[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTLIHC-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/LIHC-TP/10006007/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/10686854/transformed.cor.cli.txt"

nPatients in clinical file=176, in cluster file=202, common to both=160
[1] "Reduce the number of clustering variables from 103 to 101."
[1] 101 160
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            45            115 
  TP53 MUTATED TP53 WILD-TYPE 
            45            115 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              48              112 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              48              112 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              141 
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              141 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           14           146 
  RB1 MUTATED RB1 WILD-TYPE 
           14           146 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              8             152 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              8             152 
[1] "KRTAP5-11 MUTATION ANALYSIS"
[1] 3
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
                  5                 155 
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
                  5                 155 
[1] "AHCTF1 MUTATION ANALYSIS"
[1] 3
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              12              148 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              12              148 
[1] "GPATCH4 MUTATION ANALYSIS"
[1] 3
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
               10               150 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
               10               150 
[1] "CD207 MUTATION ANALYSIS"
[1] 3
  CD207 MUTATED CD207 WILD-TYPE 
              8             152 
  CD207 MUTATED CD207 WILD-TYPE 
              8             152 
[1] "EEF1A1 MUTATION ANALYSIS"
[1] 3
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               8              152 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               8              152 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            11            149 
  BAP1 MUTATED BAP1 WILD-TYPE 
            11            149 
[1] "CHIT1 MUTATION ANALYSIS"
[1] 3
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              5             155 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              5             155 
[1] "PPIAL4G MUTATION ANALYSIS"
[1] 3
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
                7               153 
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
                7               153 
[1] "ALB MUTATION ANALYSIS"
[1] 3
  ALB MUTATED ALB WILD-TYPE 
           23           137 
  ALB MUTATED ALB WILD-TYPE 
           23           137 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               8              152 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               8              152 
[1] "TREML2 MUTATION ANALYSIS"
[1] 3
  TREML2 MUTATED TREML2 WILD-TYPE 
               6              154 
  TREML2 MUTATED TREML2 WILD-TYPE 
               6              154 
[1] "PRH2 MUTATION ANALYSIS"
[1] 3
  PRH2 MUTATED PRH2 WILD-TYPE 
             6            154 
  PRH2 MUTATED PRH2 WILD-TYPE 
             6            154 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             137 
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             137 
[1] "AZIN1 MUTATION ANALYSIS"
[1] 3
  AZIN1 MUTATED AZIN1 WILD-TYPE 
             11             149 
  AZIN1 MUTATED AZIN1 WILD-TYPE 
             11             149 
[1] "NBPF3 MUTATION ANALYSIS"
[1] 3
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              7             153 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              7             153 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              13              147 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              13              147 
[1] "SCRN3 MUTATION ANALYSIS"
[1] 3
  SCRN3 MUTATED SCRN3 WILD-TYPE 
              9             151 
  SCRN3 MUTATED SCRN3 WILD-TYPE 
              9             151 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            21            139 
  MUC6 MUTATED MUC6 WILD-TYPE 
            21            139 
[1] "UGT2B28 MUTATION ANALYSIS"
[1] 3
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
               10               150 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
               10               150 
[1] "CDHR5 MUTATION ANALYSIS"
[1] 3
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             149 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             149 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              6             154 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              6             154 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             13             147 
  CDC27 MUTATED CDC27 WILD-TYPE 
             13             147 
[1] "CR1 MUTATION ANALYSIS"
[1] 3
  CR1 MUTATED CR1 WILD-TYPE 
           18           142 
  CR1 MUTATED CR1 WILD-TYPE 
           18           142 
[1] "TCEAL6 MUTATION ANALYSIS"
[1] 3
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              156 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              156 
[1] "LILRA6 MUTATION ANALYSIS"
[1] 3
  LILRA6 MUTATED LILRA6 WILD-TYPE 
              11              149 
  LILRA6 MUTATED LILRA6 WILD-TYPE 
              11              149 
[1] "BIK MUTATION ANALYSIS"
[1] 3
  BIK MUTATED BIK WILD-TYPE 
            3           157 
  BIK MUTATED BIK WILD-TYPE 
            3           157 
[1] "SRRM3 MUTATION ANALYSIS"
[1] 3
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              4             156 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              4             156 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
             15             145 
  MKI67 MUTATED MKI67 WILD-TYPE 
             15             145 
[1] "ALDH3B1 MUTATION ANALYSIS"
[1] 3
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
                5               155 
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
                5               155 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
              7             153 
  POTEG MUTATED POTEG WILD-TYPE 
              7             153 
[1] "ZNF658 MUTATION ANALYSIS"
[1] 3
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               7              153 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               7              153 
[1] "TCHH MUTATION ANALYSIS"
[1] 3
  TCHH MUTATED TCHH WILD-TYPE 
            20            140 
  TCHH MUTATED TCHH WILD-TYPE 
            20            140 
[1] "TMEM176A MUTATION ANALYSIS"
[1] 3
  TMEM176A MUTATED TMEM176A WILD-TYPE 
                 4                156 
  TMEM176A MUTATED TMEM176A WILD-TYPE 
                 4                156 
[1] "RP1L1 MUTATION ANALYSIS"
[1] 3
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             19             141 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             19             141 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
            13            147 
  TSC2 MUTATED TSC2 WILD-TYPE 
            13            147 
[1] "PRKDC MUTATION ANALYSIS"
[1] 3
  PRKDC MUTATED PRKDC WILD-TYPE 
             22             138 
  PRKDC MUTATED PRKDC WILD-TYPE 
             22             138 
[1] "NRD1 MUTATION ANALYSIS"
[1] 3
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            151 
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            151 
[1] "TAS2R20 MUTATION ANALYSIS"
[1] 3
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
                4               156 
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
                4               156 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            153 
  PTEN MUTATED PTEN WILD-TYPE 
             7            153 
[1] "CYFIP2 MUTATION ANALYSIS"
[1] 3
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
              13              147 
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
              13              147 
[1] "PRAMEF1 MUTATION ANALYSIS"
[1] 3
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
                9               151 
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
                9               151 
[1] "MST1 MUTATION ANALYSIS"
[1] 3
  MST1 MUTATED MST1 WILD-TYPE 
             8            152 
  MST1 MUTATED MST1 WILD-TYPE 
             8            152 
[1] "ZC3H7A MUTATION ANALYSIS"
[1] 3
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
              11              149 
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
              11              149 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            27            133 
  MLL3 MUTATED MLL3 WILD-TYPE 
            27            133 
[1] "HNRNPCL1 MUTATION ANALYSIS"
[1] 3
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                11                149 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                11                149 
[1] "TUBA3E MUTATION ANALYSIS"
[1] 3
  TUBA3E MUTATED TUBA3E WILD-TYPE 
               7              153 
  TUBA3E MUTATED TUBA3E WILD-TYPE 
               7              153 
[1] "MUC21 MUTATION ANALYSIS"
[1] 3
  MUC21 MUTATED MUC21 WILD-TYPE 
             15             145 
  MUC21 MUTATED MUC21 WILD-TYPE 
             15             145 
[1] "HPS4 MUTATION ANALYSIS"
[1] 3
  HPS4 MUTATED HPS4 WILD-TYPE 
             3            157 
  HPS4 MUTATED HPS4 WILD-TYPE 
             3            157 
[1] "OR2T4 MUTATION ANALYSIS"
[1] 3
  OR2T4 MUTATED OR2T4 WILD-TYPE 
             12             148 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
             12             148 
[1] "SPDYE1 MUTATION ANALYSIS"
[1] 3
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
               4              156 
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
               4              156 
[1] "COG2 MUTATION ANALYSIS"
[1] 3
  COG2 MUTATED COG2 WILD-TYPE 
             6            154 
  COG2 MUTATED COG2 WILD-TYPE 
             6            154 
[1] "SEC63 MUTATION ANALYSIS"
[1] 3
  SEC63 MUTATED SEC63 WILD-TYPE 
             10             150 
  SEC63 MUTATED SEC63 WILD-TYPE 
             10             150 
[1] "LILRA3 MUTATION ANALYSIS"
[1] 3
  LILRA3 MUTATED LILRA3 WILD-TYPE 
               4              156 
  LILRA3 MUTATED LILRA3 WILD-TYPE 
               4              156 
[1] "CYP2A6 MUTATION ANALYSIS"
[1] 3
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               5              155 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               5              155 
[1] "ZC3H11A MUTATION ANALYSIS"
[1] 3
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               157 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               157 
[1] "LCE4A MUTATION ANALYSIS"
[1] 3
  LCE4A MUTATED LCE4A WILD-TYPE 
              9             151 
  LCE4A MUTATED LCE4A WILD-TYPE 
              9             151 
[1] "ATXN3 MUTATION ANALYSIS"
[1] 3
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              4             156 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              4             156 
[1] "GTF2IRD2B MUTATION ANALYSIS"
[1] 3
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
                  5                 155 
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
                  5                 155 
[1] "QRICH2 MUTATION ANALYSIS"
[1] 3
  QRICH2 MUTATED QRICH2 WILD-TYPE 
              17              143 
  QRICH2 MUTATED QRICH2 WILD-TYPE 
              17              143 
[1] "PLAU MUTATION ANALYSIS"
[1] 3
  PLAU MUTATED PLAU WILD-TYPE 
             6            154 
  PLAU MUTATED PLAU WILD-TYPE 
             6            154 
[1] "MAPKAPK2 MUTATION ANALYSIS"
[1] 3
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
                 4                156 
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
                 4                156 
[1] "NAP1L1 MUTATION ANALYSIS"
[1] 3
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               5              155 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               5              155 
[1] "FAM118A MUTATION ANALYSIS"
[1] 3
  FAM118A MUTATED FAM118A WILD-TYPE 
                4               156 
  FAM118A MUTATED FAM118A WILD-TYPE 
                4               156 
[1] "SLC7A6OS MUTATION ANALYSIS"
[1] 3
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
                 4                156 
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
                 4                156 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              151 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              151 
[1] "ZXDC MUTATION ANALYSIS"
[1] 3
  ZXDC MUTATED ZXDC WILD-TYPE 
             6            154 
  ZXDC MUTATED ZXDC WILD-TYPE 
             6            154 
[1] "TAS2R30 MUTATION ANALYSIS"
[1] 3
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
                8               152 
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
                8               152 
[1] "KRTAP10-2 MUTATION ANALYSIS"
[1] 3
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
                  6                 154 
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
                  6                 154 
[1] "PPA2 MUTATION ANALYSIS"
[1] 3
  PPA2 MUTATED PPA2 WILD-TYPE 
             4            156 
  PPA2 MUTATED PPA2 WILD-TYPE 
             4            156 
[1] "SEPT2 MUTATION ANALYSIS"
[1] 3
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              6             154 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              6             154 
[1] "DRD3 MUTATION ANALYSIS"
[1] 3
  DRD3 MUTATED DRD3 WILD-TYPE 
             5            155 
  DRD3 MUTATED DRD3 WILD-TYPE 
             5            155 
[1] "PSRC1 MUTATION ANALYSIS"
[1] 3
  PSRC1 MUTATED PSRC1 WILD-TYPE 
              4             156 
  PSRC1 MUTATED PSRC1 WILD-TYPE 
              4             156 
[1] "KRTAP10-9 MUTATION ANALYSIS"
[1] 3
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  3                 157 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  3                 157 
[1] "SPATA12 MUTATION ANALYSIS"
[1] 3
  SPATA12 MUTATED SPATA12 WILD-TYPE 
                6               154 
  SPATA12 MUTATED SPATA12 WILD-TYPE 
                6               154 
[1] "GPR112 MUTATION ANALYSIS"
[1] 3
  GPR112 MUTATED GPR112 WILD-TYPE 
              14              146 
  GPR112 MUTATED GPR112 WILD-TYPE 
              14              146 
[1] "CLTCL1 MUTATION ANALYSIS"
[1] 3
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              15              145 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              15              145 
[1] "OR2A14 MUTATION ANALYSIS"
[1] 3
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               4              156 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               4              156 
[1] "OR4C16 MUTATION ANALYSIS"
[1] 3
  OR4C16 MUTATED OR4C16 WILD-TYPE 
               7              153 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
               7              153 
[1] "GBP1 MUTATION ANALYSIS"
[1] 3
  GBP1 MUTATED GBP1 WILD-TYPE 
             7            153 
  GBP1 MUTATED GBP1 WILD-TYPE 
             7            153 
[1] "OR6B3 MUTATION ANALYSIS"
[1] 3
  OR6B3 MUTATED OR6B3 WILD-TYPE 
              4             156 
  OR6B3 MUTATED OR6B3 WILD-TYPE 
              4             156 
[1] "OR2T27 MUTATION ANALYSIS"
[1] 3
  OR2T27 MUTATED OR2T27 WILD-TYPE 
               9              151 
  OR2T27 MUTATED OR2T27 WILD-TYPE 
               9              151 
[1] "RAET1E MUTATION ANALYSIS"
[1] 3
  RAET1E MUTATED RAET1E WILD-TYPE 
               5              155 
  RAET1E MUTATED RAET1E WILD-TYPE 
               5              155 
[1] "SHROOM1 MUTATION ANALYSIS"
[1] 3
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
                3               157 
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
                3               157 
[1] "OR52I2 MUTATION ANALYSIS"
[1] 3
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               6              154 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               6              154 
[1] "OR13C2 MUTATION ANALYSIS"
[1] 3
  OR13C2 MUTATED OR13C2 WILD-TYPE 
               4              156 
  OR13C2 MUTATED OR13C2 WILD-TYPE 
               4              156 
[1] "LIPC MUTATION ANALYSIS"
[1] 3
  LIPC MUTATED LIPC WILD-TYPE 
             5            155 
  LIPC MUTATED LIPC WILD-TYPE 
             5            155 
[1] "FAM22F MUTATION ANALYSIS"
[1] 3
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              156 
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              156 
[1] "GLRX3 MUTATION ANALYSIS"
[1] 3
  GLRX3 MUTATED GLRX3 WILD-TYPE 
              4             156 
  GLRX3 MUTATED GLRX3 WILD-TYPE 
              4             156 
[1] "HOXA4 MUTATION ANALYSIS"
[1] 3
  HOXA4 MUTATED HOXA4 WILD-TYPE 
              5             155 
  HOXA4 MUTATED HOXA4 WILD-TYPE 
              5             155 
[1] "DENND4B MUTATION ANALYSIS"
[1] 3
  DENND4B MUTATED DENND4B WILD-TYPE 
                8               152 
  DENND4B MUTATED DENND4B WILD-TYPE 
                8               152 
[1] "ESX1 MUTATION ANALYSIS"
[1] 3
  ESX1 MUTATED ESX1 WILD-TYPE 
             5            155 
  ESX1 MUTATED ESX1 WILD-TYPE 
             5            155 
[1] "SLFN12L MUTATION ANALYSIS"
[1] 3
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                6               154 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                6               154 
[1] "FKBP4 MUTATION ANALYSIS"
[1] 3
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             156 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             156 
[1] "AQP7 MUTATION ANALYSIS"
[1] 3
  AQP7 MUTATED AQP7 WILD-TYPE 
             8            152 
  AQP7 MUTATED AQP7 WILD-TYPE 
             8            152 
[1] "MAP4K5 MUTATION ANALYSIS"
[1] 3
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               8              152 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               8              152 
[1] "BCL11A MUTATION ANALYSIS"
[1] 3
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              154 
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              154 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 160 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
         849           NA           NA           NA           NA           NA 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        1351          421            8          680          289          444 
TCGA-BC-A69I TCGA-BW-A5NQ TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
         387           NA            2            5           NA           12 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 
          NA           NA           NA           NA           NA            3 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
           2            3            4         2425           NA           NA 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
          NA         3437           NA           79           NA          662 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
          NA           NA         2415         2017          602         2301 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
          NA           NA         1495          183          887           NA 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
          NA           NA           NA         1008          989         2232 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
          NA          428          445          433          561          458 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
          NA         1711           NA         2245         2849           NA 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
          NA           NA         2018          334           NA          230 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
         334           44          843         3071          408          386 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
         482          423          406            7            6            6 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
           6            6            6            6          570          608 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
         357          334           NA          303          363           NA 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
          NA          987           NA           NA          848           NA 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
          NA            4            1           10         1836           12 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
          37         1553         1636          860          935           NA 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
         655          673          780          180          594          585 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
         447          364          302          243          133          236 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
         182           NA           NA           NA          122           NA 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
         360          407           15          291          155          433 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
         391          265           NA          135 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 160 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
67 40 43  9 
[1] "table(vv)"
vv
T1 T2 T3 T4 
67 40 43  9 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
67 40 43  9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
67 40 43  9 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   28 16
  TP53 WILD-TYPE 62 50
  TP53 MUTATED TP53 WILD-TYPE 
            44            112 
  TP53 MUTATED TP53 WILD-TYPE 
            16             50 
$`TP53 MUTATED`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       10.13        27.52        44.42        13.84        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
       14.60        12.72         0.07         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EB 
        0.10         0.07         0.10        37.78         2.60        66.31 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A7 
       45.11         6.02        13.64         5.62        25.81        13.78 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ES-A2HT 
       12.26        13.41         0.20         0.20         0.20        14.40 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U 
        8.12         6.38         0.33        60.36         0.39        53.79 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M9 
       28.27        21.53        19.53        11.97         4.37         1.84 
TCGA-MI-A75G TCGA-MI-A75I 
       14.24         8.71 

$`TP53 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5259 
       23.34         1.12        69.57         5.03         0.26         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        2.86         0.39         0.13        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
       79.40        19.79        75.65        12.95        49.15        29.16 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81        93.67         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        22.85        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W 
       27.88         0.13         0.03         1.22        51.06        30.74 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        9.93         7.99         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        12.85        58.88         4.44 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
         66.31         113.00 
  TP53 MUTATED TP53 WILD-TYPE 
        11.050         15.455 
[1] "0.1 - 66.3 (11.1)"  "0.0 - 113.0 (15.5)"
[1] "hr=" "1.4"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED        16       14         0          9          2          1
  TP53 WILD-TYPE      48       22         2         23          3          5
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TP53 MUTATED          0         0         0
  TP53 WILD-TYPE        1         1         2
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              16             48
  STAGE II             14             22
  STAGE III             0              2
  STAGE IIIA            9             23
  STAGE IIIB            2              3
  STAGE IIIC            1              5
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of 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   16 16 12  1
  TP53 WILD-TYPE 51 24 31  8
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           16             51
  T2           16             24
  T3           12             31
  T4            1              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  TP53 MUTATED   25  0
  TP53 WILD-TYPE 76  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     25    0
  TP53 WILD-TYPE   76    3
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           25             76
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TP53 MUTATED   37  0  8
  TP53 WILD-TYPE 85  3 27
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           37             85
  M1            0              3
  MX            8             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED    9 36
  TP53 WILD-TYPE 52 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9   36
  TP53 WILD-TYPE   52   63
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            9             52
  MALE             36             63
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TP53 MUTATED                         0                       45
  TP53 WILD-TYPE                       1                      112
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TP53 MUTATED                                  0
  TP53 WILD-TYPE                                2
D1V8, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   45            112
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   37  3  0  3
  TP53 WILD-TYPE 95  7  1  9
D1V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           37             95
  R1            3              7
  R2            0              1
  RX            3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1    15
  TP53 WILD-TYPE                                0    22
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           5    22
  TP53 WILD-TYPE                         3    86
D1V10, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                      15             22
  BLACK OR AFRICAN AMERICAN                   5              3
  WHITE                                      22             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                cls
clus               0   1
  TP53 MUTATED     1  39
  TP53 WILD-TYPE   3 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   39
  TP53 WILD-TYPE    3  104
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           39            104
[1] 2 2
[1] FALSE

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED   28 18
  CTNNB1 WILD-TYPE 62 48
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              46              110 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              18               48 
$`CTNNB1 MUTATED`
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5262 
       46.78        27.52         9.50        14.60        12.72         3.39 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EJ 
       53.33         7.33        51.29        79.40        75.65        29.16 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A4NF 
       13.64        21.14         5.62        17.59        20.12        14.07 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73D 
       18.44        39.78        56.25        80.75        10.98        10.98 
TCGA-DD-A73E TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        1.45         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25Z 
        0.62         9.96        11.93         0.39         1.22        21.53 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-K7-A6G5 
       19.53        19.23        11.97         7.99         7.76         4.01 
TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75H TCGA-O8-A75V 
        2.14         9.57        12.85         4.44 

