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              1               18
  STAGE IIB              2               80
  STAGE III              0                4
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  GRIN3B MUTATED    1  0     3
  GRIN3B WILD-TYPE  4 17    99
D652V4, multiclass
       clus
vv      GRIN3B MUTATED GRIN3B WILD-TYPE
  T1                 1                4
  T2                 0               17
  T3+T4              3               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V5, binary
                  cls
clus                0  1
  GRIN3B MUTATED    1  2
  GRIN3B WILD-TYPE 34 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN3B MUTATED      1    2
  GRIN3B WILD-TYPE   34   87
   clus
vv  GRIN3B MUTATED GRIN3B WILD-TYPE
  0              1               34
  1              2               87
[1] 2 2
[1] FALSE
D652V6, binary
                  cls
clus                0  1
  GRIN3B MUTATED    3  0
  GRIN3B WILD-TYPE 54  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN3B MUTATED      3    0
  GRIN3B WILD-TYPE   54    3
   clus
vv  GRIN3B MUTATED GRIN3B WILD-TYPE
  0              3               54
  1              0                3
[1] 2 2
[1] FALSE
D652V7, binary
                  cls
clus                0  1
  GRIN3B MUTATED    3  1
  GRIN3B WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN3B MUTATED      3    1
  GRIN3B WILD-TYPE   48   74
        clus
vv       GRIN3B MUTATED GRIN3B WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D652V8, binary
                  cls
clus                0  1
  GRIN3B MUTATED    3  0
  GRIN3B WILD-TYPE 85 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN3B MUTATED      3    0
  GRIN3B WILD-TYPE   85   30
     clus
vv    GRIN3B MUTATED GRIN3B WILD-TYPE
  NO               3               85
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GRIN3B MUTATED                                     2
  GRIN3B WILD-TYPE                                 103
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GRIN3B MUTATED                                       2
  GRIN3B WILD-TYPE                                    16
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GRIN3B MUTATED                                                  0
  GRIN3B WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  GRIN3B MUTATED                                     0
  GRIN3B WILD-TYPE                                   1
D652V9, multiclass
                                                  clus
vv                                                 GRIN3B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 GRIN3B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           103
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          16
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V10, continuous
[1] "Remove cluster labels:" "GRIN3B MUTATED"        
clus
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               1               38 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-A78T 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-FB-AAPQ       TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-IB-AAUU       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-XN-A8T5       TCGA-YY-A8LH 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
D652V11, continuous
[1] "Remove cluster labels:" "GRIN3B MUTATED"        
clus
  GRIN3B MUTATED GRIN3B WILD-TYPE 
               1               32 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPQ 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
      TCGA-OE-A75W       TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" "GRIN3B WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  GRIN3B MUTATED    4  0  0  0
  GRIN3B WILD-TYPE 76 35  4  2
D652V12, multiclass
    clus
vv   GRIN3B MUTATED GRIN3B WILD-TYPE
  R0              4               76
  R1              0               35
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GRIN3B MUTATED       0                         0     4
  GRIN3B WILD-TYPE     6                         5   110
D652V14, multiclass
                           clus
vv                          GRIN3B MUTATED GRIN3B WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V15, binary
                  cls
clus                0  1
  GRIN3B MUTATED    0  2
  GRIN3B WILD-TYPE  5 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN3B MUTATED      0    2
  GRIN3B WILD-TYPE    5   89
                        clus
vv                       GRIN3B MUTATED GRIN3B WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2               89
[1] 2 2
[1] FALSE

Clustering(653) Variable = ENTPD2 MUTATION ANALYSIS
D653V1, survival
                  sevent
clus2               0  1
  ENTPD2 MUTATED    1  3
  ENTPD2 WILD-TYPE 62 59
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              121 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               3               59 
$`ENTPD2 MUTATED`
TCGA-2L-AAQJ TCGA-FB-A78T TCGA-HZ-A77P TCGA-IB-7651 
       12.95        12.33        10.85        19.82 

$`ENTPD2 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
        3.39         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-AAPP TCGA-FB-AAPQ 
       19.46         3.12        17.00        16.37        15.95        37.15 
TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
        7.50        12.53        23.54        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A8P1 
       31.86        20.19        17.00        10.13         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.82        36.69        41.33        15.19        12.00        15.85 
TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        20.88        21.90         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           10.85             0.23 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           19.82            90.12 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           12.64            15.32 
[1] "10.8 - 19.8 (12.6)" "0.2 - 90.1 (15.3)" 
[1] "hr=" "2"  
D653V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  ENTPD2 MUTATED         0        0        0         0         3         1
  ENTPD2 WILD-TYPE       1        3       12        19        79         3