$`CTNNB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
        0.26        22.36         0.07         0.16         2.86         0.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        90.71        66.31        19.79        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15         6.02        18.35        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
        7.66        70.06       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG 
       30.61        33.14        32.52        73.38        21.70        14.63 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       14.24        15.06        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
        0.30        66.35         9.30         7.56        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS 
        0.20         0.20         0.20         0.20        10.98        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U 
        0.13         0.03         0.33        60.36        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        14.86        22.13        25.64         5.92 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       14.70         9.93         4.37         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G 
        2.66        11.84        13.38         0.49         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 
        8.71        58.88 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.20             0.03 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           80.75           113.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          12.785           14.240 
[1] "0.2 - 80.8 (12.8)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.1"
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CTNNB1 MUTATED        24        9         0          7          1          2
  CTNNB1 WILD-TYPE      40       27         2         25          4          4
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CTNNB1 MUTATED          1         1         0
  CTNNB1 WILD-TYPE        0         0         2
D2V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                24               40
  STAGE II                9               27
  STAGE III               0                2
  STAGE IIIA              7               25
  STAGE IIIB              1                4
  STAGE IIIC              2                4
  STAGE IV                1                0
  STAGE IVA               1                0
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CTNNB1 MUTATED   26 10 10  1
  CTNNB1 WILD-TYPE 41 30 33  8
D2V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1             26               41
  T2             10               30
  T3             10               33
  T4              1                8
[1] 4 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
  CTNNB1 MUTATED   26  2
  CTNNB1 WILD-TYPE 75  1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     26    2
  CTNNB1 WILD-TYPE   75    1
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             26               75
  1              2                1
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  CTNNB1 MUTATED   33  1 14
  CTNNB1 WILD-TYPE 89  2 21
D2V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  M0             33               89
  M1              1                2
  MX             14               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    7 41
  CTNNB1 WILD-TYPE 54 58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      7   41
  CTNNB1 WILD-TYPE   54   58
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              7               54
  MALE               41               58
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CTNNB1 MUTATED                         0                       48
  CTNNB1 WILD-TYPE                       1                      109
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CTNNB1 MUTATED                                  0
  CTNNB1 WILD-TYPE                                2
D2V8, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     48              109
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               R0 R1 R2 RX
  CTNNB1 MUTATED   37  4  1  2
  CTNNB1 WILD-TYPE 95  6  0 10
D2V9, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             37               95
  R1              4                6
  R2              1                0
  RX              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  1    10
  CTNNB1 WILD-TYPE                                0    27
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           3    33
  CTNNB1 WILD-TYPE                         5    75
D2V10, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                        10               27
  BLACK OR AFRICAN AMERICAN                     3                5
  WHITE                                        33               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    1 45
  CTNNB1 WILD-TYPE  3 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1   45
  CTNNB1 WILD-TYPE    3   98
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             45               98
[1] 2 2
[1] FALSE

Clustering(3) Variable = ARID1A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    7 10
  ARID1A WILD-TYPE 83 56
  ARID1A MUTATED ARID1A WILD-TYPE 
              17              139 
  ARID1A MUTATED ARID1A WILD-TYPE 
              10               56 
$`ARID1A MUTATED`
TCGA-BC-A10Z TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5262 TCGA-DD-A11A TCGA-DD-A1EH 
        1.12        12.72         0.07         3.39         2.60        49.15 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NR TCGA-EP-A2KB TCGA-ES-A2HT 
       21.14        55.69         5.62         0.30        10.98        14.40 
TCGA-FV-A23B TCGA-G3-A25S TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-LG-A6GG 
       32.45         1.22        22.13        19.53         0.49 

$`ARID1A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5259 
       13.84         0.26        22.36         9.50        14.60         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         0.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        29.16        18.35        13.64        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62         9.96        11.93        22.85        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.07             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           55.69           113.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
           10.98            14.07 
[1] "0.1 - 55.7 (11.0)"  "0.0 - 113.0 (14.1)"
[1] "hr=" "2.3"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ARID1A MUTATED        11        5         1          1          0          1
  ARID1A WILD-TYPE      53       31         1         31          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ARID1A MUTATED          0         0         0
  ARID1A WILD-TYPE        1         1         2
D3V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                11               53
  STAGE II                5               31
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of 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   11  5  2  1
  ARID1A WILD-TYPE 56 35 41  8
D3V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1             11               56
  T2              5               35
  T3              2               41
  T4              1                8
[1] 4 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
  ARID1A MUTATED   12  0
  ARID1A WILD-TYPE 89  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     12    0
  ARID1A WILD-TYPE   89    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             12               89
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  ARID1A MUTATED    15   0   4
  ARID1A WILD-TYPE 107   3  31
D3V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0             15              107
  M1              0                3
  MX              4               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    7 12
  ARID1A WILD-TYPE 54 87
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      7   12
  ARID1A WILD-TYPE   54   87
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              7               54
  MALE               12               87
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ARID1A MUTATED                         0                       19
  ARID1A WILD-TYPE                       1                      138
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ARID1A MUTATED                                  0
  ARID1A WILD-TYPE                                2
D3V8, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     19              138
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    13   2   0   3
  ARID1A WILD-TYPE 119   8   1   9
D3V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             13              119
  R1              2                8
  R2              0                1
  RX              3                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  1     4
  ARID1A WILD-TYPE                                0    33
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2    12
  ARID1A WILD-TYPE                         6    96
D3V10, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         4               33
  BLACK OR AFRICAN AMERICAN                     2                6
  WHITE                                        12               96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  18
  ARID1A WILD-TYPE   4 125
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   18
  ARID1A WILD-TYPE    4  125
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             18              125
[1] 2 2
[1] FALSE

Clustering(4) Variable = RB1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    8  5
  RB1 WILD-TYPE 82 61
  RB1 MUTATED RB1 WILD-TYPE 
           13           143 
  RB1 MUTATED RB1 WILD-TYPE 
            5            61 
$`RB1 MUTATED`
TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A4NE 
       10.13         2.99        22.36        79.73        37.78        21.70 
TCGA-DD-A4NJ TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CH 
       15.06         0.23         0.20        53.79        14.86        25.64 
TCGA-G3-A5SI 
       14.70 

$`RB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 
        0.26         9.50        14.60        12.72         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10         0.13        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        73.38        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       14.24        18.44        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       51.06        28.27        30.74        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  RB1 MUTATED RB1 WILD-TYPE 
         0.20          0.03 
  RB1 MUTATED RB1 WILD-TYPE 
        79.73        113.00 
  RB1 MUTATED RB1 WILD-TYPE 
        15.06         13.64 
[1] "0.2 - 79.7 (15.1)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "1.1"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RB1 MUTATED         2        6         0          4          0          0
  RB1 WILD-TYPE      62       30         2         28          5          6
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  RB1 MUTATED          0         0         0
  RB1 WILD-TYPE        1         1         2
D4V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              2            62
  STAGE II             6            30
  STAGE III            0             2
  STAGE IIIA           4            28
  STAGE IIIB           0             5
  STAGE IIIC           0             6
  STAGE IV             0             1
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  RB1 MUTATED    2  6  5  1
  RB1 WILD-TYPE 65 34 38  8
D4V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           2            65
  T2           6            34
  T3           5            38
  T4           1             8
[1] 4 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
  RB1 MUTATED   10  0
  RB1 WILD-TYPE 91  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     10    0
  RB1 WILD-TYPE   91    3
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          10            91
  1           0             3
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  RB1 MUTATED    12   0   2
  RB1 WILD-TYPE 110   3  33
D4V6, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  M0          12           110
  M1           0             3
  MX           2            33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
               cls
clus             0  1
  RB1 MUTATED    8  6
  RB1 WILD-TYPE 53 93
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      8    6
  RB1 WILD-TYPE   53   93
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           8            53
  MALE             6            93
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RB1 MUTATED                         0                       14
  RB1 WILD-TYPE                       1                      143
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  RB1 MUTATED                                  0
  RB1 WILD-TYPE                                2
D4V8, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  14           143
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    12   1   0   1
  RB1 WILD-TYPE 120   9   1  11
D4V9, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          12           120
  R1           1             9
  R2           0             1
  RX           1            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     8
  RB1 WILD-TYPE                                1    29
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           1     5
  RB1 WILD-TYPE                         7   103
D4V10, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      8            29
  BLACK OR AFRICAN AMERICAN                  1             7
  WHITE                                      5           103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
               cls
clus              0   1
  RB1 MUTATED     1  13
  RB1 WILD-TYPE   3 130
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   13
  RB1 WILD-TYPE    3  130
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             3
  NOT HISPANIC OR LATINO          13           130
[1] 2 2
[1] FALSE

Clustering(5) Variable = AXIN1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  AXIN1 MUTATED    2  6
  AXIN1 WILD-TYPE 88 60
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              8             148 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              6              60 
$`AXIN1 MUTATED`
TCGA-CC-5261 TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A39Z TCGA-ES-A2HS TCGA-FV-A23B 
        0.39         0.46        49.15        19.76        22.85        32.45 
TCGA-FV-A3R2 TCGA-MI-A75G 
        6.38        14.24 

$`AXIN1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.07         0.16         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        45.11         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69         5.62        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       10.98         0.62         9.96        11.93        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  AXIN1 MUTATED AXIN1 WILD-TYPE 
           0.39            0.03 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          49.15          113.00 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          17.00           13.81 
[1] "0.4 - 49.1 (17.0)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.3"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AXIN1 MUTATED         3        4         1          0          0          0
  AXIN1 WILD-TYPE      61       32         1         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  AXIN1 MUTATED          0         0         0
  AXIN1 WILD-TYPE        1         1         2
D5V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I                3              61
  STAGE II               4              32
  STAGE III              1               1
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  AXIN1 MUTATED    3  4  1  0
  AXIN1 WILD-TYPE 64 36 42  9
D5V4, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  T1             3              64
  T2             4              36
  T3             1              42
  T4             0               9
[1] 4 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
  AXIN1 MUTATED    5  0
  AXIN1 WILD-TYPE 96  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      5    0
  AXIN1 WILD-TYPE   96    3
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0             5              96
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  AXIN1 MUTATED     6   0   2
  AXIN1 WILD-TYPE 116   3  33
D5V6, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  M0             6             116
  M1             0               3
  MX             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                 cls
clus               0  1
  AXIN1 MUTATED    2  6
  AXIN1 WILD-TYPE 59 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      2    6
  AXIN1 WILD-TYPE   59   93
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             2              59
  MALE               6              93
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AXIN1 MUTATED                         0                        8
  AXIN1 WILD-TYPE                       1                      149
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AXIN1 MUTATED                                  0
  AXIN1 WILD-TYPE                                2
D5V8, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     8             149
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AXIN1 MUTATED     6   0   0   2
  AXIN1 WILD-TYPE 126  10   1  10
D5V9, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  R0             6             126
  R1             0              10
  R2             0               1
  RX             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN1 MUTATED                                  0     1
  AXIN1 WILD-TYPE                                1    36
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN1 MUTATED                           0     6
  AXIN1 WILD-TYPE                         8   102
D5V10, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              36
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        6             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                 cls
clus                0   1
  AXIN1 MUTATED     0   7
  AXIN1 WILD-TYPE   4 136
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      0    7
  AXIN1 WILD-TYPE    4  136
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             136
[1] 2 2
[1] FALSE

Clustering(6) Variable = KRTAP5-11 MUTATION ANALYSIS
D6V1, survival
                     sevent
clus2                  0  1
  KRTAP5-11 MUTATED    1  4
  KRTAP5-11 WILD-TYPE 89 62
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
                  5                 151 
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
                  4                  62 
$`KRTAP5-11 MUTATED`
TCGA-BC-A10T TCGA-BC-A10W TCGA-CC-5260 TCGA-DD-A11A TCGA-ES-A2HS 
       27.52         2.99         2.86         2.60        22.85 

$`KRTAP5-11 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.16         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
               2.60                0.03 
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
              27.52              113.00 
  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE 
               2.99               13.91 
[1] "2.6 - 27.5 (3.0)"   "0.0 - 113.0 (13.9)"
[1] "hr=" "3.4"
D6V2, continuous
                     vv
clus                  STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  KRTAP5-11 MUTATED         2        0         0          0          0
  KRTAP5-11 WILD-TYPE      62       36         2         32          5
                     vv
clus                  STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  KRTAP5-11 MUTATED            1        0         0         0
  KRTAP5-11 WILD-TYPE          5        1         1         2
D6V3, multiclass
            clus
vv           KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  STAGE I                    2                  62
  STAGE II                   0                  36
  STAGE III                  0                   2
  STAGE IIIA                 0                  32
  STAGE IIIB                 0                   5
  STAGE IIIC                 1                   5
  STAGE IV                   0                   1
  STAGE IVA                  0                   1
  STAGE IVB                  0                   2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3 T4
  KRTAP5-11 MUTATED    2  0  0  3
  KRTAP5-11 WILD-TYPE 65 40 43  6
D6V4, multiclass
    clus
vv   KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  T1                 2                  65
  T2                 0                  40
  T3                 0                  43
  T4                 3                   6
[1] 4 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
  KRTAP5-11 MUTATED    2  0
  KRTAP5-11 WILD-TYPE 99  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-11 MUTATED      2    0
  KRTAP5-11 WILD-TYPE   99    3
   clus
vv  KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  0                 2                  99
  1                 0                   3
[1] 2 2
[1] FALSE
                     vv
clus                   M0  M1  MX
  KRTAP5-11 MUTATED     2   0   3
  KRTAP5-11 WILD-TYPE 120   3  32
D6V6, multiclass
    clus
vv   KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  M0                 2                 120
  M1                 0                   3
  MX                 3                  32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                     cls
clus                   0  1
  KRTAP5-11 MUTATED    1  4
  KRTAP5-11 WILD-TYPE 60 95
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-11 MUTATED      1    4
  KRTAP5-11 WILD-TYPE   60   95
        clus
vv       KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  FEMALE                 1                  60
  MALE                   4                  95
[1] 2 2
[1] FALSE
                     vv
clus                  FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRTAP5-11 MUTATED                         0                        5
  KRTAP5-11 WILD-TYPE                       1                      152
                     vv
clus                  HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRTAP5-11 MUTATED                                  0
  KRTAP5-11 WILD-TYPE                                2
D6V8, multiclass
                                  clus
vv                                 KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                          0                   1
  HEPATOCELLULAR CARCINOMA                         5                 152
  HEPATOCHOLANGIOCARCINOMA (MIXED)                 0                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP5-11 MUTATED     2   2   0   1
  KRTAP5-11 WILD-TYPE 130   8   1  11
D6V9, multiclass
    clus
vv   KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  R0                 2                 130
  R1                 2                   8
  R2                 0                   1
  RX                 1                  11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-11 MUTATED                                  0     2
  KRTAP5-11 WILD-TYPE                                1    35
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-11 MUTATED                           1     2
  KRTAP5-11 WILD-TYPE                         7   106
D6V10, multiclass
                                  clus
vv                                 KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            2                  35
  BLACK OR AFRICAN AMERICAN                        1                   7
  WHITE                                            2                 106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                     cls
clus                    0   1
  KRTAP5-11 MUTATED     0   5
  KRTAP5-11 WILD-TYPE   4 138
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP5-11 MUTATED      0    5
  KRTAP5-11 WILD-TYPE    4  138
                        clus
vv                       KRTAP5-11 MUTATED KRTAP5-11 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 5                 138
[1] 2 2
[1] FALSE

Clustering(7) Variable = AHCTF1 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  AHCTF1 MUTATED    8  4
  AHCTF1 WILD-TYPE 82 62
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              12              144 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               4               62 
$`AHCTF1 MUTATED`
TCGA-BC-A10S TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1ED 
       46.78        79.73        53.33         2.60        66.31        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A73E TCGA-EP-A12J TCGA-MI-A75E 
       45.11        49.15         5.62         1.45        18.74         5.10 

$`AHCTF1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        3.32         0.10         0.07         0.10         0.13        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       90.71        79.40        19.79        12.95         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       10.98        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20         0.20        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        9.57        14.24        12.85         8.71        58.88         4.44 

  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
            1.45             0.03 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
           79.73           113.00 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          45.945           13.710 
[1] "1.4 - 79.7 (45.9)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "2"  
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AHCTF1 MUTATED         7        1         1          1          0          1
  AHCTF1 WILD-TYPE      57       35         1         31          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  AHCTF1 MUTATED          0         0         0
  AHCTF1 WILD-TYPE        1         1         2
D7V3, multiclass
            clus
vv           AHCTF1 MUTATED AHCTF1 WILD-TYPE
  STAGE I                 7               57
  STAGE II                1               35
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  AHCTF1 MUTATED    7  1  3  1
  AHCTF1 WILD-TYPE 60 39 40  8
D7V4, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  T1              7               60
  T2              1               39
  T3              3               40
  T4              1                8
[1] 4 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
  AHCTF1 MUTATED    9  0
  AHCTF1 WILD-TYPE 92  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      9    0
  AHCTF1 WILD-TYPE   92    3
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0              9               92
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  AHCTF1 MUTATED    10   0   2
  AHCTF1 WILD-TYPE 112   3  33
D7V6, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  M0             10              112
  M1              0                3
  MX              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                  cls
clus                0  1
  AHCTF1 MUTATED    2 10
  AHCTF1 WILD-TYPE 59 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      2   10
  AHCTF1 WILD-TYPE   59   89
        clus
vv       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FEMALE              2               59
  MALE               10               89
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AHCTF1 MUTATED                         0                       12
  AHCTF1 WILD-TYPE                       1                      145
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  AHCTF1 MUTATED                                  0
  AHCTF1 WILD-TYPE                                2
D7V8, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     12              145
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AHCTF1 MUTATED    12   0   0   0
  AHCTF1 WILD-TYPE 120  10   1  12
D7V9, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  R0             12              120
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCTF1 MUTATED                                  0     2
  AHCTF1 WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHCTF1 MUTATED                           2     7
  AHCTF1 WILD-TYPE                         6   101
D7V10, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     2                6
  WHITE                                         7              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     0  11
  AHCTF1 WILD-TYPE   4 132
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      0   11
  AHCTF1 WILD-TYPE    4  132
                        clus
vv                       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              132
[1] 2 2
[1] FALSE

Clustering(8) Variable = GPATCH4 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  GPATCH4 MUTATED    5  4
  GPATCH4 WILD-TYPE 85 62
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                9               147 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
                4                62 
$`GPATCH4 MUTATED`
TCGA-BC-A10U TCGA-CC-A3MA TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EH 
       27.52         0.07         7.33         2.60        45.11        49.15 
TCGA-DD-A3A0 TCGA-FV-A495 TCGA-G3-A25Z 
       25.81         0.03        21.53 

$`GPATCH4 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33       113.00         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
             0.03              0.07 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            49.15            113.00 
  GPATCH4 MUTATED GPATCH4 WILD-TYPE 
            21.53             13.84 
[1] "0.0 - 49.1 (21.5)"  "0.1 - 113.0 (13.8)"
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GPATCH4 MUTATED         5        1         1          1          0          0
  GPATCH4 WILD-TYPE      59       35         1         31          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  GPATCH4 MUTATED          1         0         0
  GPATCH4 WILD-TYPE        0         1         2
D8V3, multiclass
            clus
vv           GPATCH4 MUTATED GPATCH4 WILD-TYPE
  STAGE I                  5                59
  STAGE II                 1                35
  STAGE III                1                 1
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 1                 0
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  GPATCH4 MUTATED    5  2  3  0
  GPATCH4 WILD-TYPE 62 38 40  9
D8V4, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  T1               5                62
  T2               2                38
  T3               3                40
  T4               0                 9
[1] 4 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
  GPATCH4 MUTATED    6  0
  GPATCH4 WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      6    0
  GPATCH4 WILD-TYPE   95    3
   clus
vv  GPATCH4 MUTATED GPATCH4 WILD-TYPE
  0               6                95
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  GPATCH4 MUTATED     7   1   2
  GPATCH4 WILD-TYPE 115   2  33
D8V6, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  M0               7               115
  M1               1                 2
  MX               2                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  GPATCH4 MUTATED    1  9
  GPATCH4 WILD-TYPE 60 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      1    9
  GPATCH4 WILD-TYPE   60   90
        clus
vv       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FEMALE               1                60
  MALE                 9                90
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GPATCH4 MUTATED                         0                       10
  GPATCH4 WILD-TYPE                       1                      147
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  GPATCH4 MUTATED                                  0
  GPATCH4 WILD-TYPE                                2
D8V8, multiclass
                                  clus
vv                                 GPATCH4 MUTATED GPATCH4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                      10               147
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPATCH4 MUTATED     7   1   1   1
  GPATCH4 WILD-TYPE 125   9   0  11
D8V9, multiclass
    clus
vv   GPATCH4 MUTATED GPATCH4 WILD-TYPE
  R0               7               125
  R1               1                 9
  R2               1                 0
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPATCH4 MUTATED                                  0     3
  GPATCH4 WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GPATCH4 MUTATED                           1     6
  GPATCH4 WILD-TYPE                         7   102
D8V10, multiclass
                                  clus
vv                                 GPATCH4 MUTATED GPATCH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                34
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                          6               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                   cls
clus                  0   1
  GPATCH4 MUTATED     0  10
  GPATCH4 WILD-TYPE   4 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH4 MUTATED      0   10
  GPATCH4 WILD-TYPE    4  133
                        clus
vv                       GPATCH4 MUTATED GPATCH4 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               133
[1] 2 2
[1] FALSE

Clustering(9) Variable = CD207 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2              0  1
  CD207 MUTATED    2  6
  CD207 WILD-TYPE 88 60
  CD207 MUTATED CD207 WILD-TYPE 
              8             148 
  CD207 MUTATED CD207 WILD-TYPE 
              6              60 
$`CD207 MUTATED`
TCGA-BC-A69I TCGA-CC-5261 TCGA-DD-A1EG TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       12.72         0.39        45.11        55.69         5.62        25.81 
TCGA-FV-A2QR TCGA-G3-A3CJ 
       19.10        19.53 

$`CD207 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         0.16         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        32.45        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.86        21.53        22.13        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  CD207 MUTATED CD207 WILD-TYPE 
           0.39            0.03 
  CD207 MUTATED CD207 WILD-TYPE 
          55.69          113.00 
  CD207 MUTATED CD207 WILD-TYPE 
         19.315          13.810 
[1] "0.4 - 55.7 (19.3)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.9"
D9V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CD207 MUTATED         6        2         0          0          0          0
  CD207 WILD-TYPE      58       34         2         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CD207 MUTATED          0         0         0
  CD207 WILD-TYPE        1         1         2
D9V3, multiclass
            clus
vv           CD207 MUTATED CD207 WILD-TYPE
  STAGE I                6              58
  STAGE II               2              34
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  CD207 MUTATED    6  2  0  0
  CD207 WILD-TYPE 61 38 43  9
D9V4, multiclass
    clus
vv   CD207 MUTATED CD207 WILD-TYPE
  T1             6              61
  T2             2              38
  T3             0              43
  T4             0               9
[1] 4 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
  CD207 MUTATED    5  0
  CD207 WILD-TYPE 96  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD207 MUTATED      5    0
  CD207 WILD-TYPE   96    3
   clus
vv  CD207 MUTATED CD207 WILD-TYPE
  0             5              96
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  CD207 MUTATED     8   0   0
  CD207 WILD-TYPE 114   3  35
D9V6, multiclass
    clus
vv   CD207 MUTATED CD207 WILD-TYPE
  M0             8             114
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                 cls
clus               0  1
  CD207 MUTATED    1  7
  CD207 WILD-TYPE 60 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD207 MUTATED      1    7
  CD207 WILD-TYPE   60   92
        clus
vv       CD207 MUTATED CD207 WILD-TYPE
  FEMALE             1              60
  MALE               7              92
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CD207 MUTATED                         0                        8
  CD207 WILD-TYPE                       1                      149
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CD207 MUTATED                                  0
  CD207 WILD-TYPE                                2
D9V8, multiclass
                                  clus
vv                                 CD207 MUTATED CD207 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     8             149
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CD207 MUTATED     6   0   0   2
  CD207 WILD-TYPE 126  10   1  10
D9V9, multiclass
    clus
vv   CD207 MUTATED CD207 WILD-TYPE
  R0             6             126
  R1             0              10
  R2             0               1
  RX             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD207 MUTATED                                  1     2
  CD207 WILD-TYPE                                0    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD207 MUTATED                           0     5
  CD207 WILD-TYPE                         8   103
D9V10, multiclass
                                  clus
vv                                 CD207 MUTATED CD207 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        5             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                 cls
clus                0   1
  CD207 MUTATED     0   7
  CD207 WILD-TYPE   4 136
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD207 MUTATED      0    7
  CD207 WILD-TYPE    4  136
                        clus
vv                       CD207 MUTATED CD207 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             136
[1] 2 2
[1] FALSE

Clustering(10) Variable = EEF1A1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  EEF1A1 MUTATED    4  4
  EEF1A1 WILD-TYPE 86 62
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               8              148 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               4               62 
$`EEF1A1 MUTATED`
TCGA-BC-A10S TCGA-DD-A11B TCGA-DD-A73D TCGA-ES-A2HS TCGA-G3-A25V TCGA-G3-A5SM 
       46.78         0.46        10.98        22.85        28.27         4.37 
TCGA-K7-A6G5 TCGA-KR-A7K0 
        4.01         2.14 

$`EEF1A1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
        7.56         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         7.76         5.98         1.84         1.02         2.66 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
            0.46             0.03 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           46.78           113.00 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           7.675           13.990 
[1] "0.5 - 46.8 (7.7)"   "0.0 - 113.0 (14.0)"
[1] "hr=" "1.7"
D10V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EEF1A1 MUTATED         5        2         0          0          0          0
  EEF1A1 WILD-TYPE      59       34         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  EEF1A1 MUTATED          0         0         0
  EEF1A1 WILD-TYPE        1         1         2
D10V3, multiclass
            clus
vv           EEF1A1 MUTATED EEF1A1 WILD-TYPE
  STAGE I                 5               59
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  EEF1A1 MUTATED    5  2  1  0
  EEF1A1 WILD-TYPE 62 38 42  9
D10V4, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  T1              5               62
  T2              2               38
  T3              1               42
  T4              0                9
[1] 4 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
  EEF1A1 MUTATED    4  0
  EEF1A1 WILD-TYPE 97  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      4    0
  EEF1A1 WILD-TYPE   97    3
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              4               97
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  EEF1A1 MUTATED     4   0   4
  EEF1A1 WILD-TYPE 118   3  31
D10V6, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  M0              4              118
  M1              0                3
  MX              4               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                  cls
clus                0  1
  EEF1A1 MUTATED    1  7
  EEF1A1 WILD-TYPE 60 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      1    7
  EEF1A1 WILD-TYPE   60   92
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FEMALE              1               60
  MALE                7               92
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  EEF1A1 MUTATED                         0                        8
  EEF1A1 WILD-TYPE                       1                      149
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  EEF1A1 MUTATED                                  0
  EEF1A1 WILD-TYPE                                2
D10V8, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      8              149
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EEF1A1 MUTATED     6   0   0   2
  EEF1A1 WILD-TYPE 126  10   1  10
D10V9, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  R0              6              126
  R1              0               10
  R2              0                1
  RX              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1A1 MUTATED                                  0     0
  EEF1A1 WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EEF1A1 MUTATED                           0     8
  EEF1A1 WILD-TYPE                         8   100
D10V10, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         8              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     0   7
  EEF1A1 WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      0    7
  EEF1A1 WILD-TYPE    4  136
                        clus
vv                       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(11) Variable = BAP1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED    7  4
  BAP1 WILD-TYPE 83 62
  BAP1 MUTATED BAP1 WILD-TYPE 
            11            145 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4             62 
$`BAP1 MUTATED`
TCGA-BC-A10Q TCGA-CC-5260 TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A3A9 TCGA-DD-A4NA 
       37.32         2.86       113.00        12.95        30.61        33.14 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A7PX TCGA-FV-A3I0 TCGA-G3-A25T 
      100.96        12.69         0.20        27.88        51.06 

$`BAP1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         0.16         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       13.41        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.03         0.33        60.36         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.20           0.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
        113.00         107.11 
  BAP1 MUTATED BAP1 WILD-TYPE 
         30.61          13.78 
[1] "0.2 - 113.0 (30.6)" "0.0 - 107.1 (13.8)"
[1] "hr=" "2.2"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BAP1 MUTATED         2        4         0          1          0          2
  BAP1 WILD-TYPE      62       32         2         31          5          4
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED          0         0         1
  BAP1 WILD-TYPE        1         1         1
D11V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               2             62
  STAGE II              4             32
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            2              4
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  BAP1 MUTATED    2  6  1  2
  BAP1 WILD-TYPE 65 34 42  7
D11V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            2             65
  T2            6             34
  T3            1             42
  T4            2              7
[1] 4 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
  BAP1 MUTATED    7  1
  BAP1 WILD-TYPE 94  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    1
  BAP1 WILD-TYPE   94    2
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            7             94
  1            1              2
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  BAP1 MUTATED     9   1   1
  BAP1 WILD-TYPE 113   2  34
D11V6, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  M0            9            113
  M1            1              2
  MX            1             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"
D11V7, binary
                cls
clus              0  1
  BAP1 MUTATED   10  1
  BAP1 WILD-TYPE 51 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     10    1
  BAP1 WILD-TYPE   51   98
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE           10             51
  MALE              1             98
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BAP1 MUTATED                         0                       10
  BAP1 WILD-TYPE                       1                      147
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BAP1 MUTATED                                  1
  BAP1 WILD-TYPE                                1
D11V8, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   10            147
  HEPATOCHOLANGIOCARCINOMA (MIXED)            1              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED     9   1   0   1
  BAP1 WILD-TYPE 123   9   1  11
D11V9, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0            9            123
  R1            1              9
  R2            0              1
  RX            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     3
  BAP1 WILD-TYPE                                1    34
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           0     8
  BAP1 WILD-TYPE                         8   100
D11V10, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3             34
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       8            100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                cls
clus               0   1
  BAP1 MUTATED     0  11
  BAP1 WILD-TYPE   4 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0   11
  BAP1 WILD-TYPE    4  132
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           11            132
[1] 2 2
[1] FALSE

Clustering(12) Variable = CHIT1 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  CHIT1 MUTATED    2  3
  CHIT1 WILD-TYPE 88 63
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              5             151 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              3              63 
$`CHIT1 MUTATED`
TCGA-BC-A69I TCGA-DD-A1ED TCGA-DD-A1EF TCGA-ES-A2HS TCGA-NI-A4U2 
       12.72        75.65        12.95        22.85        58.88 

$`CHIT1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-O8-A75V 
        4.44 

  CHIT1 MUTATED CHIT1 WILD-TYPE 
          12.72            0.03 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
          75.65          113.00 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
          22.85           13.84 
[1] "12.7 - 75.7 (22.9)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CHIT1 MUTATED         4        0         0          1          0          0
  CHIT1 WILD-TYPE      60       36         2         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CHIT1 MUTATED          0         0         0
  CHIT1 WILD-TYPE        1         1         2
D12V3, multiclass
            clus
vv           CHIT1 MUTATED CHIT1 WILD-TYPE
  STAGE I                4              60
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  CHIT1 MUTATED    4  0  1  0
  CHIT1 WILD-TYPE 63 40 42  9
D12V4, multiclass
    clus
vv   CHIT1 MUTATED CHIT1 WILD-TYPE
  T1             4              63
  T2             0              40
  T3             1              42
  T4             0               9
[1] 4 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
  CHIT1 MUTATED    3  0
  CHIT1 WILD-TYPE 98  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      3    0
  CHIT1 WILD-TYPE   98    3
   clus
vv  CHIT1 MUTATED CHIT1 WILD-TYPE
  0             3              98
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  CHIT1 MUTATED     3   0   2
  CHIT1 WILD-TYPE 119   3  33
D12V6, multiclass
    clus
vv   CHIT1 MUTATED CHIT1 WILD-TYPE
  M0             3             119
  M1             0               3
  MX             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                 cls
clus               0  1
  CHIT1 MUTATED    1  4
  CHIT1 WILD-TYPE 60 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      1    4
  CHIT1 WILD-TYPE   60   95
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  FEMALE             1              60
  MALE               4              95
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CHIT1 MUTATED                         0                        5
  CHIT1 WILD-TYPE                       1                      152
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CHIT1 MUTATED                                  0
  CHIT1 WILD-TYPE                                2
D12V8, multiclass
                                  clus
vv                                 CHIT1 MUTATED CHIT1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     5             152
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHIT1 MUTATED     5   0   0   0
  CHIT1 WILD-TYPE 127  10   1  12
D12V9, multiclass
    clus
vv   CHIT1 MUTATED CHIT1 WILD-TYPE
  R0             5             127
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHIT1 MUTATED                                  0     0
  CHIT1 WILD-TYPE                                1    37
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHIT1 MUTATED                           0     5
  CHIT1 WILD-TYPE                         8   103
D12V10, multiclass
                                  clus
vv                                 CHIT1 MUTATED CHIT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              37
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        5             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                 cls
clus                0   1
  CHIT1 MUTATED     0   4
  CHIT1 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      0    4
  CHIT1 WILD-TYPE    4  139
                        clus
vv                       CHIT1 MUTATED CHIT1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(13) Variable = PPIAL4G MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  PPIAL4G MUTATED    5  2
  PPIAL4G WILD-TYPE 85 64
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
                7               149 
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
                2                64 
$`PPIAL4G MUTATED`
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EH 
       53.33         2.60        79.40        66.31        12.95        49.15 
TCGA-EP-A12J 
       18.74 

$`PPIAL4G WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG 
       21.76        51.29        90.71        19.79        75.65        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
             2.60              0.03 
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
             79.4             113.0 
  PPIAL4G MUTATED PPIAL4G WILD-TYPE 
            49.15             13.78 
[1] "2.6 - 79.4 (49.1)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.4"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PPIAL4G MUTATED         4        1         1          1          0          0
  PPIAL4G WILD-TYPE      60       35         1         31          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  PPIAL4G MUTATED          0         0         0
  PPIAL4G WILD-TYPE        1         1         2
D13V3, multiclass
            clus
vv           PPIAL4G MUTATED PPIAL4G WILD-TYPE
  STAGE I                  4                60
  STAGE II                 1                35
  STAGE III                1                 1
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  PPIAL4G MUTATED    4  1  2  0
  PPIAL4G WILD-TYPE 63 39 41  9
D13V4, multiclass
    clus
vv   PPIAL4G MUTATED PPIAL4G WILD-TYPE
  T1               4                63
  T2               1                39
  T3               2                41
  T4               0                 9
[1] 4 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
  PPIAL4G MUTATED    6  0
  PPIAL4G WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4G MUTATED      6    0
  PPIAL4G WILD-TYPE   95    3
   clus
vv  PPIAL4G MUTATED PPIAL4G WILD-TYPE
  0               6                95
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  PPIAL4G MUTATED     6   0   1
  PPIAL4G WILD-TYPE 116   3  34
D13V6, multiclass
    clus
vv   PPIAL4G MUTATED PPIAL4G WILD-TYPE
  M0               6               116
  M1               0                 3
  MX               1                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"
D13V7, binary
                   cls
clus                 0  1
  PPIAL4G MUTATED    2  5
  PPIAL4G WILD-TYPE 59 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4G MUTATED      2    5
  PPIAL4G WILD-TYPE   59   94
        clus
vv       PPIAL4G MUTATED PPIAL4G WILD-TYPE
  FEMALE               2                59
  MALE                 5                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PPIAL4G MUTATED                         0                        7
  PPIAL4G WILD-TYPE                       1                      150
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  PPIAL4G MUTATED                                  0
  PPIAL4G WILD-TYPE                                2
D13V8, multiclass
                                  clus
vv                                 PPIAL4G MUTATED PPIAL4G WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       7               150
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPIAL4G MUTATED     7   0   0   0
  PPIAL4G WILD-TYPE 125  10   1  12
D13V9, multiclass
    clus
vv   PPIAL4G MUTATED PPIAL4G WILD-TYPE
  R0               7               125
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIAL4G MUTATED                                  0     2
  PPIAL4G WILD-TYPE                                1    35
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPIAL4G MUTATED                           2     2
  PPIAL4G WILD-TYPE                         6   106
D13V10, multiclass
                                  clus
vv                                 PPIAL4G MUTATED PPIAL4G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                35
  BLACK OR AFRICAN AMERICAN                      2                 6
  WHITE                                          2               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  PPIAL4G MUTATED     0   6
  PPIAL4G WILD-TYPE   4 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPIAL4G MUTATED      0    6
  PPIAL4G WILD-TYPE    4  137
                        clus
vv                       PPIAL4G MUTATED PPIAL4G WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               137
[1] 2 2
[1] FALSE

Clustering(14) Variable = ALB MUTATION ANALYSIS
D14V1, survival
               sevent
clus2            0  1
  ALB MUTATED   13  9
  ALB WILD-TYPE 77 57
  ALB MUTATED ALB WILD-TYPE 
           22           134 
  ALB MUTATED ALB WILD-TYPE 
            9            57 
$`ALB MUTATED`
TCGA-BC-4073 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A39X 
       27.91       113.00        90.71        12.95        45.11        55.69 
TCGA-DD-A4NI TCGA-DD-A4NK TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       18.44        39.78        19.99         0.62         9.96        22.85 
TCGA-FV-A23B TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CJ TCGA-G3-A5SJ 
       32.45         0.33         1.22        30.74        19.53        11.97 
TCGA-G3-A5SK TCGA-K7-A6G5 TCGA-MI-A75E TCGA-MI-A75G 
        9.93         4.01         5.10        14.24 

$`ALB WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       14.24        15.06        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
       11.74        10.98        11.93        14.40        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        53.79        28.27        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.92        19.23        14.70         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-KR-A7K0 
        7.76         5.98         1.84         1.02         2.66         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I 
       11.84        13.38         0.49         9.57        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  ALB MUTATED ALB WILD-TYPE 
         0.33          0.03 
  ALB MUTATED ALB WILD-TYPE 
       113.00        107.11 
  ALB MUTATED ALB WILD-TYPE 
       18.985        13.710 
[1] "0.3 - 113.0 (19.0)" "0.0 - 107.1 (13.7)"
[1] "hr=" "1.3"
D14V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALB MUTATED        13        5         0          2          1          1
  ALB WILD-TYPE      51       31         2         30          4          5
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  ALB MUTATED          0         1         0
  ALB WILD-TYPE        1         0         2
D14V3, multiclass
            clus
vv           ALB MUTATED ALB WILD-TYPE
  STAGE I             13            51
  STAGE II             5            31
  STAGE III            0             2
  STAGE IIIA           2            30
  STAGE IIIB           1             4
  STAGE IIIC           1             5
  STAGE IV             0             1
  STAGE IVA            1             0
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  ALB MUTATED   14  5  3  1
  ALB WILD-TYPE 53 35 40  8
D14V4, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  T1          14            53
  T2           5            35
  T3           3            40
  T4           1             8
[1] 4 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
  ALB MUTATED   14  1
  ALB WILD-TYPE 87  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     14    1
  ALB WILD-TYPE   87    2
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          14            87
  1           1             2
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  ALB MUTATED    16   0   7
  ALB WILD-TYPE 106   3  28
D14V6, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  M0          16           106
  M1           0             3
  MX           7            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
               cls
clus             0  1
  ALB MUTATED    7 16
  ALB WILD-TYPE 54 83
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      7   16
  ALB WILD-TYPE   54   83
        clus
vv       ALB MUTATED ALB WILD-TYPE
  FEMALE           7            54
  MALE            16            83
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALB MUTATED                         0                       23
  ALB WILD-TYPE                       1                      134
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALB MUTATED                                  0
  ALB WILD-TYPE                                2
D14V8, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  23           134
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ALB MUTATED    18   2   0   1
  ALB WILD-TYPE 114   8   1  11
D14V9, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  R0          18           114
  R1           2             8
  R2           0             1
  RX           1            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALB MUTATED                                  1     0
  ALB WILD-TYPE                                0    37
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALB MUTATED                           1    21
  ALB WILD-TYPE                         7    87
D14V10, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      0            37
  BLACK OR AFRICAN AMERICAN                  1             7
  WHITE                                     21            87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
               cls
clus              0   1
  ALB MUTATED     0  23
  ALB WILD-TYPE   4 120
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      0   23
  ALB WILD-TYPE    4  120
                        clus
vv                       ALB MUTATED ALB WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          23           120
[1] 2 2
[1] FALSE

Clustering(15) Variable = PABPC1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    5  3
  PABPC1 WILD-TYPE 85 63
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               8              148 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               3               63 
$`PABPC1 MUTATED`
TCGA-BC-4073 TCGA-BC-A216 TCGA-DD-A118 TCGA-DD-A1EJ TCGA-DD-A3A2 TCGA-EP-A2KA 
       27.91        44.42       113.00        29.16        70.06        11.74 
TCGA-G3-A25V TCGA-G3-A3CH 
       28.27        25.64 