                  vv
clus               STAGE IV
  ENTPD2 MUTATED          0
  ENTPD2 WILD-TYPE        3
D653V3, multiclass
           clus
vv          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  STAGE I                0                1
  STAGE IA               0                3
  STAGE IB               0               12
  STAGE IIA              0               19
  STAGE IIB              3               79
  STAGE III              1                3
  STAGE IV               0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  ENTPD2 MUTATED    0  0     4
  ENTPD2 WILD-TYPE  5 17    98
D653V4, multiclass
       clus
vv      ENTPD2 MUTATED ENTPD2 WILD-TYPE
  T1                 0                5
  T2                 0               17
  T3+T4              4               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V5, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    1  3
  ENTPD2 WILD-TYPE 34 86
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      1    3
  ENTPD2 WILD-TYPE   34   86
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              1               34
  1              3               86
[1] 2 2
[1] FALSE
D653V6, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    2  0
  ENTPD2 WILD-TYPE 55  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      2    0
  ENTPD2 WILD-TYPE   55    3
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              2               55
  1              0                3
[1] 2 2
[1] FALSE
D653V7, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    3  1
  ENTPD2 WILD-TYPE 48 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      3    1
  ENTPD2 WILD-TYPE   48   74
        clus
vv       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  FEMALE              3               48
  MALE                1               74
[1] 2 2
[1] FALSE
D653V8, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    4  0
  ENTPD2 WILD-TYPE 84 30
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      4    0
  ENTPD2 WILD-TYPE   84   30
     clus
vv    ENTPD2 MUTATED ENTPD2 WILD-TYPE
  NO               4               84
  YES              0               30
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ENTPD2 MUTATED                                     3
  ENTPD2 WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ENTPD2 MUTATED                                       1
  ENTPD2 WILD-TYPE                                    17
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ENTPD2 MUTATED                                                  0
  ENTPD2 WILD-TYPE                                                1
                  vv
clus               PANCREAS-UNDIFFERENTIATED CARCINOMA
  ENTPD2 MUTATED                                     0
  ENTPD2 WILD-TYPE                                   1
D653V9, multiclass
                                                  clus
vv                                                 ENTPD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                           0
                                                  clus
vv                                                 ENTPD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V10, continuous
[1] "Remove cluster labels:" "ENTPD2 MUTATED"        
clus
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               2               37 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABA 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO       TCGA-2J-AABV 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-2L-AAQA       TCGA-2L-AAQE       TCGA-3A-A9I9       TCGA-3A-A9IB 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-F2-A8YN       TCGA-FB-A5VM       TCGA-FB-AAPQ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-FB-AAPS       TCGA-H8-A6C1       TCGA-HV-AA8V       TCGA-HZ-A8P1 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A6UF       TCGA-IB-A6UG 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IB-A7M4       TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUU 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-XN-A8T5 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-YY-A8LH 
"ENTPD2 WILD-TYPE" 
D653V11, continuous
[1] "Remove cluster labels:" "ENTPD2 MUTATED"        
clus
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               2               31 
      TCGA-3A-A9IJ       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-IB-A5SS 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-XD-AAUL       TCGA-2J-AAB1       TCGA-2J-AABE 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-2J-AABF       TCGA-2J-AABO       TCGA-3A-A9IB       TCGA-3A-A9IR 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-3A-A9IX       TCGA-FB-A5VM       TCGA-FB-AAPQ       TCGA-FB-AAPS 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-H8-A6C1       TCGA-HZ-A8P1       TCGA-IB-7885       TCGA-IB-8126 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUV       TCGA-LB-A9Q5       TCGA-OE-A75W 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
      TCGA-XD-AAUI       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" "ENTPD2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ENTPD2 MUTATED    3  1  0  0
  ENTPD2 WILD-TYPE 77 34  4  2
D653V12, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  R0              3               77
  R1              1               34
  R2              0                4
  RX              0                2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENTPD2 MUTATED       0                         0     4
  ENTPD2 WILD-TYPE     6                         5   110
D653V14, multiclass
                           clus
vv                          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V15, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    0  3
  ENTPD2 WILD-TYPE  5 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      0    3
  ENTPD2 WILD-TYPE    5   88
                        clus
vv                       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3               88
[1] 2 2
[1] FALSE

Clustering(654) Variable = STK11 MUTATION ANALYSIS
D654V1, survival
                 sevent
clus2              0  1
  STK11 MUTATED    1  2
  STK11 WILD-TYPE 62 60
  STK11 MUTATED STK11 WILD-TYPE 