$`PABPC1 WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 
       25.32        23.34         1.12        69.57         5.03        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        53.79        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        22.13         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
           11.74             0.03 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          113.00           107.11 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          28.715           13.525 
[1] "11.7 - 113.0 (28.7)" "0.0 - 107.1 (13.5)" 
[1] "hr=" "2.5"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PABPC1 MUTATED         2        1         0          4          0          1
  PABPC1 WILD-TYPE      62       35         2         28          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  PABPC1 MUTATED          0         0         0
  PABPC1 WILD-TYPE        1         1         2
D15V3, multiclass
            clus
vv           PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE I                 2               62
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              4               28
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  PABPC1 MUTATED    3  1  4  0
  PABPC1 WILD-TYPE 64 39 39  9
D15V4, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  T1              3               64
  T2              1               39
  T3              4               39
  T4              0                9
[1] 4 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
  PABPC1 MUTATED    5  1
  PABPC1 WILD-TYPE 96  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      5    1
  PABPC1 WILD-TYPE   96    2
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              5               96
  1              1                2
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  PABPC1 MUTATED     6   0   2
  PABPC1 WILD-TYPE 116   3  33
D15V6, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  M0              6              116
  M1              0                3
  MX              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    5  3
  PABPC1 WILD-TYPE 56 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      5    3
  PABPC1 WILD-TYPE   56   96
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              5               56
  MALE                3               96
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PABPC1 MUTATED                         0                        8
  PABPC1 WILD-TYPE                       1                      149
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  PABPC1 MUTATED                                  0
  PABPC1 WILD-TYPE                                2
D15V8, multiclass
                                  clus
vv                                 PABPC1 MUTATED PABPC1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      8              149
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PABPC1 MUTATED     7   1   0   0
  PABPC1 WILD-TYPE 125   9   1  12
D15V9, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  R0              7              125
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PABPC1 MUTATED                                  0     1
  PABPC1 WILD-TYPE                                1    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED                           0     7
  PABPC1 WILD-TYPE                         8   101
D15V10, multiclass
                                  clus
vv                                 PABPC1 MUTATED PABPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         7              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                  cls
clus                 0   1
  PABPC1 MUTATED     0   7
  PABPC1 WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    7
  PABPC1 WILD-TYPE    4  136
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(16) Variable = TREML2 MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  TREML2 MUTATED    4  2
  TREML2 WILD-TYPE 86 64
  TREML2 MUTATED TREML2 WILD-TYPE 
               6              150 
  TREML2 MUTATED TREML2 WILD-TYPE 
               2               64 
$`TREML2 MUTATED`
TCGA-BC-A3KF TCGA-DD-A4NE TCGA-DD-A4NO TCGA-DD-A73D TCGA-DD-A73E TCGA-ES-A2HT 
        0.26        21.70        73.81        10.98         1.45        14.40 

$`TREML2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       32.52        73.38        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        29.56        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        22.85        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  TREML2 MUTATED TREML2 WILD-TYPE 
            0.26             0.03 
  TREML2 MUTATED TREML2 WILD-TYPE 
           73.81           113.00 
  TREML2 MUTATED TREML2 WILD-TYPE 
          12.690           13.875 
[1] "0.3 - 73.8 (12.7)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.1"
D16V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TREML2 MUTATED         4        1         0          1          0          0
  TREML2 WILD-TYPE      60       35         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  TREML2 MUTATED          0         0         0
  TREML2 WILD-TYPE        1         1         2
D16V3, multiclass
            clus
vv           TREML2 MUTATED TREML2 WILD-TYPE
  STAGE I                 4               60
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  TREML2 MUTATED    4  1  1  0
  TREML2 WILD-TYPE 63 39 42  9
D16V4, multiclass
    clus
vv   TREML2 MUTATED TREML2 WILD-TYPE
  T1              4               63
  T2              1               39
  T3              1               42
  T4              0                9
[1] 4 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
  TREML2 MUTATED    3  0
  TREML2 WILD-TYPE 98  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TREML2 MUTATED      3    0
  TREML2 WILD-TYPE   98    3
   clus
vv  TREML2 MUTATED TREML2 WILD-TYPE
  0              3               98
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  TREML2 MUTATED     4   0   2
  TREML2 WILD-TYPE 118   3  33
D16V6, multiclass
    clus
vv   TREML2 MUTATED TREML2 WILD-TYPE
  M0              4              118
  M1              0                3
  MX              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                  cls
clus                0  1
  TREML2 MUTATED    3  3
  TREML2 WILD-TYPE 58 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TREML2 MUTATED      3    3
  TREML2 WILD-TYPE   58   96
        clus
vv       TREML2 MUTATED TREML2 WILD-TYPE
  FEMALE              3               58
  MALE                3               96
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TREML2 MUTATED                         0                        6
  TREML2 WILD-TYPE                       1                      151
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  TREML2 MUTATED                                  0
  TREML2 WILD-TYPE                                2
D16V8, multiclass
                                  clus
vv                                 TREML2 MUTATED TREML2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      6              151
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TREML2 MUTATED     6   0   0   0
  TREML2 WILD-TYPE 126  10   1  12
D16V9, multiclass
    clus
vv   TREML2 MUTATED TREML2 WILD-TYPE
  R0              6              126
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TREML2 MUTATED                                  0     0
  TREML2 WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TREML2 MUTATED                           1     5
  TREML2 WILD-TYPE                         7   103
D16V10, multiclass
                                  clus
vv                                 TREML2 MUTATED TREML2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         5              103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                  cls
clus                 0   1
  TREML2 MUTATED     1   4
  TREML2 WILD-TYPE   3 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TREML2 MUTATED      1    4
  TREML2 WILD-TYPE    3  139
                        clus
vv                       TREML2 MUTATED TREML2 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(17) Variable = PRH2 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  PRH2 MUTATED    4  2
  PRH2 WILD-TYPE 86 64
  PRH2 MUTATED PRH2 WILD-TYPE 
             6            150 
  PRH2 MUTATED PRH2 WILD-TYPE 
             2             64 
$`PRH2 MUTATED`
TCGA-BC-4073 TCGA-BC-A10U TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH 
       27.91        27.52        66.31        75.65        12.95        49.15 

$`PRH2 WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EG 
       21.76        51.29        90.71        79.40        19.79        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  PRH2 MUTATED PRH2 WILD-TYPE 
         12.95           0.03 
  PRH2 MUTATED PRH2 WILD-TYPE 
         75.65         113.00 
  PRH2 MUTATED PRH2 WILD-TYPE 
         38.53          13.71 
[1] "12.9 - 75.7 (38.5)" "0.0 - 113.0 (13.7)"
[1] "hr=" "2.3"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PRH2 MUTATED         3        0         1          1          0          0
  PRH2 WILD-TYPE      61       36         1         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PRH2 MUTATED          0         0         0
  PRH2 WILD-TYPE        1         1         2
D17V3, multiclass
            clus
vv           PRH2 MUTATED PRH2 WILD-TYPE
  STAGE I               3             61
  STAGE II              0             36
  STAGE III             1              1
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PRH2 MUTATED    3  1  2  0
  PRH2 WILD-TYPE 64 39 41  9
D17V4, multiclass
    clus
vv   PRH2 MUTATED PRH2 WILD-TYPE
  T1            3             64
  T2            1             39
  T3            2             41
  T4            0              9
[1] 4 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
  PRH2 MUTATED    5  0
  PRH2 WILD-TYPE 96  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRH2 MUTATED      5    0
  PRH2 WILD-TYPE   96    3
   clus
vv  PRH2 MUTATED PRH2 WILD-TYPE
  0            5             96
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  PRH2 MUTATED     4   0   2
  PRH2 WILD-TYPE 118   3  33
D17V6, multiclass
    clus
vv   PRH2 MUTATED PRH2 WILD-TYPE
  M0            4            118
  M1            0              3
  MX            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                cls
clus              0  1
  PRH2 MUTATED    2  4
  PRH2 WILD-TYPE 59 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRH2 MUTATED      2    4
  PRH2 WILD-TYPE   59   95
        clus
vv       PRH2 MUTATED PRH2 WILD-TYPE
  FEMALE            2             59
  MALE              4             95
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PRH2 MUTATED                         0                        6
  PRH2 WILD-TYPE                       1                      151
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PRH2 MUTATED                                  0
  PRH2 WILD-TYPE                                2
D17V8, multiclass
                                  clus
vv                                 PRH2 MUTATED PRH2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    6            151
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PRH2 MUTATED     4   2   0   0
  PRH2 WILD-TYPE 128   8   1  12
D17V9, multiclass
    clus
vv   PRH2 MUTATED PRH2 WILD-TYPE
  R0            4            128
  R1            2              8
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRH2 MUTATED                                  0     0
  PRH2 WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PRH2 MUTATED                           0     5
  PRH2 WILD-TYPE                         8   103
D17V10, multiclass
                                  clus
vv                                 PRH2 MUTATED PRH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       5            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                cls
clus               0   1
  PRH2 MUTATED     0   5
  PRH2 WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRH2 MUTATED      0    5
  PRH2 WILD-TYPE    4  138
                        clus
vv                       PRH2 MUTATED PRH2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(18) Variable = MUC17 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  MUC17 MUTATED   11 10
  MUC17 WILD-TYPE 79 56
  MUC17 MUTATED MUC17 WILD-TYPE 
             21             135 
  MUC17 MUTATED MUC17 WILD-TYPE 
             10              56 
$`MUC17 MUTATED`
TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A69I TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       46.78         5.03        12.72         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A39X 
        4.24         0.10        79.40        75.65        12.95        55.69 
TCGA-DD-A73E TCGA-ED-A5KG TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A2KB TCGA-ES-A2HS 
        1.45        15.85         0.20        18.74        10.98        22.85 
TCGA-G3-A25V TCGA-MI-A75E TCGA-MI-A75I 
       28.27         5.10         8.71 

$`MUC17 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 
        0.26        22.36         9.50        14.60         0.07         0.16 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.07         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EG 
       21.76        51.29        90.71        66.31        19.79        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G 
       10.98         9.30         7.56        10.98        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       13.41        12.69        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        0.62         9.96        11.93        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        53.79        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G 
        2.14        11.84        13.38         0.49         9.57        14.24 
TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85        58.88         4.44 

  MUC17 MUTATED MUC17 WILD-TYPE 
           0.10            0.03 
  MUC17 MUTATED MUC17 WILD-TYPE 
           79.4           113.0 
  MUC17 MUTATED MUC17 WILD-TYPE 
          10.98           14.24 
[1] "0.1 - 79.4 (11.0)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "1.4"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC17 MUTATED         9        4         0          3          0          3
  MUC17 WILD-TYPE      55       32         2         29          5          3
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  MUC17 MUTATED          0         1         0
  MUC17 WILD-TYPE        1         0         2
D18V3, multiclass
            clus
vv           MUC17 MUTATED MUC17 WILD-TYPE
  STAGE I                9              55
  STAGE II               4              32
  STAGE III              0               2
  STAGE IIIA             3              29
  STAGE IIIB             0               5
  STAGE IIIC             3               3
  STAGE IV               0               1
  STAGE IVA              1               0
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  MUC17 MUTATED   10  5  5  3
  MUC17 WILD-TYPE 57 35 38  6
D18V4, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  T1            10              57
  T2             5              35
  T3             5              38
  T4             3               6
[1] 4 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
  MUC17 MUTATED   14  1
  MUC17 WILD-TYPE 87  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     14    1
  MUC17 WILD-TYPE   87    2
   clus
vv  MUC17 MUTATED MUC17 WILD-TYPE
  0            14              87
  1             1               2
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  MUC17 MUTATED    16   0   7
  MUC17 WILD-TYPE 106   3  28
D18V6, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  M0            16             106
  M1             0               3
  MX             7              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                 cls
clus               0  1
  MUC17 MUTATED    6 17
  MUC17 WILD-TYPE 55 82
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      6   17
  MUC17 WILD-TYPE   55   82
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE             6              55
  MALE              17              82
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MUC17 MUTATED                         0                       23
  MUC17 WILD-TYPE                       1                      134
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  MUC17 MUTATED                                  0
  MUC17 WILD-TYPE                                2
D18V8, multiclass
                                  clus
vv                                 MUC17 MUTATED MUC17 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    23             134
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MUC17 MUTATED    18   0   0   4
  MUC17 WILD-TYPE 114  10   1   8
D18V9, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  R0            18             114
  R1             0              10
  R2             0               1
  RX             4               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC17 MUTATED                                  0     9
  MUC17 WILD-TYPE                                1    28
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED                           2    12
  MUC17 WILD-TYPE                         6    96
D18V10, multiclass
                                  clus
vv                                 MUC17 MUTATED MUC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        9              28
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                       12              96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                 cls
clus                0   1
  MUC17 MUTATED     0  22
  MUC17 WILD-TYPE   4 121
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      0   22
  MUC17 WILD-TYPE    4  121
                        clus
vv                       MUC17 MUTATED MUC17 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            22             121
[1] 2 2
[1] FALSE

Clustering(19) Variable = AZIN1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  AZIN1 MUTATED    5  6
  AZIN1 WILD-TYPE 85 60
  AZIN1 MUTATED AZIN1 WILD-TYPE 
             11             145 
  AZIN1 MUTATED AZIN1 WILD-TYPE 
              6              60 
$`AZIN1 MUTATED`
TCGA-BC-4073 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D 
       27.91         4.24         3.32        83.57         0.46        51.29 
TCGA-DD-A1EB TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CJ 
       66.31         1.22        53.79        28.27        19.53 

$`AZIN1 WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        0.07         0.16         2.86         0.39         3.39         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         7.33         2.60        21.76        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39        51.06        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  AZIN1 MUTATED AZIN1 WILD-TYPE 
           0.46            0.03 
  AZIN1 MUTATED AZIN1 WILD-TYPE 
          83.57          113.00 
  AZIN1 MUTATED AZIN1 WILD-TYPE 
          27.91           13.78 
[1] "0.5 - 83.6 (27.9)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AZIN1 MUTATED         6        1         0          4          0          0
  AZIN1 WILD-TYPE      58       35         2         28          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  AZIN1 MUTATED          0         0         0
  AZIN1 WILD-TYPE        1         1         2
D19V3, multiclass
            clus
vv           AZIN1 MUTATED AZIN1 WILD-TYPE
  STAGE I                6              58
  STAGE II               1              35
  STAGE III              0               2
  STAGE IIIA             4              28
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  AZIN1 MUTATED    6  1  4  0
  AZIN1 WILD-TYPE 61 39 39  9
D19V4, multiclass
    clus
vv   AZIN1 MUTATED AZIN1 WILD-TYPE
  T1             6              61
  T2             1              39
  T3             4              39
  T4             0               9
[1] 4 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
  AZIN1 MUTATED   11  0
  AZIN1 WILD-TYPE 90  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZIN1 MUTATED     11    0
  AZIN1 WILD-TYPE   90    3
   clus
vv  AZIN1 MUTATED AZIN1 WILD-TYPE
  0            11              90
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  AZIN1 MUTATED    10   0   1
  AZIN1 WILD-TYPE 112   3  34
D19V6, multiclass
    clus
vv   AZIN1 MUTATED AZIN1 WILD-TYPE
  M0            10             112
  M1             0               3
  MX             1              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"
D19V7, binary
                 cls
clus               0  1
  AZIN1 MUTATED    3  8
  AZIN1 WILD-TYPE 58 91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZIN1 MUTATED      3    8
  AZIN1 WILD-TYPE   58   91
        clus
vv       AZIN1 MUTATED AZIN1 WILD-TYPE
  FEMALE             3              58
  MALE               8              91
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AZIN1 MUTATED                         0                       11
  AZIN1 WILD-TYPE                       1                      146
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AZIN1 MUTATED                                  0
  AZIN1 WILD-TYPE                                2
D19V8, multiclass
                                  clus
vv                                 AZIN1 MUTATED AZIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    11             146
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AZIN1 MUTATED     6   2   0   2
  AZIN1 WILD-TYPE 126   8   1  10
D19V9, multiclass
    clus
vv   AZIN1 MUTATED AZIN1 WILD-TYPE
  R0             6             126
  R1             2               8
  R2             0               1
  RX             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AZIN1 MUTATED                                  1     3
  AZIN1 WILD-TYPE                                0    34
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AZIN1 MUTATED                           0     6
  AZIN1 WILD-TYPE                         8   102
D19V10, multiclass
                                  clus
vv                                 AZIN1 MUTATED AZIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        3              34
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        6             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                 cls
clus                0   1
  AZIN1 MUTATED     0   9
  AZIN1 WILD-TYPE   4 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AZIN1 MUTATED      0    9
  AZIN1 WILD-TYPE    4  134
                        clus
vv                       AZIN1 MUTATED AZIN1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             134
[1] 2 2
[1] FALSE

Clustering(20) Variable = NBPF3 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2              0  1
  NBPF3 MUTATED    4  3
  NBPF3 WILD-TYPE 86 63
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              7             149 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
              3              63 
$`NBPF3 MUTATED`
TCGA-BC-A216 TCGA-CC-A3MA TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A25V 
       44.42         0.07        45.11         5.62        25.81        28.27 
TCGA-G3-A3CJ 
       19.53 

$`NBPF3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  NBPF3 MUTATED NBPF3 WILD-TYPE 
           0.07            0.03 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
          45.11          113.00 
  NBPF3 MUTATED NBPF3 WILD-TYPE 
          25.81           13.78 
[1] "0.1 - 45.1 (25.8)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D20V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NBPF3 MUTATED         4        1         0          2          0          0
  NBPF3 WILD-TYPE      60       35         2         30          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  NBPF3 MUTATED          0         0         0
  NBPF3 WILD-TYPE        1         1         2
D20V3, multiclass
            clus
vv           NBPF3 MUTATED NBPF3 WILD-TYPE
  STAGE I                4              60
  STAGE II               1              35
  STAGE III              0               2
  STAGE IIIA             2              30
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    4  1  2  0
  NBPF3 WILD-TYPE 63 39 41  9
D20V4, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  T1             4              63
  T2             1              39
  T3             2              41
  T4             0               9
[1] 4 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
  NBPF3 MUTATED    4  0
  NBPF3 WILD-TYPE 97  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      4    0
  NBPF3 WILD-TYPE   97    3
   clus
vv  NBPF3 MUTATED NBPF3 WILD-TYPE
  0             4              97
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  NBPF3 MUTATED     7   0   0
  NBPF3 WILD-TYPE 115   3  35
D20V6, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  M0             7             115
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                 cls
clus               0  1
  NBPF3 MUTATED    1  6
  NBPF3 WILD-TYPE 60 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      1    6
  NBPF3 WILD-TYPE   60   93
        clus
vv       NBPF3 MUTATED NBPF3 WILD-TYPE
  FEMALE             1              60
  MALE               6              93
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NBPF3 MUTATED                         0                        7
  NBPF3 WILD-TYPE                       1                      150
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  NBPF3 MUTATED                                  0
  NBPF3 WILD-TYPE                                2
D20V8, multiclass
                                  clus
vv                                 NBPF3 MUTATED NBPF3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     7             150
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NBPF3 MUTATED     7   0   0   0
  NBPF3 WILD-TYPE 125  10   1  12
D20V9, multiclass
    clus
vv   NBPF3 MUTATED NBPF3 WILD-TYPE
  R0             7             125
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF3 MUTATED                                  1     2
  NBPF3 WILD-TYPE                                0    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NBPF3 MUTATED                           0     4
  NBPF3 WILD-TYPE                         8   104
D20V10, multiclass
                                  clus
vv                                 NBPF3 MUTATED NBPF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        4             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                 cls
clus                0   1
  NBPF3 MUTATED     0   6
  NBPF3 WILD-TYPE   4 137
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF3 MUTATED      0    6
  NBPF3 WILD-TYPE    4  137
                        clus
vv                       NBPF3 MUTATED NBPF3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             137
[1] 2 2
[1] FALSE

Clustering(21) Variable = BCLAF1 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  BCLAF1 MUTATED    8  5
  BCLAF1 WILD-TYPE 82 61
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              13              143 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               5               61 
$`BCLAF1 MUTATED`
TCGA-BC-A112 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A4NN TCGA-ED-A7PZ 
        5.03         2.60        79.40        66.31        29.56         0.20 
TCGA-EP-A12J TCGA-ES-A2HT TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A3CG 
       18.74        14.40        60.36         1.22        14.86        22.13 
TCGA-G3-A5SJ 
       11.97 

$`BCLAF1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       21.76        51.29        90.71        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        22.85        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38         0.13         0.03         0.33         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        30.74        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            0.20             0.03 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            79.4            113.0 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           14.86            13.78 
[1] "0.2 - 79.4 (14.9)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D21V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BCLAF1 MUTATED         9        2         0          1          0          0
  BCLAF1 WILD-TYPE      55       34         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  BCLAF1 MUTATED          0         0         0
  BCLAF1 WILD-TYPE        1         1         2
D21V3, multiclass
            clus
vv           BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE I                 9               55
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  BCLAF1 MUTATED    9  2  2  0
  BCLAF1 WILD-TYPE 58 38 41  9
D21V4, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1              9               58
  T2              2               38
  T3              2               41
  T4              0                9
[1] 4 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
  BCLAF1 MUTATED    7  0
  BCLAF1 WILD-TYPE 94  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      7    0
  BCLAF1 WILD-TYPE   94    3
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              7               94
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  BCLAF1 MUTATED    10   0   3
  BCLAF1 WILD-TYPE 112   3  32
D21V6, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  M0             10              112
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    3 10
  BCLAF1 WILD-TYPE 58 89
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      3   10
  BCLAF1 WILD-TYPE   58   89
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              3               58
  MALE               10               89
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BCLAF1 MUTATED                         0                       13
  BCLAF1 WILD-TYPE                       1                      144
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  BCLAF1 MUTATED                                  0
  BCLAF1 WILD-TYPE                                2
D21V8, multiclass
                                  clus
vv                                 BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     13              144
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCLAF1 MUTATED    10   3   0   0
  BCLAF1 WILD-TYPE 122   7   1  12
D21V9, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  R0             10              122
  R1              3                7
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCLAF1 MUTATED                                  0     3
  BCLAF1 WILD-TYPE                                1    34
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED                           3     6
  BCLAF1 WILD-TYPE                         5   102
D21V10, multiclass
                                  clus
vv                                 BCLAF1 MUTATED BCLAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3               34
  BLACK OR AFRICAN AMERICAN                     3                5
  WHITE                                         6              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     0  12
  BCLAF1 WILD-TYPE   4 131
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0   12
  BCLAF1 WILD-TYPE    4  131
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             12              131
[1] 2 2
[1] FALSE

Clustering(22) Variable = SCRN3 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2              0  1
  SCRN3 MUTATED    4  5
  SCRN3 WILD-TYPE 86 61
  SCRN3 MUTATED SCRN3 WILD-TYPE 
              9             147 
  SCRN3 MUTATED SCRN3 WILD-TYPE 
              5              61 
$`SCRN3 MUTATED`
TCGA-BC-A3KF TCGA-CC-A3MA TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EG TCGA-DD-A39Z 
        0.26         0.07         2.60        51.29        45.11        19.76 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A3CJ 
       14.40        19.10        19.53 

$`SCRN3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         0.46        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 
        9.96        11.93        22.85        32.45        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  SCRN3 MUTATED SCRN3 WILD-TYPE 
           0.07            0.03 
  SCRN3 MUTATED SCRN3 WILD-TYPE 
          51.29          113.00 
  SCRN3 MUTATED SCRN3 WILD-TYPE 
          19.10           13.78 
[1] "0.1 - 51.3 (19.1)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.7"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SCRN3 MUTATED         6        2         0          1          0          0
  SCRN3 WILD-TYPE      58       34         2         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SCRN3 MUTATED          0         0         0
  SCRN3 WILD-TYPE        1         1         2
D22V3, multiclass
            clus
vv           SCRN3 MUTATED SCRN3 WILD-TYPE
  STAGE I                6              58
  STAGE II               2              34
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  SCRN3 MUTATED    6  2  1  0
  SCRN3 WILD-TYPE 61 38 42  9
D22V4, multiclass
    clus
vv   SCRN3 MUTATED SCRN3 WILD-TYPE
  T1             6              61
  T2             2              38
  T3             1              42
  T4             0               9
[1] 4 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
  SCRN3 MUTATED    6  0
  SCRN3 WILD-TYPE 95  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRN3 MUTATED      6    0
  SCRN3 WILD-TYPE   95    3
   clus
vv  SCRN3 MUTATED SCRN3 WILD-TYPE
  0             6              95
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  SCRN3 MUTATED     8   0   1
  SCRN3 WILD-TYPE 114   3  34
D22V6, multiclass
    clus
vv   SCRN3 MUTATED SCRN3 WILD-TYPE
  M0             8             114
  M1             0               3
  MX             1              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"
D22V7, binary
                 cls
clus               0  1
  SCRN3 MUTATED    3  6
  SCRN3 WILD-TYPE 58 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRN3 MUTATED      3    6
  SCRN3 WILD-TYPE   58   93
        clus
vv       SCRN3 MUTATED SCRN3 WILD-TYPE
  FEMALE             3              58
  MALE               6              93
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SCRN3 MUTATED                         0                        9
  SCRN3 WILD-TYPE                       1                      148
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SCRN3 MUTATED                                  0
  SCRN3 WILD-TYPE                                2
D22V8, multiclass
                                  clus
vv                                 SCRN3 MUTATED SCRN3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             148
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCRN3 MUTATED     8   0   0   1
  SCRN3 WILD-TYPE 124  10   1  11
D22V9, multiclass
    clus
vv   SCRN3 MUTATED SCRN3 WILD-TYPE
  R0             8             124
  R1             0              10
  R2             0               1
  RX             1              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCRN3 MUTATED                                  1     1
  SCRN3 WILD-TYPE                                0    36
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCRN3 MUTATED                           2     4
  SCRN3 WILD-TYPE                         6   104
D22V10, multiclass
                                  clus
vv                                 SCRN3 MUTATED SCRN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              36
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                        4             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                 cls
clus                0   1
  SCRN3 MUTATED     0   7
  SCRN3 WILD-TYPE   4 136
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRN3 MUTATED      0    7
  SCRN3 WILD-TYPE    4  136
                        clus
vv                       SCRN3 MUTATED SCRN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             136
[1] 2 2
[1] FALSE

Clustering(23) Variable = MUC6 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  MUC6 MUTATED    9 12
  MUC6 WILD-TYPE 81 54
  MUC6 MUTATED MUC6 WILD-TYPE 
            21            135 
  MUC6 MUTATED MUC6 WILD-TYPE 
            12             54 
$`MUC6 MUTATED`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A217 TCGA-CC-5261 TCGA-CC-5263 
       27.91        10.13        27.52        13.84         0.39         4.24 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         2.60        51.29        79.40        66.31 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB 
       12.95        45.11        49.15        18.74        11.74        10.98 
TCGA-G3-A25S TCGA-G3-A3CJ TCGA-MI-A75G 
        1.22        19.53        14.24 

$`MUC6 WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       37.32        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
        9.50        14.60        12.72         0.07         0.16         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       79.73        37.78        83.57       113.00         0.46        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       90.71        19.79        75.65         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KC 
        0.20         0.20         0.20         0.20        19.99         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.86        21.53        22.13        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         0.49         9.57         5.10        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  MUC6 MUTATED MUC6 WILD-TYPE 
          0.39           0.03 
  MUC6 MUTATED MUC6 WILD-TYPE 
          79.4          113.0 
  MUC6 MUTATED MUC6 WILD-TYPE 
         14.24          13.78 
[1] "0.4 - 79.4 (14.2)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.4"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC6 MUTATED         8        5         1          4          0          0
  MUC6 WILD-TYPE      56       31         1         28          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  MUC6 MUTATED          1         0         0
  MUC6 WILD-TYPE        0         1         2
D23V3, multiclass
            clus
vv           MUC6 MUTATED MUC6 WILD-TYPE
  STAGE I               8             56
  STAGE II              5             31
  STAGE III             1              1
  STAGE IIIA            4             28
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              1              0
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MUC6 MUTATED    8  5  7  1
  MUC6 WILD-TYPE 59 35 36  8
D23V4, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  T1            8             59
  T2            5             35
  T3            7             36
  T4            1              8
[1] 4 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
  MUC6 MUTATED   15  0
  MUC6 WILD-TYPE 86  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     15    0
  MUC6 WILD-TYPE   86    3
   clus
vv  MUC6 MUTATED MUC6 WILD-TYPE
  0           15             86
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  MUC6 MUTATED    14   1   6
  MUC6 WILD-TYPE 108   2  29
D23V6, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  M0           14            108
  M1            1              2
  MX            6             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                cls
clus              0  1
  MUC6 MUTATED    7 14
  MUC6 WILD-TYPE 54 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      7   14
  MUC6 WILD-TYPE   54   85
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  FEMALE            7             54
  MALE             14             85
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MUC6 MUTATED                         0                       21
  MUC6 WILD-TYPE                       1                      136
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  MUC6 MUTATED                                  0
  MUC6 WILD-TYPE                                2
D23V8, multiclass
                                  clus
vv                                 MUC6 MUTATED MUC6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   21            136
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MUC6 MUTATED    15   3   1   2
  MUC6 WILD-TYPE 117   7   0  10
D23V9, multiclass
    clus
vv   MUC6 MUTATED MUC6 WILD-TYPE
  R0           15            117
  R1            3              7
  R2            1              0
  RX            2             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC6 MUTATED                                  1     5
  MUC6 WILD-TYPE                                0    32
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MUC6 MUTATED                           2    12
  MUC6 WILD-TYPE                         6    96
D23V10, multiclass
                                  clus
vv                                 MUC6 MUTATED MUC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       5             32
  BLACK OR AFRICAN AMERICAN                   2              6
  WHITE                                      12             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                cls
clus               0   1
  MUC6 MUTATED     0  19
  MUC6 WILD-TYPE   4 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      0   19
  MUC6 WILD-TYPE    4  124
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           19            124
[1] 2 2
[1] FALSE

Clustering(24) Variable = UGT2B28 MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2                0  1
  UGT2B28 MUTATED    5  5
  UGT2B28 WILD-TYPE 85 61
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
               10               146 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
                5                61 
$`UGT2B28 MUTATED`
TCGA-BC-A10S TCGA-DD-A116 TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A4NN 
       46.78        53.33        12.95        49.15        55.69        29.56 
TCGA-ED-A7XP TCGA-EP-A12J TCGA-G3-A25T TCGA-G3-A3CJ 
        0.20        18.74        51.06        19.53 

$`UGT2B28 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       75.65        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
             0.20              0.03 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
            55.69            113.00 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
           38.170            13.525 
[1] "0.2 - 55.7 (38.2)"  "0.0 - 113.0 (13.5)"
[1] "hr=" "1.2"
D24V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  UGT2B28 MUTATED         4        2         1          2          0          0
  UGT2B28 WILD-TYPE      60       34         1         30          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  UGT2B28 MUTATED          0         0         0
  UGT2B28 WILD-TYPE        1         1         2
D24V3, multiclass
            clus
vv           UGT2B28 MUTATED UGT2B28 WILD-TYPE
  STAGE I                  4                60
  STAGE II                 2                34
  STAGE III                1                 1
  STAGE IIIA               2                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  UGT2B28 MUTATED    4  2  4  0
  UGT2B28 WILD-TYPE 63 38 39  9
D24V4, multiclass
    clus
vv   UGT2B28 MUTATED UGT2B28 WILD-TYPE
  T1               4                63
  T2               2                38
  T3               4                39
  T4               0                 9
[1] 4 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
  UGT2B28 MUTATED    7  0
  UGT2B28 WILD-TYPE 94  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT2B28 MUTATED      7    0
  UGT2B28 WILD-TYPE   94    3
   clus
vv  UGT2B28 MUTATED UGT2B28 WILD-TYPE
  0               7                94
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  UGT2B28 MUTATED     8   0   2
  UGT2B28 WILD-TYPE 114   3  33
D24V6, multiclass
    clus
vv   UGT2B28 MUTATED UGT2B28 WILD-TYPE
  M0               8               114
  M1               0                 3
  MX               2                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                   cls
clus                 0  1
  UGT2B28 MUTATED    5  5
  UGT2B28 WILD-TYPE 56 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT2B28 MUTATED      5    5
  UGT2B28 WILD-TYPE   56   94
        clus
vv       UGT2B28 MUTATED UGT2B28 WILD-TYPE
  FEMALE               5                56
  MALE                 5                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  UGT2B28 MUTATED                         0                       10
  UGT2B28 WILD-TYPE                       1                      147
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  UGT2B28 MUTATED                                  0
  UGT2B28 WILD-TYPE                                2
D24V8, multiclass
                                  clus
vv                                 UGT2B28 MUTATED UGT2B28 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                      10               147
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  UGT2B28 MUTATED    10   0   0   0
  UGT2B28 WILD-TYPE 122  10   1  12
D24V9, multiclass
    clus
vv   UGT2B28 MUTATED UGT2B28 WILD-TYPE
  R0              10               122
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT2B28 MUTATED                                  1     2
  UGT2B28 WILD-TYPE                                0    35
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  UGT2B28 MUTATED                           1     6
  UGT2B28 WILD-TYPE                         7   102
D24V10, multiclass
                                  clus
vv                                 UGT2B28 MUTATED UGT2B28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                35
  BLACK OR AFRICAN AMERICAN                      1                 7
  WHITE                                          6               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                   cls
clus                  0   1
  UGT2B28 MUTATED     0  10
  UGT2B28 WILD-TYPE   4 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT2B28 MUTATED      0   10
  UGT2B28 WILD-TYPE    4  133
                        clus
vv                       UGT2B28 MUTATED UGT2B28 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO              10               133
[1] 2 2
[1] FALSE

Clustering(25) Variable = CDHR5 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2              0  1
  CDHR5 MUTATED    4  7
  CDHR5 WILD-TYPE 86 59
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             11             145 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              7              59 
$`CDHR5 MUTATED`
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EF 
       10.13        46.78        27.52        53.33         2.60        12.95 
TCGA-DD-A1EH TCGA-DD-A39Y TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL 
       49.15         5.62        18.74         0.62         9.96 

$`CDHR5 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 
       22.36         9.50        14.60        12.72         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI 
       79.40        66.31        19.79        75.65        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S 
        0.20         0.20         0.20         0.20         0.20        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74        10.98        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  CDHR5 MUTATED CDHR5 WILD-TYPE 
           0.62            0.03 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
          53.33          113.00 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
          12.95           13.91 
[1] "0.6 - 53.3 (12.9)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.7"
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDHR5 MUTATED         6        0         1          1          0          0
  CDHR5 WILD-TYPE      58       36         1         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CDHR5 MUTATED          0         0         0
  CDHR5 WILD-TYPE        1         1         2
D25V3, multiclass
            clus
vv           CDHR5 MUTATED CDHR5 WILD-TYPE
  STAGE I                6              58
  STAGE II               0              36
  STAGE III              1               1
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  CDHR5 MUTATED    6  0  4  1
  CDHR5 WILD-TYPE 61 40 39  8
D25V4, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  T1             6              61
  T2             0              40
  T3             4              39
  T4             1               8
[1] 4 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
  CDHR5 MUTATED    4  0
  CDHR5 WILD-TYPE 97  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      4    0
  CDHR5 WILD-TYPE   97    3
   clus
vv  CDHR5 MUTATED CDHR5 WILD-TYPE
  0             4              97
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  CDHR5 MUTATED     5   0   6
  CDHR5 WILD-TYPE 117   3  29
D25V6, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  M0             5             117
  M1             0               3
  MX             6              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                 cls
clus               0  1
  CDHR5 MUTATED    2  9
  CDHR5 WILD-TYPE 59 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      2    9
  CDHR5 WILD-TYPE   59   90
        clus
vv       CDHR5 MUTATED CDHR5 WILD-TYPE
  FEMALE             2              59
  MALE               9              90
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CDHR5 MUTATED                         0                       11
  CDHR5 WILD-TYPE                       1                      146
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CDHR5 MUTATED                                  0
  CDHR5 WILD-TYPE                                2
D25V8, multiclass
                                  clus
vv                                 CDHR5 MUTATED CDHR5 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    11             146
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDHR5 MUTATED     9   1   0   0
  CDHR5 WILD-TYPE 123   9   1  12
D25V9, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  R0             9             123
  R1             1               9
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDHR5 MUTATED                                  0     2
  CDHR5 WILD-TYPE                                1    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDHR5 MUTATED                           3     6
  CDHR5 WILD-TYPE                         5   102
D25V10, multiclass
                                  clus
vv                                 CDHR5 MUTATED CDHR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    3               5
  WHITE                                        6             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                 cls
clus                0   1
  CDHR5 MUTATED     0  11
  CDHR5 WILD-TYPE   4 132
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      0   11
  CDHR5 WILD-TYPE    4  132
                        clus
vv                       CDHR5 MUTATED CDHR5 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            11             132
[1] 2 2
[1] FALSE

Clustering(26) Variable = KCTD3 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2              0  1
  KCTD3 MUTATED    3  3
  KCTD3 WILD-TYPE 87 63
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              6             150 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              3              63 
$`KCTD3 MUTATED`
TCGA-BC-A10W TCGA-BC-A10Y TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EH TCGA-EP-A12J 
        2.99        23.34        53.33         2.60        49.15        18.74 

$`KCTD3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       25.32         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
           2.60            0.03 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          53.33          113.00 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          21.04           13.81 
[1] "2.6 - 53.3 (21.0)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KCTD3 MUTATED         2        0         1          1          0          0
  KCTD3 WILD-TYPE      62       36         1         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KCTD3 MUTATED          0         0         0
  KCTD3 WILD-TYPE        1         1         2
D26V3, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                2              62
  STAGE II               0              36
  STAGE III              1               1
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    2  0  2  2
  KCTD3 WILD-TYPE 65 40 41  7
D26V4, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  T1             2              65
  T2             0              40
  T3             2              41
  T4             2               7
[1] 4 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
  KCTD3 MUTATED    3  0
  KCTD3 WILD-TYPE 98  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      3    0
  KCTD3 WILD-TYPE   98    3
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0             3              98
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  KCTD3 MUTATED     3   0   3
  KCTD3 WILD-TYPE 119   3  32
D26V6, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  M0             3             119
  M1             0               3
  MX             3              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                 cls
clus               0  1
  KCTD3 MUTATED    0  6
  KCTD3 WILD-TYPE 61 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0    6
  KCTD3 WILD-TYPE   61   93
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             0              61
  MALE               6              93
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KCTD3 MUTATED                         0                        6
  KCTD3 WILD-TYPE                       1                      151
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KCTD3 MUTATED                                  0
  KCTD3 WILD-TYPE                                2
D26V8, multiclass
                                  clus
vv                                 KCTD3 MUTATED KCTD3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     6             151
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCTD3 MUTATED     5   1   0   0
  KCTD3 WILD-TYPE 127   9   1  12
D26V9, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0             5             127
  R1             1               9
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD3 MUTATED                                  0     2
  KCTD3 WILD-TYPE                                1    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD3 MUTATED                           2     2
  KCTD3 WILD-TYPE                         6   106
D26V10, multiclass
                                  clus
vv                                 KCTD3 MUTATED KCTD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                        2             106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                 cls
clus                0   1
  KCTD3 MUTATED     0   6
  KCTD3 WILD-TYPE   4 137
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      0    6
  KCTD3 WILD-TYPE    4  137
                        clus
vv                       KCTD3 MUTATED KCTD3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             137
[1] 2 2
[1] FALSE

Clustering(27) Variable = CDC27 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    7  6
  CDC27 WILD-TYPE 83 60
  CDC27 MUTATED CDC27 WILD-TYPE 
             13             143 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6              60 
$`CDC27 MUTATED`
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
       53.33         2.60        79.40        12.95        49.15        29.16 
TCGA-DD-A39Z TCGA-DD-A4NR TCGA-ED-A82E TCGA-EP-A12J TCGA-FV-A23B TCGA-G3-A3CJ 
       19.76         0.30         0.20        18.74        32.45        19.53 
TCGA-G3-A3CK 
       19.23 