              3             122 
  STK11 MUTATED STK11 WILD-TYPE 
              2              60 
$`STK11 MUTATED`
TCGA-3A-A9IH TCGA-IB-7651 TCGA-IB-A6UG 
       33.57        19.82         1.35 

$`STK11 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
       10.85         0.23        19.82        36.69        41.33        15.19 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX 
       12.00        15.85         7.20        20.88        21.90         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  STK11 MUTATED STK11 WILD-TYPE 
           1.35            0.23 
  STK11 MUTATED STK11 WILD-TYPE 
          33.57           90.12 
  STK11 MUTATED STK11 WILD-TYPE 
         19.820          15.205 
[1] "1.4 - 33.6 (19.8)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.3"
D654V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  STK11 MUTATED         0        1        0         0         3         0
  STK11 WILD-TYPE       1        2       12        19        79         4
                 vv
clus              STAGE IV
  STK11 MUTATED          0
  STK11 WILD-TYPE        3
D654V3, multiclass
           clus
vv          STK11 MUTATED STK11 WILD-TYPE
  STAGE I               0               1
  STAGE IA              1               2
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             3              79
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  STK11 MUTATED    1  0     3
  STK11 WILD-TYPE  4 17    99
D654V4, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  T1                1               4
  T2                0              17
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V5, binary
                 cls
clus               0  1
  STK11 MUTATED    1  3
  STK11 WILD-TYPE 34 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      1    3
  STK11 WILD-TYPE   34   86
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0             1              34
  1             3              86
[1] 2 2
[1] FALSE
D654V6, binary
                 cls
clus               0  1
  STK11 MUTATED    2  0
  STK11 WILD-TYPE 55  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      2    0
  STK11 WILD-TYPE   55    3
   clus
vv  STK11 MUTATED STK11 WILD-TYPE
  0             2              55
  1             0               3
[1] 2 2
[1] FALSE
D654V7, binary
                 cls
clus               0  1
  STK11 MUTATED    2  2
  STK11 WILD-TYPE 49 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      2    2
  STK11 WILD-TYPE   49   73
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE             2              49
  MALE               2              73
[1] 2 2
[1] FALSE
D654V8, binary
                 cls
clus               0  1
  STK11 MUTATED    3  0
  STK11 WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      3    0
  STK11 WILD-TYPE   85   30
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STK11 MUTATED                                     4
  STK11 WILD-TYPE                                 101
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STK11 MUTATED                                       0
  STK11 WILD-TYPE                                    18
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STK11 MUTATED                                                  0
  STK11 WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  STK11 MUTATED                                     0
  STK11 WILD-TYPE                                   1
D654V9, multiclass
                                                  clus
vv                                                 STK11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 STK11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V10, continuous
D654V11, continuous
                 vv
clus              R0 R1 R2 RX
  STK11 MUTATED    3  1  0  0
  STK11 WILD-TYPE 77 34  4  2
D654V12, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0             3              77
  R1             1              34
  R2             0               4
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STK11 MUTATED       0                         0     4
  STK11 WILD-TYPE     6                         5   110
D654V14, multiclass
                           clus
vv                          STK11 MUTATED STK11 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V15, binary
                 cls
clus               0  1
  STK11 MUTATED    0  4
  STK11 WILD-TYPE  5 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      0    4
  STK11 WILD-TYPE    5   87
                        clus
vv                       STK11 MUTATED STK11 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4              87
[1] 2 2
[1] FALSE

Clustering(655) Variable = LBR MUTATION ANALYSIS
D655V1, survival
               sevent
clus2            0  1
  LBR MUTATED    2  2
  LBR WILD-TYPE 61 60
  LBR MUTATED LBR WILD-TYPE 
            4           121 
  LBR MUTATED LBR WILD-TYPE 
            2            60 
$`LBR MUTATED`
TCGA-2J-AABF TCGA-FB-AAPZ TCGA-IB-7651 TCGA-IB-A6UF 
       22.72        23.54        19.82        21.90 

$`LBR WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       20.61        19.96        22.22        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 
       37.15         7.50        12.53        15.55         4.04         5.03 
TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 TCGA-FZ-5923 
        1.02        24.36         2.01         5.10        36.20        20.35 
TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V TCGA-HV-AA8X 
       17.79        22.06         8.28        32.15        30.25        17.49 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85         7.20        20.88         1.35         8.22        15.88 
TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR 
        0.26         4.73         7.86        14.17         6.02        11.11 
TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 TCGA-LB-A9Q5 
        7.40         8.05        13.28         7.56        12.46        10.29 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-RL-AAAS 
        8.78        13.68         3.12        15.32         9.40         0.30 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80         0.39        18.67        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  LBR MUTATED LBR WILD-TYPE 