$`CDC27 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
       45.11         6.02        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.20            0.03 
  CDC27 MUTATED CDC27 WILD-TYPE 
           79.4           113.0 
  CDC27 MUTATED CDC27 WILD-TYPE 
          19.53           13.64 
[1] "0.2 - 79.4 (19.5)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "1"  
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDC27 MUTATED         5        4         1          2          0          1
  CDC27 WILD-TYPE      59       32         1         30          5          5
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CDC27 MUTATED          0         0         0
  CDC27 WILD-TYPE        1         1         2
D27V3, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                5              59
  STAGE II               4              32
  STAGE III              1               1
  STAGE IIIA             2              30
  STAGE IIIB             0               5
  STAGE IIIC             1               5
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    6  4  3  0
  CDC27 WILD-TYPE 61 36 40  9
D27V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             6              61
  T2             4              36
  T3             3              40
  T4             0               9
[1] 4 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
  CDC27 MUTATED   10  1
  CDC27 WILD-TYPE 91  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     10    1
  CDC27 WILD-TYPE   91    2
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0            10              91
  1             1               2
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  CDC27 MUTATED    12   0   1
  CDC27 WILD-TYPE 110   3  34
D27V6, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  M0            12             110
  M1             0               3
  MX             1              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"
D27V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    6  7
  CDC27 WILD-TYPE 55 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      6    7
  CDC27 WILD-TYPE   55   92
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             6              55
  MALE               7              92
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CDC27 MUTATED                         0                       13
  CDC27 WILD-TYPE                       1                      144
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CDC27 MUTATED                                  0
  CDC27 WILD-TYPE                                2
D27V8, multiclass
                                  clus
vv                                 CDC27 MUTATED CDC27 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    13             144
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC27 MUTATED    13   0   0   0
  CDC27 WILD-TYPE 119  10   1  12
D27V9, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0            13             119
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC27 MUTATED                                  1     4
  CDC27 WILD-TYPE                                0    33
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED                           2     5
  CDC27 WILD-TYPE                         6   103
D27V10, multiclass
                                  clus
vv                                 CDC27 MUTATED CDC27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        4              33
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                        5             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                 cls
clus                0   1
  CDC27 MUTATED     0  12
  CDC27 WILD-TYPE   4 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0   12
  CDC27 WILD-TYPE    4  131
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             131
[1] 2 2
[1] FALSE

Clustering(28) Variable = CR1 MUTATION ANALYSIS
D28V1, survival
               sevent
clus2            0  1
  CR1 MUTATED   10  8
  CR1 WILD-TYPE 80 58
  CR1 MUTATED CR1 WILD-TYPE 
           18           138 
  CR1 MUTATED CR1 WILD-TYPE 
            8            58 
$`CR1 MUTATED`
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10Z TCGA-BC-A112 TCGA-CC-A3MB TCGA-DD-A116 
       37.32        46.78         1.12         5.03         0.10        53.33 
TCGA-DD-A11A TCGA-DD-A1ED TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-ED-A459 
        2.60        75.65        21.14         5.62        17.59        13.41 
TCGA-EP-A12J TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CI TCGA-G3-A3CJ 
       18.74        53.79        28.27        30.74         5.92        19.53 

$`CR1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34        69.57        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
        9.50        14.60        12.72         0.07         0.16         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.39         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        37.78        83.57       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        13.64        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72       100.96        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39         1.22        51.06        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       25.64        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  CR1 MUTATED CR1 WILD-TYPE 
         0.10          0.03 
  CR1 MUTATED CR1 WILD-TYPE 
        75.65        113.00 
  CR1 MUTATED CR1 WILD-TYPE 
       19.135        13.710 
[1] "0.1 - 75.7 (19.1)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "1"  
D28V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CR1 MUTATED         9        3         0          2          1          0
  CR1 WILD-TYPE      55       33         2         30          4          6
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  CR1 MUTATED          0         0         0
  CR1 WILD-TYPE        1         1         2
D28V3, multiclass
            clus
vv           CR1 MUTATED CR1 WILD-TYPE
  STAGE I              9            55
  STAGE II             3            33
  STAGE III            0             2
  STAGE IIIA           2            30
  STAGE IIIB           1             4
  STAGE IIIC           0             6
  STAGE IV             0             1
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  CR1 MUTATED    9  4  5  0
  CR1 WILD-TYPE 58 36 38  9
D28V4, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  T1           9            58
  T2           4            36
  T3           5            38
  T4           0             9
[1] 4 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
  CR1 MUTATED   12  0
  CR1 WILD-TYPE 89  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED     12    0
  CR1 WILD-TYPE   89    3
   clus
vv  CR1 MUTATED CR1 WILD-TYPE
  0          12            89
  1           0             3
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  CR1 MUTATED    13   0   5
  CR1 WILD-TYPE 109   3  30
D28V6, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  M0          13           109
  M1           0             3
  MX           5            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
               cls
clus             0  1
  CR1 MUTATED    4 14
  CR1 WILD-TYPE 57 85
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      4   14
  CR1 WILD-TYPE   57   85
        clus
vv       CR1 MUTATED CR1 WILD-TYPE
  FEMALE           4            57
  MALE            14            85
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CR1 MUTATED                         0                       18
  CR1 WILD-TYPE                       1                      139
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  CR1 MUTATED                                  0
  CR1 WILD-TYPE                                2
D28V8, multiclass
                                  clus
vv                                 CR1 MUTATED CR1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  18           139
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CR1 MUTATED    17   1   0   0
  CR1 WILD-TYPE 115   9   1  12
D28V9, multiclass
    clus
vv   CR1 MUTATED CR1 WILD-TYPE
  R0          17           115
  R1           1             9
  R2           0             1
  RX           0            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CR1 MUTATED                                  1     6
  CR1 WILD-TYPE                                0    31
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CR1 MUTATED                           2     9
  CR1 WILD-TYPE                         6    99
D28V10, multiclass
                                  clus
vv                                 CR1 MUTATED CR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      6            31
  BLACK OR AFRICAN AMERICAN                  2             6
  WHITE                                      9            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
               cls
clus              0   1
  CR1 MUTATED     0  18
  CR1 WILD-TYPE   4 125
[1] "tbl2"
               cls
clus            [,1] [,2]
  CR1 MUTATED      0   18
  CR1 WILD-TYPE    4  125
                        clus
vv                       CR1 MUTATED CR1 WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO          18           125
[1] 2 2
[1] FALSE

Clustering(29) Variable = TCEAL6 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  TCEAL6 MUTATED    1  3
  TCEAL6 WILD-TYPE 89 63
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              152 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               3               63 
$`TCEAL6 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A3CJ 
       45.11         5.62        25.81        19.53 

$`TCEAL6 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
            5.62             0.03 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
           45.11           113.00 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
           22.67            13.81 
[1] "5.6 - 45.1 (22.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.7"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TCEAL6 MUTATED         3        1         0          0          0          0
  TCEAL6 WILD-TYPE      61       35         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  TCEAL6 MUTATED          0         0         0
  TCEAL6 WILD-TYPE        1         1         2
D29V3, multiclass
            clus
vv           TCEAL6 MUTATED TCEAL6 WILD-TYPE
  STAGE I                 3               61
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  TCEAL6 MUTATED    3  1  0  0
  TCEAL6 WILD-TYPE 64 39 43  9
D29V4, multiclass
    clus
vv   TCEAL6 MUTATED TCEAL6 WILD-TYPE
  T1              3               64
  T2              1               39
  T3              0               43
  T4              0                9
[1] 4 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
  TCEAL6 MUTATED    2  0
  TCEAL6 WILD-TYPE 99  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      2    0
  TCEAL6 WILD-TYPE   99    3
   clus
vv  TCEAL6 MUTATED TCEAL6 WILD-TYPE
  0              2               99
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  TCEAL6 MUTATED     4   0   0
  TCEAL6 WILD-TYPE 118   3  35
D29V6, multiclass
    clus
vv   TCEAL6 MUTATED TCEAL6 WILD-TYPE
  M0              4              118
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                  cls
clus                0  1
  TCEAL6 MUTATED    0  4
  TCEAL6 WILD-TYPE 61 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      0    4
  TCEAL6 WILD-TYPE   61   95
        clus
vv       TCEAL6 MUTATED TCEAL6 WILD-TYPE
  FEMALE              0               61
  MALE                4               95
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TCEAL6 MUTATED                         0                        4
  TCEAL6 WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  TCEAL6 MUTATED                                  0
  TCEAL6 WILD-TYPE                                2
D29V8, multiclass
                                  clus
vv                                 TCEAL6 MUTATED TCEAL6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCEAL6 MUTATED     4   0   0   0
  TCEAL6 WILD-TYPE 128  10   1  12
D29V9, multiclass
    clus
vv   TCEAL6 MUTATED TCEAL6 WILD-TYPE
  R0              4              128
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL6 MUTATED                                  1     1
  TCEAL6 WILD-TYPE                                0    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL6 MUTATED                           0     2
  TCEAL6 WILD-TYPE                         8   106
D29V10, multiclass
                                  clus
vv                                 TCEAL6 MUTATED TCEAL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         2              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     0   4
  TCEAL6 WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      0    4
  TCEAL6 WILD-TYPE    4  139
                        clus
vv                       TCEAL6 MUTATED TCEAL6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(30) Variable = LILRA6 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2               0  1
  LILRA6 MUTATED    7  4
  LILRA6 WILD-TYPE 83 62
  LILRA6 MUTATED LILRA6 WILD-TYPE 
              11              145 
  LILRA6 MUTATED LILRA6 WILD-TYPE 
               4               62 
$`LILRA6 MUTATED`
TCGA-BC-A10S TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF 
       46.78        53.33        79.40        66.31        75.65        12.95 
TCGA-DD-A39Y TCGA-EP-A12J TCGA-EP-A3JL TCGA-G3-A3CJ TCGA-MI-A75G 
        5.62        18.74         9.96        19.53        14.24 

$`LILRA6 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EG TCGA-DD-A1EH 
       21.76        51.29        90.71        19.79        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         0.62        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         9.57         5.10        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  LILRA6 MUTATED LILRA6 WILD-TYPE 
            5.62             0.03 
  LILRA6 MUTATED LILRA6 WILD-TYPE 
            79.4            113.0 
  LILRA6 MUTATED LILRA6 WILD-TYPE 
           19.53            13.64 
[1] "5.6 - 79.4 (19.5)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "1.7"
D30V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LILRA6 MUTATED         6        3         0          1          0          0
  LILRA6 WILD-TYPE      58       33         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  LILRA6 MUTATED          0         0         0
  LILRA6 WILD-TYPE        1         1         2
D30V3, multiclass
            clus
vv           LILRA6 MUTATED LILRA6 WILD-TYPE
  STAGE I                 6               58
  STAGE II                3               33
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  LILRA6 MUTATED    6  3  2  0
  LILRA6 WILD-TYPE 61 37 41  9
D30V4, multiclass
    clus
vv   LILRA6 MUTATED LILRA6 WILD-TYPE
  T1              6               61
  T2              3               37
  T3              2               41
  T4              0                9
[1] 4 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
  LILRA6 MUTATED    7  0
  LILRA6 WILD-TYPE 94  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA6 MUTATED      7    0
  LILRA6 WILD-TYPE   94    3
   clus
vv  LILRA6 MUTATED LILRA6 WILD-TYPE
  0              7               94
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  LILRA6 MUTATED     8   0   3
  LILRA6 WILD-TYPE 114   3  32
D30V6, multiclass
    clus
vv   LILRA6 MUTATED LILRA6 WILD-TYPE
  M0              8              114
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                  cls
clus                0  1
  LILRA6 MUTATED    2  9
  LILRA6 WILD-TYPE 59 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA6 MUTATED      2    9
  LILRA6 WILD-TYPE   59   90
        clus
vv       LILRA6 MUTATED LILRA6 WILD-TYPE
  FEMALE              2               59
  MALE                9               90
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LILRA6 MUTATED                         0                       11
  LILRA6 WILD-TYPE                       1                      146
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  LILRA6 MUTATED                                  0
  LILRA6 WILD-TYPE                                2
D30V8, multiclass
                                  clus
vv                                 LILRA6 MUTATED LILRA6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     11              146
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LILRA6 MUTATED    10   0   0   0
  LILRA6 WILD-TYPE 122  10   1  12
D30V9, multiclass
    clus
vv   LILRA6 MUTATED LILRA6 WILD-TYPE
  R0             10              122
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LILRA6 MUTATED                                  1     3
  LILRA6 WILD-TYPE                                0    34
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LILRA6 MUTATED                           1     5
  LILRA6 WILD-TYPE                         7   103
D30V10, multiclass
                                  clus
vv                                 LILRA6 MUTATED LILRA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         3               34
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         5              103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                  cls
clus                 0   1
  LILRA6 MUTATED     0  10
  LILRA6 WILD-TYPE   4 133
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA6 MUTATED      0   10
  LILRA6 WILD-TYPE    4  133
                        clus
vv                       LILRA6 MUTATED LILRA6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             10              133
[1] 2 2
[1] FALSE

Clustering(31) Variable = BIK MUTATION ANALYSIS
D31V1, survival
               sevent
clus2            0  1
  BIK MUTATED    0  3
  BIK WILD-TYPE 90 63
  BIK MUTATED BIK WILD-TYPE 
            3           153 
  BIK MUTATED BIK WILD-TYPE 
            3            63 
$`BIK MUTATED`
TCGA-DD-A115 TCGA-DD-A1EF TCGA-G3-A25S 
       83.57        12.95         1.22 

$`BIK WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  BIK MUTATED BIK WILD-TYPE 
         1.22          0.03 
  BIK MUTATED BIK WILD-TYPE 
        83.57        113.00 
  BIK MUTATED BIK WILD-TYPE 
        12.95         13.91 
[1] "1.2 - 83.6 (12.9)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.8"
D31V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BIK MUTATED         2        0         0          1          0          0
  BIK WILD-TYPE      62       36         2         31          5          6
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  BIK MUTATED          0         0         0
  BIK WILD-TYPE        1         1         2
D31V3, multiclass
            clus
vv           BIK MUTATED BIK WILD-TYPE
  STAGE I              2            62
  STAGE II             0            36
  STAGE III            0             2
  STAGE IIIA           1            31
  STAGE IIIB           0             5
  STAGE IIIC           0             6
  STAGE IV             0             1
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  BIK MUTATED    2  0  1  0
  BIK WILD-TYPE 65 40 42  9
D31V4, multiclass
    clus
vv   BIK MUTATED BIK WILD-TYPE
  T1           2            65
  T2           0            40
  T3           1            42
  T4           0             9
[1] 4 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
  BIK MUTATED    3  0
  BIK WILD-TYPE 98  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  BIK MUTATED      3    0
  BIK WILD-TYPE   98    3
   clus
vv  BIK MUTATED BIK WILD-TYPE
  0           3            98
  1           0             3
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  BIK MUTATED     3   0   0
  BIK WILD-TYPE 119   3  35
D31V6, multiclass
    clus
vv   BIK MUTATED BIK WILD-TYPE
  M0           3           119
  M1           0             3
  MX           0            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
               cls
clus             0  1
  BIK MUTATED    1  2
  BIK WILD-TYPE 60 97
[1] "tbl2"
               cls
clus            [,1] [,2]
  BIK MUTATED      1    2
  BIK WILD-TYPE   60   97
        clus
vv       BIK MUTATED BIK WILD-TYPE
  FEMALE           1            60
  MALE             2            97
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BIK MUTATED                         0                        3
  BIK WILD-TYPE                       1                      154
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  BIK MUTATED                                  0
  BIK WILD-TYPE                                2
D31V8, multiclass
                                  clus
vv                                 BIK MUTATED BIK WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                   3           154
  HEPATOCHOLANGIOCARCINOMA (MIXED)           0             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  BIK MUTATED     2   1   0   0
  BIK WILD-TYPE 130   9   1  12
D31V9, multiclass
    clus
vv   BIK MUTATED BIK WILD-TYPE
  R0           2           130
  R1           1             9
  R2           0             1
  RX           0            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BIK MUTATED                                  0     0
  BIK WILD-TYPE                                1    37
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BIK MUTATED                           0     3
  BIK WILD-TYPE                         8   105
D31V10, multiclass
                                  clus
vv                                 BIK MUTATED BIK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            37
  BLACK OR AFRICAN AMERICAN                  0             8
  WHITE                                      3           105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, binary
               cls
clus              0   1
  BIK MUTATED     0   2
  BIK WILD-TYPE   4 141
[1] "tbl2"
               cls
clus            [,1] [,2]
  BIK MUTATED      0    2
  BIK WILD-TYPE    4  141
                        clus
vv                       BIK MUTATED BIK WILD-TYPE
  HISPANIC OR LATINO               0             4
  NOT HISPANIC OR LATINO           2           141
[1] 2 2
[1] FALSE

Clustering(32) Variable = SRRM3 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  SRRM3 MUTATED    2  2
  SRRM3 WILD-TYPE 88 64
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              4             152 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              2              64 
$`SRRM3 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-ED-A7PZ TCGA-G3-A3CJ 
       45.11         5.62         0.20        19.53 

$`SRRM3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  SRRM3 MUTATED SRRM3 WILD-TYPE 
           0.20            0.03 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
          45.11          113.00 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
         12.575          13.875 
[1] "0.2 - 45.1 (12.6)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.6"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SRRM3 MUTATED         2        2         0          0          0          0
  SRRM3 WILD-TYPE      62       34         2         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SRRM3 MUTATED          0         0         0
  SRRM3 WILD-TYPE        1         1         2
D32V3, multiclass
            clus
vv           SRRM3 MUTATED SRRM3 WILD-TYPE
  STAGE I                2              62
  STAGE II               2              34
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  SRRM3 MUTATED    2  2  0  0
  SRRM3 WILD-TYPE 65 38 43  9
D32V4, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  T1             2              65
  T2             2              38
  T3             0              43
  T4             0               9
[1] 4 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
  SRRM3 MUTATED    2  0
  SRRM3 WILD-TYPE 99  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      2    0
  SRRM3 WILD-TYPE   99    3
   clus
vv  SRRM3 MUTATED SRRM3 WILD-TYPE
  0             2              99
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  SRRM3 MUTATED     4   0   0
  SRRM3 WILD-TYPE 118   3  35
D32V6, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  M0             4             118
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                 cls
clus               0  1
  SRRM3 MUTATED    0  4
  SRRM3 WILD-TYPE 61 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      0    4
  SRRM3 WILD-TYPE   61   95
        clus
vv       SRRM3 MUTATED SRRM3 WILD-TYPE
  FEMALE             0              61
  MALE               4              95
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SRRM3 MUTATED                         0                        4
  SRRM3 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SRRM3 MUTATED                                  0
  SRRM3 WILD-TYPE                                2
D32V8, multiclass
                                  clus
vv                                 SRRM3 MUTATED SRRM3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SRRM3 MUTATED     4   0   0   0
  SRRM3 WILD-TYPE 128  10   1  12
D32V9, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  R0             4             128
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRRM3 MUTATED                                  1     2
  SRRM3 WILD-TYPE                                0    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SRRM3 MUTATED                           0     1
  SRRM3 WILD-TYPE                         8   107
D32V10, multiclass
                                  clus
vv                                 SRRM3 MUTATED SRRM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        1             107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                 cls
clus                0   1
  SRRM3 MUTATED     0   4
  SRRM3 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      0    4
  SRRM3 WILD-TYPE    4  139
                        clus
vv                       SRRM3 MUTATED SRRM3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(33) Variable = MKI67 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  MKI67 MUTATED   10  4
  MKI67 WILD-TYPE 80 62
  MKI67 MUTATED MKI67 WILD-TYPE 
             14             142 
  MKI67 MUTATED MKI67 WILD-TYPE 
              4              62 
$`MKI67 MUTATED`
TCGA-BC-A10S TCGA-BC-A69I TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
       46.78        12.72         0.07        83.57        53.33         2.60 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A39Y TCGA-ED-A66X TCGA-EP-A12J 
       66.31        75.65        49.15         5.62        13.35        18.74 
TCGA-FV-A4ZQ TCGA-G3-A25U 
        0.39        53.79 

$`MKI67 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       13.84         0.26        22.36         9.50        14.60         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 
        0.10         0.10         0.13        79.73        37.78       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        12.95        45.11         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       60.36         1.22        51.06        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  MKI67 MUTATED MKI67 WILD-TYPE 
           0.07            0.03 
  MKI67 MUTATED MKI67 WILD-TYPE 
          83.57          113.00 
  MKI67 MUTATED MKI67 WILD-TYPE 
          32.76           13.81 
[1] "0.1 - 83.6 (32.8)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.2"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MKI67 MUTATED         8        0         1          5          0          0
  MKI67 WILD-TYPE      56       36         1         27          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  MKI67 MUTATED          0         0         0
  MKI67 WILD-TYPE        1         1         2
D33V3, multiclass
            clus
vv           MKI67 MUTATED MKI67 WILD-TYPE
  STAGE I                8              56
  STAGE II               0              36
  STAGE III              1               1
  STAGE IIIA             5              27
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    8  0  7  0
  MKI67 WILD-TYPE 59 40 36  9
D33V4, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  T1             8              59
  T2             0              40
  T3             7              36
  T4             0               9
[1] 4 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
  MKI67 MUTATED   11  0
  MKI67 WILD-TYPE 90  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     11    0
  MKI67 WILD-TYPE   90    3
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0            11              90
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  MKI67 MUTATED    13   0   2
  MKI67 WILD-TYPE 109   3  33
D33V6, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  M0            13             109
  M1             0               3
  MX             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                 cls
clus               0  1
  MKI67 MUTATED    3 12
  MKI67 WILD-TYPE 58 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      3   12
  MKI67 WILD-TYPE   58   87
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  FEMALE             3              58
  MALE              12              87
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MKI67 MUTATED                         0                       15
  MKI67 WILD-TYPE                       1                      142
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  MKI67 MUTATED                                  0
  MKI67 WILD-TYPE                                2
D33V8, multiclass
                                  clus
vv                                 MKI67 MUTATED MKI67 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    15             142
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MKI67 MUTATED    14   0   0   1
  MKI67 WILD-TYPE 118  10   1  11
D33V9, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            14             118
  R1             0              10
  R2             0               1
  RX             1              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKI67 MUTATED                                  0     6
  MKI67 WILD-TYPE                                1    31
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MKI67 MUTATED                           2     6
  MKI67 WILD-TYPE                         6   102
D33V10, multiclass
                                  clus
vv                                 MKI67 MUTATED MKI67 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        6              31
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                        6             102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                 cls
clus                0   1
  MKI67 MUTATED     0  12
  MKI67 WILD-TYPE   4 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED      0   12
  MKI67 WILD-TYPE    4  131
                        clus
vv                       MKI67 MUTATED MKI67 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            12             131
[1] 2 2
[1] FALSE

Clustering(34) Variable = ALDH3B1 MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  ALDH3B1 MUTATED    1  4
  ALDH3B1 WILD-TYPE 89 62
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
                5               151 
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
                4                62 
$`ALDH3B1 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-ES-A2HS TCGA-G3-A3CJ 
       45.11         5.62        25.81        22.85        19.53 

$`ALDH3B1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
             5.62              0.03 
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
            45.11            113.00 
  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE 
            22.85             13.78 
[1] "5.6 - 45.1 (22.9)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.8"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALDH3B1 MUTATED         4        1         0          0          0          0
  ALDH3B1 WILD-TYPE      60       35         2         32          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  ALDH3B1 MUTATED          0         0         0
  ALDH3B1 WILD-TYPE        1         1         2
D34V3, multiclass
            clus
vv           ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  STAGE I                  4                60
  STAGE II                 1                35
  STAGE III                0                 2
  STAGE IIIA               0                32
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  ALDH3B1 MUTATED    4  1  0  0
  ALDH3B1 WILD-TYPE 63 39 43  9
D34V4, multiclass
    clus
vv   ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  T1               4                63
  T2               1                39
  T3               0                43
  T4               0                 9
[1] 4 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
  ALDH3B1 MUTATED    2  0
  ALDH3B1 WILD-TYPE 99  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3B1 MUTATED      2    0
  ALDH3B1 WILD-TYPE   99    3
   clus
vv  ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  0               2                99
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  ALDH3B1 MUTATED     4   0   1
  ALDH3B1 WILD-TYPE 118   3  34
D34V6, multiclass
    clus
vv   ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  M0               4               118
  M1               0                 3
  MX               1                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"
D34V7, binary
                   cls
clus                 0  1
  ALDH3B1 MUTATED    0  5
  ALDH3B1 WILD-TYPE 61 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3B1 MUTATED      0    5
  ALDH3B1 WILD-TYPE   61   94
        clus
vv       ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  FEMALE               0                61
  MALE                 5                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALDH3B1 MUTATED                         0                        5
  ALDH3B1 WILD-TYPE                       1                      152
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALDH3B1 MUTATED                                  0
  ALDH3B1 WILD-TYPE                                2
D34V8, multiclass
                                  clus
vv                                 ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       5               152
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ALDH3B1 MUTATED     5   0   0   0
  ALDH3B1 WILD-TYPE 127  10   1  12
D34V9, multiclass
    clus
vv   ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  R0               5               127
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDH3B1 MUTATED                                  1     1
  ALDH3B1 WILD-TYPE                                0    36
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ALDH3B1 MUTATED                           0     3
  ALDH3B1 WILD-TYPE                         8   105
D34V10, multiclass
                                  clus
vv                                 ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                36
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          3               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                   cls
clus                  0   1
  ALDH3B1 MUTATED     0   5
  ALDH3B1 WILD-TYPE   4 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH3B1 MUTATED      0    5
  ALDH3B1 WILD-TYPE    4  138
                        clus
vv                       ALDH3B1 MUTATED ALDH3B1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               138
[1] 2 2
[1] FALSE

Clustering(35) Variable = POTEG MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  POTEG MUTATED    3  4
  POTEG WILD-TYPE 87 62
  POTEG MUTATED POTEG WILD-TYPE 
              7             149 
  POTEG MUTATED POTEG WILD-TYPE 
              4              62 
$`POTEG MUTATED`
TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A3A0 
        0.13        53.33         2.60        12.95         5.62        25.81 
TCGA-DD-A73C 
        7.56 

$`POTEG WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
        4.24         3.32         0.10         0.07         0.10        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57       113.00         7.33         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        55.69        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         9.30        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  POTEG MUTATED POTEG WILD-TYPE 
           0.13            0.03 
  POTEG MUTATED POTEG WILD-TYPE 
          53.33          113.00 
  POTEG MUTATED POTEG WILD-TYPE 
           7.56           14.07 
[1] "0.1 - 53.3 (7.6)"   "0.0 - 113.0 (14.1)"
[1] "hr=" "2"  
D35V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  POTEG MUTATED         4        0         0          3          0          0
  POTEG WILD-TYPE      60       36         2         29          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  POTEG MUTATED          0         0         0
  POTEG WILD-TYPE        1         1         2
D35V3, multiclass
            clus
vv           POTEG MUTATED POTEG WILD-TYPE
  STAGE I                4              60
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             3              29
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  POTEG MUTATED    4  0  3  0
  POTEG WILD-TYPE 63 40 40  9
D35V4, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  T1             4              63
  T2             0              40
  T3             3              40
  T4             0               9
[1] 4 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
  POTEG MUTATED    5  0
  POTEG WILD-TYPE 96  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      5    0
  POTEG WILD-TYPE   96    3
   clus
vv  POTEG MUTATED POTEG WILD-TYPE
  0             5              96
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  POTEG MUTATED     7   0   0
  POTEG WILD-TYPE 115   3  35
D35V6, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  M0             7             115
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                 cls
clus               0  1
  POTEG MUTATED    2  5
  POTEG WILD-TYPE 59 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      2    5
  POTEG WILD-TYPE   59   94
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  FEMALE             2              59
  MALE               5              94
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  POTEG MUTATED                         0                        7
  POTEG WILD-TYPE                       1                      150
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  POTEG MUTATED                                  0
  POTEG WILD-TYPE                                2
D35V8, multiclass
                                  clus
vv                                 POTEG MUTATED POTEG WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     7             150
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  POTEG MUTATED     7   0   0   0
  POTEG WILD-TYPE 125  10   1  12
D35V9, multiclass
    clus
vv   POTEG MUTATED POTEG WILD-TYPE
  R0             7             125
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POTEG MUTATED                                  0     3
  POTEG WILD-TYPE                                1    34
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  POTEG MUTATED                           1     3
  POTEG WILD-TYPE                         7   105
D35V10, multiclass
                                  clus
vv                                 POTEG MUTATED POTEG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3              34
  BLACK OR AFRICAN AMERICAN                    1               7
  WHITE                                        3             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                 cls
clus                0   1
  POTEG MUTATED     0   7
  POTEG WILD-TYPE   4 136
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      0    7
  POTEG WILD-TYPE    4  136
                        clus
vv                       POTEG MUTATED POTEG WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             7             136
[1] 2 2
[1] FALSE

Clustering(36) Variable = ZNF658 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  ZNF658 MUTATED    2  4
  ZNF658 WILD-TYPE 88 62
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               6              150 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               4               62 
$`ZNF658 MUTATED`
TCGA-BC-A112 TCGA-DD-A116 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-FV-A3I0 TCGA-G3-A3CJ 
        5.03        53.33         5.62        25.81        27.88        19.53 

$`ZNF658 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        19.10         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  ZNF658 MUTATED ZNF658 WILD-TYPE 
            5.03             0.03 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
           53.33           113.00 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
           22.67            13.81 
[1] "5.0 - 53.3 (22.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.6"
D36V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZNF658 MUTATED         2        2         0          2          0          0
  ZNF658 WILD-TYPE      62       34         2         30          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ZNF658 MUTATED          0         0         0
  ZNF658 WILD-TYPE        1         1         2
D36V3, multiclass
            clus
vv           ZNF658 MUTATED ZNF658 WILD-TYPE
  STAGE I                 2               62
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              2               30
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ZNF658 MUTATED    2  2  3  0
  ZNF658 WILD-TYPE 65 38 40  9
D36V4, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  T1              2               65
  T2              2               38
  T3              3               40
  T4              0                9
[1] 4 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
  ZNF658 MUTATED    3  0
  ZNF658 WILD-TYPE 98  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      3    0
  ZNF658 WILD-TYPE   98    3
   clus
vv  ZNF658 MUTATED ZNF658 WILD-TYPE
  0              3               98
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  ZNF658 MUTATED     6   0   1
  ZNF658 WILD-TYPE 116   3  34
D36V6, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  M0              6              116
  M1              0                3
  MX              1               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"
D36V7, binary
                  cls
clus                0  1
  ZNF658 MUTATED    1  6
  ZNF658 WILD-TYPE 60 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      1    6
  ZNF658 WILD-TYPE   60   93
        clus
vv       ZNF658 MUTATED ZNF658 WILD-TYPE
  FEMALE              1               60
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ZNF658 MUTATED                         0                        6
  ZNF658 WILD-TYPE                       1                      151
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ZNF658 MUTATED                                  1
  ZNF658 WILD-TYPE                                1
D36V8, multiclass
                                  clus
vv                                 ZNF658 MUTATED ZNF658 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      6              151
  HEPATOCHOLANGIOCARCINOMA (MIXED)              1                1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF658 MUTATED     6   0   0   1
  ZNF658 WILD-TYPE 126  10   1  11
D36V9, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  R0              6              126
  R1              0               10
  R2              0                1
  RX              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF658 MUTATED                                  1     3
  ZNF658 WILD-TYPE                                0    34
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF658 MUTATED                           0     3
  ZNF658 WILD-TYPE                         8   105
D36V10, multiclass
                                  clus
vv                                 ZNF658 MUTATED ZNF658 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         3               34
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     0   7
  ZNF658 WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      0    7
  ZNF658 WILD-TYPE    4  136
                        clus
vv                       ZNF658 MUTATED ZNF658 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(37) Variable = TCHH MUTATION ANALYSIS
D37V1, survival
                sevent
clus2             0  1
  TCHH MUTATED   11  9
  TCHH WILD-TYPE 79 57
  TCHH MUTATED TCHH WILD-TYPE 
            20            136 
  TCHH MUTATED TCHH WILD-TYPE 
             9             57 
$`TCHH MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A69I TCGA-CC-5259 
       10.13        27.52        27.52         1.12        12.72         0.16 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH 
       53.33         2.60        66.31        75.65        12.95        49.15 
TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A4NN TCGA-EP-A12J TCGA-G3-A3CJ TCGA-G3-A5SI 
       18.35        70.06        29.56        18.74        19.53        14.70 
TCGA-G3-A5SJ TCGA-O8-A75V 
       11.97         4.44 

$`TCHH WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        46.78         2.99        25.32        23.34 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        9.50        14.60         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EG 
       21.76        51.29        90.71        79.40        19.79        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81         7.66        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       25.64         5.92        19.23         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
       14.24        12.85         8.71        58.88 

  TCHH MUTATED TCHH WILD-TYPE 
          0.16           0.03 
  TCHH MUTATED TCHH WILD-TYPE 
         75.65         113.00 
  TCHH MUTATED TCHH WILD-TYPE 
        18.545         13.710 
[1] "0.2 - 75.7 (18.5)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "1"  
D37V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TCHH MUTATED        11        2         1          1          0          1
  TCHH WILD-TYPE      53       34         1         31          5          5
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TCHH MUTATED          0         0         1
  TCHH WILD-TYPE        1         1         1
D37V3, multiclass
            clus
vv           TCHH MUTATED TCHH WILD-TYPE
  STAGE I              11             53
  STAGE II              2             34
  STAGE III             1              1
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            1              5
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TCHH MUTATED   11  3  3  3
  TCHH WILD-TYPE 56 37 40  6
D37V4, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  T1           11             56
  T2            3             37
  T3            3             40
  T4            3              6
[1] 4 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
  TCHH MUTATED   14  0
  TCHH WILD-TYPE 87  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED     14    0
  TCHH WILD-TYPE   87    3
   clus
vv  TCHH MUTATED TCHH WILD-TYPE
  0           14             87
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  TCHH MUTATED    13   1   6
  TCHH WILD-TYPE 109   2  29
D37V6, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  M0           13            109
  M1            1              2
  MX            6             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                cls
clus              0  1
  TCHH MUTATED    8 12
  TCHH WILD-TYPE 53 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      8   12
  TCHH WILD-TYPE   53   87
        clus
vv       TCHH MUTATED TCHH WILD-TYPE
  FEMALE            8             53
  MALE             12             87
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TCHH MUTATED                         0                       20
  TCHH WILD-TYPE                       1                      137
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TCHH MUTATED                                  0
  TCHH WILD-TYPE                                2
D37V8, multiclass
                                  clus
vv                                 TCHH MUTATED TCHH WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   20            137
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TCHH MUTATED    17   3   0   0
  TCHH WILD-TYPE 115   7   1  12
D37V9, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  R0           17            115
  R1            3              7
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCHH MUTATED                                  1     3
  TCHH WILD-TYPE                                0    34
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TCHH MUTATED                           2    12
  TCHH WILD-TYPE                         6    96
D37V10, multiclass
                                  clus
vv                                 TCHH MUTATED TCHH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3             34
  BLACK OR AFRICAN AMERICAN                   2              6
  WHITE                                      12             96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                cls
clus               0   1
  TCHH MUTATED     1  17
  TCHH WILD-TYPE   3 126
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      1   17
  TCHH WILD-TYPE    3  126
                        clus
vv                       TCHH MUTATED TCHH WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           17            126
[1] 2 2
[1] FALSE

Clustering(38) Variable = TMEM176A MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  TMEM176A MUTATED    1  3
  TMEM176A WILD-TYPE 89 63
  TMEM176A MUTATED TMEM176A WILD-TYPE 
                 4                152 
  TMEM176A MUTATED TMEM176A WILD-TYPE 
                 3                 63 
$`TMEM176A MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A5SM 
       45.11         5.62        25.81         4.37 

$`TMEM176A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       11.97         9.93         7.99         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  TMEM176A MUTATED TMEM176A WILD-TYPE 
              4.37               0.03 
  TMEM176A MUTATED TMEM176A WILD-TYPE 
             45.11             113.00 
  TMEM176A MUTATED TMEM176A WILD-TYPE 
            15.715             13.875 
[1] "4.4 - 45.1 (15.7)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "2"  
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  TMEM176A MUTATED         3        1         0          0          0
  TMEM176A WILD-TYPE      61       35         2         32          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  TMEM176A MUTATED            0        0         0         0
  TMEM176A WILD-TYPE          6        1         1         2
D38V3, multiclass
            clus
vv           TMEM176A MUTATED TMEM176A WILD-TYPE
  STAGE I                   3                 61
  STAGE II                  1                 35
  STAGE III                 0                  2
  STAGE IIIA                0                 32
  STAGE IIIB                0                  5
  STAGE IIIC                0                  6
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  TMEM176A MUTATED    3  1  0  0
  TMEM176A WILD-TYPE 64 39 43  9
D38V4, multiclass
    clus
vv   TMEM176A MUTATED TMEM176A WILD-TYPE
  T1                3                 64
  T2                1                 39
  T3                0                 43
  T4                0                  9
[1] 4 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
  TMEM176A MUTATED     1   0
  TMEM176A WILD-TYPE 100   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM176A MUTATED      1    0
  TMEM176A WILD-TYPE  100    3
   clus
vv  TMEM176A MUTATED TMEM176A WILD-TYPE
  0                1                100
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  TMEM176A MUTATED     4   0   0
  TMEM176A WILD-TYPE 118   3  35
D38V6, multiclass
    clus
vv   TMEM176A MUTATED TMEM176A WILD-TYPE
  M0                4                118
  M1                0                  3
  MX                0                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                  0  1
  TMEM176A MUTATED    0  4
  TMEM176A WILD-TYPE 61 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM176A MUTATED      0    4
  TMEM176A WILD-TYPE   61   95
        clus
vv       TMEM176A MUTATED TMEM176A WILD-TYPE
  FEMALE                0                 61
  MALE                  4                 95
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TMEM176A MUTATED                         0                        4
  TMEM176A WILD-TYPE                       1                      153
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  TMEM176A MUTATED                                  0
  TMEM176A WILD-TYPE                                2
D38V8, multiclass
                                  clus
vv                                 TMEM176A MUTATED TMEM176A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                        4                153
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TMEM176A MUTATED     4   0   0   0
  TMEM176A WILD-TYPE 128  10   1  12
D38V9, multiclass
    clus
vv   TMEM176A MUTATED TMEM176A WILD-TYPE
  R0                4                128
  R1                0                 10
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM176A MUTATED                                  0     1
  TMEM176A WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM176A MUTATED                           0     3
  TMEM176A WILD-TYPE                         8   105
D38V10, multiclass
                                  clus
vv                                 TMEM176A MUTATED TMEM176A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 36
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           3                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                    cls
clus                   0   1
  TMEM176A MUTATED     0   4
  TMEM176A WILD-TYPE   4 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM176A MUTATED      0    4
  TMEM176A WILD-TYPE    4  139
                        clus
vv                       TMEM176A MUTATED TMEM176A WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO                4                139
[1] 2 2
[1] FALSE

Clustering(39) Variable = RP1L1 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2              0  1
  RP1L1 MUTATED   10  9
  RP1L1 WILD-TYPE 80 57
  RP1L1 MUTATED RP1L1 WILD-TYPE 
             19             137 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
              9              57 
$`RP1L1 MUTATED`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10Y TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69I 
       27.91        46.78        23.34        13.84        22.36        12.72 
TCGA-CC-5261 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Z 
        0.39        21.76        12.95        45.11        49.15        19.76 
TCGA-DD-A3A9 TCGA-FV-A23B TCGA-FV-A4ZP TCGA-G3-A25Z TCGA-G3-A5SK TCGA-G3-A7M7 
       30.61        32.45        60.36        21.53         9.93         5.98 
TCGA-GJ-A6C0 
        1.02 

$`RP1L1 WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 
        1.12        69.57         5.03        44.42         0.26         9.50 
TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
       14.60         0.07         0.16         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       75.65         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        22.85        14.40        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         0.13         0.03         0.33         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG 
       51.06        53.79        28.27        30.74        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.99         4.37         7.76         1.84         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  RP1L1 MUTATED RP1L1 WILD-TYPE 
           0.39            0.03 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          60.36          113.00 
  RP1L1 MUTATED RP1L1 WILD-TYPE 
          21.76           13.41 
[1] "0.4 - 60.4 (21.8)"  "0.0 - 113.0 (13.4)"
[1] "hr=" "1.1"
D39V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RP1L1 MUTATED         7        6         1          2          0          0
  RP1L1 WILD-TYPE      57       30         1         30          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  RP1L1 MUTATED          0         0         1
  RP1L1 WILD-TYPE        1         1         1
D39V3, multiclass
            clus
vv           RP1L1 MUTATED RP1L1 WILD-TYPE
  STAGE I                7              57
  STAGE II               6              30
  STAGE III              1               1
  STAGE IIIA             2              30
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              1               1
[1] 9 2
[1] TRUE
[1] "dimension of 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    7  6  4  2
  RP1L1 WILD-TYPE 60 34 39  7
D39V4, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  T1             7              60
  T2             6              34
  T3             4              39
  T4             2               7
[1] 4 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
  RP1L1 MUTATED   11  0
  RP1L1 WILD-TYPE 90  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED     11    0
  RP1L1 WILD-TYPE   90    3
   clus
vv  RP1L1 MUTATED RP1L1 WILD-TYPE
  0            11              90
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  RP1L1 MUTATED    13   1   5
  RP1L1 WILD-TYPE 109   2  30
D39V6, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  M0            13             109
  M1             1               2
  MX             5              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                 cls
clus               0  1
  RP1L1 MUTATED    7 12
  RP1L1 WILD-TYPE 54 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      7   12
  RP1L1 WILD-TYPE   54   87
        clus
vv       RP1L1 MUTATED RP1L1 WILD-TYPE
  FEMALE             7              54
  MALE              12              87
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RP1L1 MUTATED                         0                       19
  RP1L1 WILD-TYPE                       1                      138
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  RP1L1 MUTATED                                  0
  RP1L1 WILD-TYPE                                2
D39V8, multiclass
                                  clus
vv                                 RP1L1 MUTATED RP1L1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    19             138
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RP1L1 MUTATED    14   2   0   3
  RP1L1 WILD-TYPE 118   8   1   9
D39V9, multiclass
    clus
vv   RP1L1 MUTATED RP1L1 WILD-TYPE
  R0            14             118
  R1             2               8
  R2             0               1
  RX             3               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RP1L1 MUTATED                                  0     2
  RP1L1 WILD-TYPE                                1    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RP1L1 MUTATED                           0    16
  RP1L1 WILD-TYPE                         8    92
D39V10, multiclass
                                  clus
vv                                 RP1L1 MUTATED RP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                       16              92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                 cls
clus                0   1
  RP1L1 MUTATED     0  16
  RP1L1 WILD-TYPE   4 127
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RP1L1 MUTATED      0   16
  RP1L1 WILD-TYPE    4  127
                        clus
vv                       RP1L1 MUTATED RP1L1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            16             127
[1] 2 2
[1] FALSE