        19.82          0.23 
  LBR MUTATED LBR WILD-TYPE 
        23.54         90.12 
  LBR MUTATED LBR WILD-TYPE 
        22.31         15.12 
[1] "19.8 - 23.5 (22.3)" "0.2 - 90.1 (15.1)" 
[1] "hr=" "1.6"
D655V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  LBR MUTATED         0        0        0         0         4         0
  LBR WILD-TYPE       1        3       12        19        78         4
               vv
clus            STAGE IV
  LBR MUTATED          0
  LBR WILD-TYPE        3
D655V3, multiclass
           clus
vv          LBR MUTATED LBR WILD-TYPE
  STAGE I             0             1
  STAGE IA            0             3
  STAGE IB            0            12
  STAGE IIA           0            19
  STAGE IIB           4            78
  STAGE III           0             4
  STAGE IV            0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3+T4
  LBR MUTATED    0  1     3
  LBR WILD-TYPE  5 16    99
D655V4, multiclass
       clus
vv      LBR MUTATED LBR WILD-TYPE
  T1              0             5
  T2              1            16
  T3+T4           3            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V5, binary
               cls
clus             0  1
  LBR MUTATED    0  4
  LBR WILD-TYPE 35 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBR MUTATED      0    4
  LBR WILD-TYPE   35   85
   clus
vv  LBR MUTATED LBR WILD-TYPE
  0           0            35
  1           4            85
[1] 2 2
[1] FALSE
D655V6, binary
               cls
clus             0  1
  LBR MUTATED    3  0
  LBR WILD-TYPE 54  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBR MUTATED      3    0
  LBR WILD-TYPE   54    3
   clus
vv  LBR MUTATED LBR WILD-TYPE
  0           3            54
  1           0             3
[1] 2 2
[1] FALSE
D655V7, binary
               cls
clus             0  1
  LBR MUTATED    1  3
  LBR WILD-TYPE 50 72
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBR MUTATED      1    3
  LBR WILD-TYPE   50   72
        clus
vv       LBR MUTATED LBR WILD-TYPE
  FEMALE           1            50
  MALE             3            72
[1] 2 2
[1] FALSE
D655V8, binary
               cls
clus             0  1
  LBR MUTATED    3  1
  LBR WILD-TYPE 85 29
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBR MUTATED      3    1
  LBR WILD-TYPE   85   29
     clus
vv    LBR MUTATED LBR WILD-TYPE
  NO            3            85
  YES           1            29
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LBR MUTATED                                     4
  LBR WILD-TYPE                                 101
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LBR MUTATED                                       0
  LBR WILD-TYPE                                    18
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LBR MUTATED                                                  0
  LBR WILD-TYPE                                                1
               vv
clus            PANCREAS-UNDIFFERENTIATED CARCINOMA
  LBR MUTATED                                     0
  LBR WILD-TYPE                                   1
D655V9, multiclass
                                                  clus
vv                                                 LBR MUTATED LBR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           101
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA           0             1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                        0             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V10, continuous
D655V11, continuous
               vv
clus            R0 R1 R2 RX
  LBR MUTATED    2  2  0  0
  LBR WILD-TYPE 78 33  4  2
D655V12, multiclass
    clus
vv   LBR MUTATED LBR WILD-TYPE
  R0           2            78
  R1           2            33
  R2           0             4
  RX           0             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LBR MUTATED       0                         0     4
  LBR WILD-TYPE     6                         5   110
D655V14, multiclass
                           clus
vv                          LBR MUTATED LBR WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V15, binary
               cls
clus             0  1
  LBR MUTATED    0  3
  LBR WILD-TYPE  5 88
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBR MUTATED      0    3
  LBR WILD-TYPE    5   88
                        clus
vv                       LBR MUTATED LBR WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3            88
[1] 2 2
[1] FALSE

Clustering(656) Variable = AKD1 MUTATION ANALYSIS
D656V1, survival
                sevent
clus2             0  1
  AKD1 MUTATED    1  2
  AKD1 WILD-TYPE 62 60
  AKD1 MUTATED AKD1 WILD-TYPE 
             3            122 
  AKD1 MUTATED AKD1 WILD-TYPE 
             2             60 
$`AKD1 MUTATED`
TCGA-IB-7651 TCGA-IB-A7M4 TCGA-IB-AAUW 
       19.82        15.88         7.56 

$`AKD1 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS 
        7.36        24.26        33.57        63.85        50.70        32.81 
TCGA-3A-A9IU TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       15.06        36.26        34.09        10.13        24.43        75.12 
TCGA-3E-AAAZ TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T 
       71.74        19.46         3.12        17.00        16.37        12.33 
TCGA-FB-AAPP TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 
       15.95        37.15         7.50        12.53        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 
        4.04         5.03         1.02        24.36         2.01         5.10 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP 
       36.20        20.35        17.79        22.06         8.28        32.15 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I 
       30.25        17.49        31.86        20.19        17.00        10.13 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 
        5.26        10.85         0.23        19.82        36.69        41.33 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF 
       15.19        12.00        15.85         7.20        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22         0.26         4.73         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-LB-A8F3 
        6.02        11.11         7.40         8.05        13.28        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  AKD1 MUTATED AKD1 WILD-TYPE 
          7.56           0.23 
  AKD1 MUTATED AKD1 WILD-TYPE 
         19.82          90.12 
  AKD1 MUTATED AKD1 WILD-TYPE 
        15.880         15.205 
[1] "7.6 - 19.8 (15.9)" "0.2 - 90.1 (15.2)"
[1] "hr=" "1.7"
D656V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AKD1 MUTATED         0        0        0         0         3         0
  AKD1 WILD-TYPE       1        3       12        19        79         4
                vv
clus             STAGE IV
  AKD1 MUTATED          0
  AKD1 WILD-TYPE        3
D656V3, multiclass
           clus
vv          AKD1 MUTATED AKD1 WILD-TYPE
  STAGE I              0              1
  STAGE IA             0              3
  STAGE IB             0             12
  STAGE IIA            0             19
  STAGE IIB            3             79
  STAGE III            0              4
  STAGE IV             0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  AKD1 MUTATED    0  0     3
  AKD1 WILD-TYPE  5 17    99
D656V4, multiclass
       clus
vv      AKD1 MUTATED AKD1 WILD-TYPE
  T1               0              5
  T2               0             17
  T3+T4            3             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V5, binary
                cls
clus              0  1
  AKD1 MUTATED    0  3
  AKD1 WILD-TYPE 35 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      0    3
  AKD1 WILD-TYPE   35   86
   clus
vv  AKD1 MUTATED AKD1 WILD-TYPE
  0            0             35
  1            3             86
[1] 2 2
[1] FALSE
D656V6, binary
                cls
clus              0  1
  AKD1 MUTATED    2  0
  AKD1 WILD-TYPE 55  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      2    0
  AKD1 WILD-TYPE   55    3
   clus
vv  AKD1 MUTATED AKD1 WILD-TYPE
  0            2             55
  1            0              3
[1] 2 2
[1] FALSE
D656V7, binary
                cls
clus              0  1
  AKD1 MUTATED    2  1
  AKD1 WILD-TYPE 49 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      2    1
  AKD1 WILD-TYPE   49   74
        clus
vv       AKD1 MUTATED AKD1 WILD-TYPE
  FEMALE            2             49
  MALE              1             74
[1] 2 2
[1] FALSE
D656V8, binary
                cls
clus              0  1
  AKD1 MUTATED    3  0
  AKD1 WILD-TYPE 85 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      3    0
  AKD1 WILD-TYPE   85   30
     clus
vv    AKD1 MUTATED AKD1 WILD-TYPE
  NO             3             85
  YES            0             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AKD1 MUTATED                                     3
  AKD1 WILD-TYPE                                 102
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AKD1 MUTATED                                       0
  AKD1 WILD-TYPE                                    18
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AKD1 MUTATED                                                  0
  AKD1 WILD-TYPE                                                1
                vv
clus             PANCREAS-UNDIFFERENTIATED CARCINOMA
  AKD1 MUTATED                                     0
  AKD1 WILD-TYPE                                   1
D656V9, multiclass
                                                  clus
vv                                                 AKD1 MUTATED AKD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             18
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                         0              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V10, continuous
[1] "Remove cluster labels:" "AKD1 MUTATED"          
clus
  AKD1 MUTATED AKD1 WILD-TYPE 
             2             37 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABA 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO     TCGA-2J-AABV 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-2L-AAQA     TCGA-2L-AAQE     TCGA-3A-A9I9     TCGA-3A-A9IB 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-F2-A8YN     TCGA-FB-A5VM     TCGA-FB-A78T 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-FB-AAPQ     TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HV-AA8V 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A6UF 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUU 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-XN-A8T5 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-YY-A8LH 
"AKD1 WILD-TYPE" 
D656V11, continuous
[1] "Remove cluster labels:" "AKD1 MUTATED"          
clus
  AKD1 MUTATED AKD1 WILD-TYPE 
             2             31 
    TCGA-3A-A9IJ     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-IB-A5SS 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-XD-AAUL     TCGA-2J-AAB1     TCGA-2J-AABE 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-2J-AABF     TCGA-2J-AABO     TCGA-3A-A9IB     TCGA-3A-A9IR 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-3A-A9IX     TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPQ 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-H8-A6C1     TCGA-HZ-A8P1     TCGA-IB-7885 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-AAUQ 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUV     TCGA-LB-A9Q5     TCGA-OE-A75W 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XN-A8T5     TCGA-YY-A8LH 
"AKD1 WILD-TYPE" "AKD1 WILD-TYPE" "AKD1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  AKD1 MUTATED    3  0  0  0
  AKD1 WILD-TYPE 77 35  4  2
D656V12, multiclass
    clus
vv   AKD1 MUTATED AKD1 WILD-TYPE
  R0            3             77
  R1            0             35
  R2            0              4
  RX            0              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKD1 MUTATED       0                         0     3
  AKD1 WILD-TYPE     6                         5   111
D656V14, multiclass
                           clus
vv                          AKD1 MUTATED AKD1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V15, binary
                cls
clus              0  1
  AKD1 MUTATED    0  3
  AKD1 WILD-TYPE  5 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKD1 MUTATED      0    3
  AKD1 WILD-TYPE    5   88
                        clus
vv                       AKD1 MUTATED AKD1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3             88
[1] 2 2
[1] FALSE

Clustering(657) Variable = GABRD MUTATION ANALYSIS
D657V1, survival
                 sevent
clus2              0  1
  GABRD MUTATED    0  4
  GABRD WILD-TYPE 63 58
  GABRD MUTATED GABRD WILD-TYPE 
              4             121 
  GABRD MUTATED GABRD WILD-TYPE 
              4              58 
$`GABRD MUTATED`
TCGA-US-A77E TCGA-HV-AA8X TCGA-IB-7651 TCGA-US-A77J 
       14.14        17.49        19.82        18.67 

$`GABRD WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AAB9 
       16.37         2.17        23.97         9.63         2.63        20.61 
TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK TCGA-2J-AABO 
       19.96        22.22        22.72        42.31        15.91        14.47 
TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI 
       15.22         9.11        21.44         4.70        22.49         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB 
       12.95         9.60        45.47        43.50        20.84         7.36 
TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IO TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
       24.26        33.57        63.85        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P 
       31.86        20.19        17.00        10.13         5.26        10.85 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
        0.23        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        0.30        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GABRD MUTATED GABRD WILD-TYPE 
          14.14            0.23 
  GABRD MUTATED GABRD WILD-TYPE 
          19.82           90.12 
  GABRD MUTATED GABRD WILD-TYPE 
          18.08           15.19 
[1] "14.1 - 19.8 (18.1)" "0.2 - 90.1 (15.2)" 
[1] "hr=" "2"  
D657V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  GABRD MUTATED         0        0        0         0         4         0
  GABRD WILD-TYPE       1        3       12        19        78         4
                 vv
clus              STAGE IV
  GABRD MUTATED          0
  GABRD WILD-TYPE        3
D657V3, multiclass
           clus
vv          GABRD MUTATED GABRD WILD-TYPE
  STAGE I               0               1
  STAGE IA              0               3
  STAGE IB              0              12
  STAGE IIA             0              19
  STAGE IIB             4              78
  STAGE III             0               4
  STAGE IV              0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  GABRD MUTATED    0  1     3
  GABRD WILD-TYPE  5 16    99
D657V4, multiclass
       clus
vv      GABRD MUTATED GABRD WILD-TYPE
  T1                0               5
  T2                1              16
  T3+T4             3              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V5, binary
                 cls
clus               0  1
  GABRD MUTATED    0  4
  GABRD WILD-TYPE 35 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRD MUTATED      0    4
  GABRD WILD-TYPE   35   85
   clus
vv  GABRD MUTATED GABRD WILD-TYPE
  0             0              35
  1             4              85
[1] 2 2
[1] FALSE
D657V6, binary
                 cls
clus               0  1
  GABRD MUTATED    1  0
  GABRD WILD-TYPE 56  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRD MUTATED      1    0
  GABRD WILD-TYPE   56    3
   clus
vv  GABRD MUTATED GABRD WILD-TYPE
  0             1              56
  1             0               3
[1] 2 2
[1] FALSE
D657V7, binary
                 cls
clus               0  1
  GABRD MUTATED    3  1
  GABRD WILD-TYPE 48 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRD MUTATED      3    1
  GABRD WILD-TYPE   48   74
        clus
vv       GABRD MUTATED GABRD WILD-TYPE
  FEMALE             3              48
  MALE               1              74
[1] 2 2
[1] FALSE
D657V8, binary
                 cls
clus               0  1
  GABRD MUTATED    3  0
  GABRD WILD-TYPE 85 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRD MUTATED      3    0
  GABRD WILD-TYPE   85   30
     clus
vv    GABRD MUTATED GABRD WILD-TYPE
  NO              3              85
  YES             0              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GABRD MUTATED                                     3
  GABRD WILD-TYPE                                 102
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GABRD MUTATED                                       1
  GABRD WILD-TYPE                                    17
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GABRD MUTATED                                                  0
  GABRD WILD-TYPE                                                1
                 vv
clus              PANCREAS-UNDIFFERENTIATED CARCINOMA
  GABRD MUTATED                                     0
  GABRD WILD-TYPE                                   1
D657V9, multiclass
                                                  clus
vv                                                 GABRD MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                          0
                                                  clus
vv                                                 GABRD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V10, continuous
[1] "Remove cluster labels:" "GABRD MUTATED"         
clus
  GABRD MUTATED GABRD WILD-TYPE 
              1              38 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABA 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO      TCGA-2J-AABV 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-2L-AAQA      TCGA-2L-AAQE      TCGA-3A-A9I9      TCGA-3A-A9IB 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-F2-A8YN      TCGA-FB-A5VM      TCGA-FB-A78T 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-FB-AAPQ      TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HV-AA8V 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UF 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-IB-AAUV      TCGA-LB-A9Q5      TCGA-OE-A75W 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" 
D657V11, continuous
[1] "Remove cluster labels:" "GABRD MUTATED"         
clus
  GABRD MUTATED GABRD WILD-TYPE 
              1              32 
     TCGA-3A-A9IJ      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-IB-A5SS 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-XD-AAUL      TCGA-2J-AAB1      TCGA-2J-AABE 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-2J-AABF      TCGA-2J-AABO      TCGA-3A-A9IB      TCGA-3A-A9IR 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-3A-A9IX      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPQ 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-H8-A6C1      TCGA-HZ-A8P1      TCGA-IB-7885 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUV      TCGA-LB-A9Q5 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
     TCGA-OE-A75W      TCGA-XD-AAUI      TCGA-XN-A8T5      TCGA-YY-A8LH 
"GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" "GABRD WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  GABRD MUTATED    2  1  1  0
  GABRD WILD-TYPE 78 34  3  2
D657V12, multiclass
    clus
vv   GABRD MUTATED GABRD WILD-TYPE
  R0             2              78
  R1             1              34
  R2             1               3
  RX             0               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GABRD MUTATED       1                         0     3
  GABRD WILD-TYPE     5                         5   111
D657V14, multiclass
                           clus
vv                          GABRD MUTATED GABRD WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V15, binary
                 cls
clus               0  1
  GABRD MUTATED    0  3
  GABRD WILD-TYPE  5 88
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRD MUTATED      0    3
  GABRD WILD-TYPE    5   88
                        clus
vv                       GABRD MUTATED GABRD WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3              88
[1] 2 2
[1] FALSE

Clustering(658) Variable = CEACAM5 MUTATION ANALYSIS
D658V1, survival
                   sevent
clus2                0  1
  CEACAM5 MUTATED    3  1
  CEACAM5 WILD-TYPE 60 61
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                4               121 
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                1                61 
$`CEACAM5 MUTATED`
TCGA-3A-A9IO TCGA-HZ-A8P1 TCGA-IB-7651 TCGA-YB-A89D 
       63.85         0.23        19.82        11.51 

$`CEACAM5 WILD-TYPE`
TCGA-2J-AABR TCGA-2J-AABT TCGA-3A-A9I5 TCGA-3A-A9IJ TCGA-3A-A9IL TCGA-F2-A44G 
       14.40        10.49        58.98        60.95        90.12         7.66 
TCGA-FB-AAQ6 TCGA-FZ-5924 TCGA-HZ-A77Q TCGA-IB-A5SS TCGA-LB-A7SX TCGA-S4-A8RO 
        8.02        15.78         1.08        15.12        12.92        17.26 
TCGA-US-A77E TCGA-XD-AAUL TCGA-2J-AAB1 TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 
       14.14        16.37         2.17        23.97         9.63         2.63 
TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABK 
       20.61        19.96        22.22        22.72        42.31        15.91 
TCGA-2J-AABO TCGA-2J-AABP TCGA-2J-AABU TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQE 
       14.47        15.22         9.11        21.44         4.70        22.49 
TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-2L-AAQM TCGA-3A-A9I7 TCGA-3A-A9I9 
        3.39        12.95         9.60        45.47        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IR TCGA-3A-A9IS TCGA-3A-A9IU 
        7.36        24.26        33.57        50.70        32.81        15.06 
TCGA-3A-A9IV TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       36.26        34.09        10.13        24.43        75.12        71.74 
TCGA-F2-7273 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPP 
       19.46         3.12        17.00        16.37        12.33        15.95 
TCGA-FB-AAPQ TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 
       37.15         7.50        12.53        23.54        15.55         4.04 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-FZ-5919 TCGA-FZ-5920 TCGA-FZ-5921 TCGA-FZ-5922 
        5.03         1.02        24.36         2.01         5.10        36.20 
TCGA-FZ-5923 TCGA-FZ-5926 TCGA-H8-A6C1 TCGA-HV-A7OL TCGA-HV-A7OP TCGA-HV-AA8V 
       20.35        17.79        22.06         8.28        32.15        30.25 
TCGA-HV-AA8X TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 TCGA-HZ-A49I TCGA-HZ-A77O 
       17.49        31.86        20.19        17.00        10.13         5.26 
TCGA-HZ-A77P TCGA-HZ-A9TJ TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
       10.85        19.82        36.69        41.33        15.19        12.00 
TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        20.88        21.90         1.35         8.22 
TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ 
       15.88         0.26         4.73         7.86        14.17         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUU TCGA-IB-AAUV TCGA-IB-AAUW TCGA-LB-A8F3 
       11.11         7.40         8.05        13.28         7.56        12.46 
TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M 
       10.29         8.78        13.68         3.12        15.32         9.40 
TCGA-RL-AAAS TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-US-A77J TCGA-XD-AAUG 
        0.30        39.98        16.80         0.39        18.67        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH 
       12.99        12.03        31.27        23.67        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
             0.23              0.26 
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
            63.85             90.12 
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
           15.665            15.220 
[1] "0.2 - 63.9 (15.7)" "0.3 - 90.1 (15.2)"
[1] "hr=" "2"  
D658V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  CEACAM5 MUTATED         0        0        1         0         2         0
  CEACAM5 WILD-TYPE       1        3       11        19        80         4
                   vv
clus                STAGE IV
  CEACAM5 MUTATED          0
  CEACAM5 WILD-TYPE        3
D658V3, multiclass
           clus
vv          CEACAM5 MUTATED CEACAM5 WILD-TYPE
  STAGE I                 0                 1
  STAGE IA                0                 3
  STAGE IB                1                11
  STAGE IIA               0                19
  STAGE IIB               2                80
  STAGE III               0                 4
  STAGE IV                0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2 T3+T4
  CEACAM5 MUTATED     0   1     2
  CEACAM5 WILD-TYPE   5  16   100
D658V4, multiclass
       clus
vv      CEACAM5 MUTATED CEACAM5 WILD-TYPE
  T1                  0                 5
  T2                  1                16
  T3+T4               2               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V5, binary
                   cls
clus                 0  1
  CEACAM5 MUTATED    1  2
  CEACAM5 WILD-TYPE 34 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM5 MUTATED      1    2
  CEACAM5 WILD-TYPE   34   87
   clus
vv  CEACAM5 MUTATED CEACAM5 WILD-TYPE
  0               1                34
  1               2                87
[1] 2 2
[1] FALSE
D658V6, binary
                   cls
clus                 0  1
  CEACAM5 MUTATED    1  0
  CEACAM5 WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM5 MUTATED      1    0
  CEACAM5 WILD-TYPE   56    3
   clus
vv  CEACAM5 MUTATED CEACAM5 WILD-TYPE
  0               1                56
  1               0                 3
[1] 2 2
[1] FALSE
D658V7, binary
                   cls
clus                 0  1
  CEACAM5 MUTATED    1  3
  CEACAM5 WILD-TYPE 50 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM5 MUTATED      1    3
  CEACAM5 WILD-TYPE   50   72
        clus
vv       CEACAM5 MUTATED CEACAM5 WILD-TYPE
  FEMALE               1                50
  MALE                 3                72
[1] 2 2
[1] FALSE
D658V8, binary
                   cls
clus                 0  1
  CEACAM5 MUTATED    2  1
  CEACAM5 WILD-TYPE 86 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM5 MUTATED      2    1
  CEACAM5 WILD-TYPE   86   29
     clus
vv    CEACAM5 MUTATED CEACAM5 WILD-TYPE
  NO                2                86
  YES               1                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEACAM5 MUTATED                                     3
  CEACAM5 WILD-TYPE                                 102
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEACAM5 MUTATED                                       1
  CEACAM5 WILD-TYPE                                    17
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEACAM5 MUTATED                                                  0
  CEACAM5 WILD-TYPE                                                1
                   vv
clus                PANCREAS-UNDIFFERENTIATED CARCINOMA
  CEACAM5 MUTATED                                     0
  CEACAM5 WILD-TYPE                                   1
D658V9, multiclass
                                                  clus
vv                                                 CEACAM5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
  PANCREAS-UNDIFFERENTIATED CARCINOMA                            0
                                                  clus
vv                                                 CEACAM5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            102
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           17
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
  PANCREAS-UNDIFFERENTIATED CARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V10, continuous
[1] "Remove cluster labels:" "CEACAM5 MUTATED"       
clus
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                2                37 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABA 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-2J-AABE        TCGA-2J-AABF        TCGA-2J-AABO        TCGA-2J-AABV 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-2L-AAQA        TCGA-2L-AAQE        TCGA-3A-A9I9        TCGA-3A-A9IB 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-F2-A8YN        TCGA-FB-A5VM        TCGA-FB-A78T 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-FB-AAPQ        TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-HV-AA8V 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A6UF        TCGA-IB-A6UG 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-IB-A7M4        TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUU 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-XN-A8T5 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-YY-A8LH 
"CEACAM5 WILD-TYPE" 
D658V11, continuous
[1] "Remove cluster labels:" "CEACAM5 MUTATED"       
clus
  CEACAM5 MUTATED CEACAM5 WILD-TYPE 
                2                31 
       TCGA-3A-A9IJ        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-IB-A5SS 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-XD-AAUL        TCGA-2J-AAB1        TCGA-2J-AABE 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-2J-AABF        TCGA-2J-AABO        TCGA-3A-A9IB        TCGA-3A-A9IR 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-3A-A9IX        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-AAPQ 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-H8-A6C1        TCGA-IB-7885        TCGA-IB-8126 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUV        TCGA-LB-A9Q5        TCGA-OE-A75W 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
       TCGA-XD-AAUI        TCGA-XN-A8T5        TCGA-YY-A8LH 
"CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" "CEACAM5 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CEACAM5 MUTATED    4  0  0  0
  CEACAM5 WILD-TYPE 76 35  4  2
D658V12, multiclass
    clus
vv   CEACAM5 MUTATED CEACAM5 WILD-TYPE
  R0               4                76
  R1               0                35
  R2               0                 4
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM5 MUTATED       0                         0     4
  CEACAM5 WILD-TYPE     6                         5   110
D658V14, multiclass
                           clus
vv                          CEACAM5 MUTATED CEACAM5 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V15, binary
                   cls
clus                 0  1
  CEACAM5 MUTATED    0  4
  CEACAM5 WILD-TYPE  5 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM5 MUTATED      0    4
  CEACAM5 WILD-TYPE    5   87
                        clus
vv                       CEACAM5 MUTATED CEACAM5 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4                87
[1] 2 2
[1] FALSE