Clustering(40) Variable = TSC2 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2             0  1
  TSC2 MUTATED    6  7
  TSC2 WILD-TYPE 84 59
  TSC2 MUTATED TSC2 WILD-TYPE 
            13            143 
  TSC2 MUTATED TSC2 WILD-TYPE 
             7             59 
$`TSC2 MUTATED`
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A3KF TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A39Z 
       46.78        27.52         0.26        37.78         2.60        19.76 
TCGA-DD-A3A6 TCGA-DD-A4NH TCGA-DD-A4NQ TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T 
      107.11        14.24        12.26        11.93         1.22        51.06 
TCGA-MI-A75I 
        8.71 

$`TSC2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 
       22.36         9.50        14.60        12.72         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI 
       32.52        73.38        21.70        14.07        14.63        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36         0.39        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85        58.88         4.44 

  TSC2 MUTATED TSC2 WILD-TYPE 
          0.26           0.03 
  TSC2 MUTATED TSC2 WILD-TYPE 
        107.11         113.00 
  TSC2 MUTATED TSC2 WILD-TYPE 
         14.24          13.84 
[1] "0.3 - 107.1 (14.2)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TSC2 MUTATED         3        4         0          2          1          0
  TSC2 WILD-TYPE      61       32         2         30          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TSC2 MUTATED          0         0         0
  TSC2 WILD-TYPE        1         1         2
D40V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               3             61
  STAGE II              4             32
  STAGE III             0              2
  STAGE IIIA            2             30
  STAGE IIIB            1              4
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TSC2 MUTATED    3  5  4  1
  TSC2 WILD-TYPE 64 35 39  8
D40V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            3             64
  T2            5             35
  T3            4             39
  T4            1              8
[1] 4 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
  TSC2 MUTATED    6  0
  TSC2 WILD-TYPE 95  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      6    0
  TSC2 WILD-TYPE   95    3
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            6             95
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  TSC2 MUTATED     9   0   4
  TSC2 WILD-TYPE 113   3  31
D40V6, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  M0            9            113
  M1            0              3
  MX            4             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                cls
clus              0  1
  TSC2 MUTATED    5  8
  TSC2 WILD-TYPE 56 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      5    8
  TSC2 WILD-TYPE   56   91
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  FEMALE            5             56
  MALE              8             91
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TSC2 MUTATED                         0                       13
  TSC2 WILD-TYPE                       1                      144
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TSC2 MUTATED                                  0
  TSC2 WILD-TYPE                                2
D40V8, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   13            144
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TSC2 MUTATED    10   2   0   0
  TSC2 WILD-TYPE 122   8   1  12
D40V9, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0           10            122
  R1            2              8
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC2 MUTATED                                  0     0
  TSC2 WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC2 MUTATED                           3     9
  TSC2 WILD-TYPE                         5    99
D40V10, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   3              5
  WHITE                                       9             99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                cls
clus               0   1
  TSC2 MUTATED     1  10
  TSC2 WILD-TYPE   3 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      1   10
  TSC2 WILD-TYPE    3  133
                        clus
vv                       TSC2 MUTATED TSC2 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10            133
[1] 2 2
[1] FALSE

Clustering(41) Variable = PRKDC MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  PRKDC MUTATED   11 11
  PRKDC WILD-TYPE 79 55
  PRKDC MUTATED PRKDC WILD-TYPE 
             22             134 
  PRKDC MUTATED PRKDC WILD-TYPE 
             11              55 
$`PRKDC MUTATED`
TCGA-BC-A10S TCGA-BC-A10Z TCGA-BC-A216 TCGA-CC-5259 TCGA-CC-5261 TCGA-DD-A114 
       46.78         1.12        44.42         0.16         0.39        37.78 
TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-A3A2 TCGA-DD-A4NF TCGA-DD-A73B 
       21.76        66.31         5.62        70.06        14.07         9.30 
TCGA-EP-A2KA TCGA-FV-A23B TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CJ TCGA-G3-A3CK 
       11.74        32.45        30.74        14.86        19.53        19.23 
TCGA-GJ-A6C0 TCGA-KR-A7K7 TCGA-MI-A75E TCGA-MI-A75G 
        1.02        13.38         5.10        14.24 

$`PRKDC WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.34        69.57         5.03        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5260 
       22.36         9.50        14.60        12.72         0.07         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        2.60         0.46        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       66.35        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       11.93        22.85        14.40        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CG 
        1.22        51.06        53.79        28.27        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       25.64         5.92        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 
        4.37         7.76         5.98         1.84         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I 
        2.14        11.84         0.49         9.57        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  PRKDC MUTATED PRKDC WILD-TYPE 
           0.16            0.03 
  PRKDC MUTATED PRKDC WILD-TYPE 
          70.06          113.00 
  PRKDC MUTATED PRKDC WILD-TYPE 
          14.55           13.71 
[1] "0.2 - 70.1 (14.6)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "1.3"
D41V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PRKDC MUTATED         9        7         0          2          1          2
  PRKDC WILD-TYPE      55       29         2         30          4          4
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PRKDC MUTATED          0         0         0
  PRKDC WILD-TYPE        1         1         2
D41V3, multiclass
            clus
vv           PRKDC MUTATED PRKDC WILD-TYPE
  STAGE I                9              55
  STAGE II               7              29
  STAGE III              0               2
  STAGE IIIA             2              30
  STAGE IIIB             1               4
  STAGE IIIC             2               4
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    9  7  4  2
  PRKDC WILD-TYPE 58 33 39  7
D41V4, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  T1             9              58
  T2             7              33
  T3             4              39
  T4             2               7
[1] 4 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
  PRKDC MUTATED   16  0
  PRKDC WILD-TYPE 85  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     16    0
  PRKDC WILD-TYPE   85    3
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0            16              85
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  PRKDC MUTATED    18   0   4
  PRKDC WILD-TYPE 104   3  31
D41V6, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  M0            18             104
  M1             0               3
  MX             4              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                 cls
clus               0  1
  PRKDC MUTATED   12 10
  PRKDC WILD-TYPE 49 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     12   10
  PRKDC WILD-TYPE   49   89
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  FEMALE            12              49
  MALE              10              89
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PRKDC MUTATED                         0                       22
  PRKDC WILD-TYPE                       1                      135
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PRKDC MUTATED                                  0
  PRKDC WILD-TYPE                                2
D41V8, multiclass
                                  clus
vv                                 PRKDC MUTATED PRKDC WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    22             135
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKDC MUTATED    19   0   0   3
  PRKDC WILD-TYPE 113  10   1   9
D41V9, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  R0            19             113
  R1             0              10
  R2             0               1
  RX             3               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKDC MUTATED                                  1     5
  PRKDC WILD-TYPE                                0    32
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKDC MUTATED                           1    14
  PRKDC WILD-TYPE                         7    94
D41V10, multiclass
                                  clus
vv                                 PRKDC MUTATED PRKDC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        5              32
  BLACK OR AFRICAN AMERICAN                    1               7
  WHITE                                       14              94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                 cls
clus                0   1
  PRKDC MUTATED     1  18
  PRKDC WILD-TYPE   3 125
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED      1   18
  PRKDC WILD-TYPE    3  125
                        clus
vv                       PRKDC MUTATED PRKDC WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO            18             125
[1] 2 2
[1] FALSE

Clustering(42) Variable = NRD1 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2             0  1
  NRD1 MUTATED    5  4
  NRD1 WILD-TYPE 85 62
  NRD1 MUTATED NRD1 WILD-TYPE 
             9            147 
  NRD1 MUTATED NRD1 WILD-TYPE 
             4             62 
$`NRD1 MUTATED`
TCGA-BC-A3KF TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A39X TCGA-DD-A3A7 TCGA-EP-A12J 
        0.26         3.32         0.07        55.69        13.78        18.74 
TCGA-FV-A2QR TCGA-G3-A3CJ TCGA-G3-A3CK 
       19.10        19.53        19.23 

$`NRD1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74       107.11         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        32.45        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI 
       14.86        21.53        22.13        25.64         5.92        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  NRD1 MUTATED NRD1 WILD-TYPE 
          0.07           0.03 
  NRD1 MUTATED NRD1 WILD-TYPE 
         55.69         113.00 
  NRD1 MUTATED NRD1 WILD-TYPE 
         18.74          13.84 
[1] "0.1 - 55.7 (18.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D42V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NRD1 MUTATED         5        1         0          2          1          0
  NRD1 WILD-TYPE      59       35         2         30          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  NRD1 MUTATED          0         0         0
  NRD1 WILD-TYPE        1         1         2
D42V3, multiclass
            clus
vv           NRD1 MUTATED NRD1 WILD-TYPE
  STAGE I               5             59
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            2             30
  STAGE IIIB            1              4
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of 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    5  1  3  0
  NRD1 WILD-TYPE 62 39 40  9
D42V4, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  T1            5             62
  T2            1             39
  T3            3             40
  T4            0              9
[1] 4 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
  NRD1 MUTATED    6  0
  NRD1 WILD-TYPE 95  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      6    0
  NRD1 WILD-TYPE   95    3
   clus
vv  NRD1 MUTATED NRD1 WILD-TYPE
  0            6             95
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  NRD1 MUTATED     8   0   1
  NRD1 WILD-TYPE 114   3  34
D42V6, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  M0            8            114
  M1            0              3
  MX            1             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"
D42V7, binary
                cls
clus              0  1
  NRD1 MUTATED    2  7
  NRD1 WILD-TYPE 59 92
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      2    7
  NRD1 WILD-TYPE   59   92
        clus
vv       NRD1 MUTATED NRD1 WILD-TYPE
  FEMALE            2             59
  MALE              7             92
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NRD1 MUTATED                         0                        9
  NRD1 WILD-TYPE                       1                      148
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  NRD1 MUTATED                                  0
  NRD1 WILD-TYPE                                2
D42V8, multiclass
                                  clus
vv                                 NRD1 MUTATED NRD1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    9            148
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRD1 MUTATED     7   0   0   1
  NRD1 WILD-TYPE 125  10   1  11
D42V9, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  R0            7            125
  R1            0             10
  R2            0              1
  RX            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRD1 MUTATED                                  1     3
  NRD1 WILD-TYPE                                0    34
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRD1 MUTATED                           1     3
  NRD1 WILD-TYPE                         7   105
D42V10, multiclass
                                  clus
vv                                 NRD1 MUTATED NRD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3             34
  BLACK OR AFRICAN AMERICAN                   1              7
  WHITE                                       3            105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                cls
clus               0   1
  NRD1 MUTATED     0   7
  NRD1 WILD-TYPE   4 136
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      0    7
  NRD1 WILD-TYPE    4  136
                        clus
vv                       NRD1 MUTATED NRD1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            136
[1] 2 2
[1] FALSE

Clustering(43) Variable = TAS2R20 MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  TAS2R20 MUTATED    3  1
  TAS2R20 WILD-TYPE 87 65
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
                4               152 
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
                1                65 
$`TAS2R20 MUTATED`
TCGA-BC-A69I TCGA-DD-A1ED TCGA-DD-A39Y TCGA-DD-A4NL 
       12.72        75.65         5.62        56.25 

$`TAS2R20 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
             5.62              0.03 
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
            75.65            113.00 
  TAS2R20 MUTATED TAS2R20 WILD-TYPE 
           34.485            13.875 
[1] "5.6 - 75.7 (34.5)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "2.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TAS2R20 MUTATED         4        0         0          0          0          0
  TAS2R20 WILD-TYPE      60       36         2         32          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  TAS2R20 MUTATED          0         0         0
  TAS2R20 WILD-TYPE        1         1         2
D43V3, multiclass
            clus
vv           TAS2R20 MUTATED TAS2R20 WILD-TYPE
  STAGE I                  4                60
  STAGE II                 0                36
  STAGE III                0                 2
  STAGE IIIA               0                32
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  TAS2R20 MUTATED    4  0  0  0
  TAS2R20 WILD-TYPE 63 40 43  9
D43V4, multiclass
    clus
vv   TAS2R20 MUTATED TAS2R20 WILD-TYPE
  T1               4                63
  T2               0                40
  T3               0                43
  T4               0                 9
[1] 4 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
  TAS2R20 MUTATED    3  0
  TAS2R20 WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R20 MUTATED      3    0
  TAS2R20 WILD-TYPE   98    3
   clus
vv  TAS2R20 MUTATED TAS2R20 WILD-TYPE
  0               3                98
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  TAS2R20 MUTATED     4   0   0
  TAS2R20 WILD-TYPE 118   3  35
D43V6, multiclass
    clus
vv   TAS2R20 MUTATED TAS2R20 WILD-TYPE
  M0               4               118
  M1               0                 3
  MX               0                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                 0  1
  TAS2R20 MUTATED    0  4
  TAS2R20 WILD-TYPE 61 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R20 MUTATED      0    4
  TAS2R20 WILD-TYPE   61   95
        clus
vv       TAS2R20 MUTATED TAS2R20 WILD-TYPE
  FEMALE               0                61
  MALE                 4                95
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TAS2R20 MUTATED                         0                        4
  TAS2R20 WILD-TYPE                       1                      153
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  TAS2R20 MUTATED                                  0
  TAS2R20 WILD-TYPE                                2
D43V8, multiclass
                                  clus
vv                                 TAS2R20 MUTATED TAS2R20 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       4               153
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TAS2R20 MUTATED     4   0   0   0
  TAS2R20 WILD-TYPE 128  10   1  12
D43V9, multiclass
    clus
vv   TAS2R20 MUTATED TAS2R20 WILD-TYPE
  R0               4               128
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAS2R20 MUTATED                                  0     1
  TAS2R20 WILD-TYPE                                1    36
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TAS2R20 MUTATED                           0     3
  TAS2R20 WILD-TYPE                         8   105
D43V10, multiclass
                                  clus
vv                                 TAS2R20 MUTATED TAS2R20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                36
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          3               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                   cls
clus                  0   1
  TAS2R20 MUTATED     0   3
  TAS2R20 WILD-TYPE   4 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R20 MUTATED      0    3
  TAS2R20 WILD-TYPE    4  140
                        clus
vv                       TAS2R20 MUTATED TAS2R20 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               140
[1] 2 2
[1] FALSE

Clustering(44) Variable = PTEN MUTATION ANALYSIS
D44V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    2  5
  PTEN WILD-TYPE 88 61
  PTEN MUTATED PTEN WILD-TYPE 
             7            149 
  PTEN MUTATED PTEN WILD-TYPE 
             5             61 
$`PTEN MUTATED`
TCGA-BC-A112 TCGA-BC-A3KF TCGA-DD-A11C TCGA-DD-A3A0 TCGA-DD-A4NE TCGA-FV-A23B 
        5.03         0.26        21.76        25.81        21.70        32.45 
TCGA-G3-A25Y 
       14.86 

$`PTEN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       13.64        21.14        55.69         5.62        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
        0.36        30.61        33.14        32.52        73.38        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         9.96        11.93        22.85        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  PTEN MUTATED PTEN WILD-TYPE 
          0.26           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         32.45         113.00 
  PTEN MUTATED PTEN WILD-TYPE 
         21.70          13.78 
[1] "0.3 - 32.5 (21.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.1"
D44V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTEN MUTATED         4        1         0          1          0          0
  PTEN WILD-TYPE      60       35         2         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PTEN MUTATED          0         0         0
  PTEN WILD-TYPE        1         1         2
D44V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               4             60
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PTEN MUTATED    4  1  2  0
  PTEN WILD-TYPE 63 39 41  9
D44V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            4             63
  T2            1             39
  T3            2             41
  T4            0              9
[1] 4 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
  PTEN MUTATED    4  0
  PTEN WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    0
  PTEN WILD-TYPE   97    3
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  PTEN MUTATED     6   0   1
  PTEN WILD-TYPE 116   3  34
D44V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  M0            6            116
  M1            0              3
  MX            1             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"
D44V7, binary
                cls
clus              0  1
  PTEN MUTATED    4  3
  PTEN WILD-TYPE 57 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE   57   96
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4             57
  MALE              3             96
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PTEN MUTATED                         0                        7
  PTEN WILD-TYPE                       1                      150
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                                2
D44V8, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    7            150
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     6   0   0   1
  PTEN WILD-TYPE 126  10   1  11
D44V9, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            6            126
  R1            0             10
  R2            0              1
  RX            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     1
  PTEN WILD-TYPE                                1    36
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           0     6
  PTEN WILD-TYPE                         8   102
D44V10, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             36
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       6            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                cls
clus               0   1
  PTEN MUTATED     1   5
  PTEN WILD-TYPE   3 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    5
  PTEN WILD-TYPE    3  138
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(45) Variable = CYFIP2 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  CYFIP2 MUTATED    6  7
  CYFIP2 WILD-TYPE 84 59
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
              13              143 
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
               7               59 
$`CYFIP2 MUTATED`
TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MB TCGA-DD-A1EG 
        5.03        14.60         2.86         0.39         0.10        45.11 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-EP-A2KC TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U 
        5.62        25.81         0.62         0.13        51.06        53.79 
TCGA-G3-A3CJ 
       19.53 

$`CYFIP2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 
       13.84         0.26        22.36         9.50        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.16         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH 
       79.40        66.31        19.79        75.65        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74        10.98         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V 
        0.03         0.33        60.36         0.39         1.22        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
            0.10             0.03 
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
           53.79           113.00 
  CYFIP2 MUTATED CYFIP2 WILD-TYPE 
            5.62            13.91 
[1] "0.1 - 53.8 (5.6)"   "0.0 - 113.0 (13.9)"
[1] "hr=" "1.8"
D45V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CYFIP2 MUTATED         6        3         0          2          0          1
  CYFIP2 WILD-TYPE      58       33         2         30          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CYFIP2 MUTATED          0         0         0
  CYFIP2 WILD-TYPE        1         1         2
D45V3, multiclass
            clus
vv           CYFIP2 MUTATED CYFIP2 WILD-TYPE
  STAGE I                 6               58
  STAGE II                3               33
  STAGE III               0                2
  STAGE IIIA              2               30
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CYFIP2 MUTATED    6  3  3  1
  CYFIP2 WILD-TYPE 61 37 40  8
D45V4, multiclass
    clus
vv   CYFIP2 MUTATED CYFIP2 WILD-TYPE
  T1              6               61
  T2              3               37
  T3              3               40
  T4              1                8
[1] 4 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
  CYFIP2 MUTATED    7  0
  CYFIP2 WILD-TYPE 94  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYFIP2 MUTATED      7    0
  CYFIP2 WILD-TYPE   94    3
   clus
vv  CYFIP2 MUTATED CYFIP2 WILD-TYPE
  0              7               94
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  CYFIP2 MUTATED    10   0   3
  CYFIP2 WILD-TYPE 112   3  32
D45V6, multiclass
    clus
vv   CYFIP2 MUTATED CYFIP2 WILD-TYPE
  M0             10              112
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                  cls
clus                0  1
  CYFIP2 MUTATED    4  9
  CYFIP2 WILD-TYPE 57 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYFIP2 MUTATED      4    9
  CYFIP2 WILD-TYPE   57   90
        clus
vv       CYFIP2 MUTATED CYFIP2 WILD-TYPE
  FEMALE              4               57
  MALE                9               90
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CYFIP2 MUTATED                         0                       13
  CYFIP2 WILD-TYPE                       1                      144
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CYFIP2 MUTATED                                  0
  CYFIP2 WILD-TYPE                                2
D45V8, multiclass
                                  clus
vv                                 CYFIP2 MUTATED CYFIP2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     13              144
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYFIP2 MUTATED    11   0   0   2
  CYFIP2 WILD-TYPE 121  10   1  10
D45V9, multiclass
    clus
vv   CYFIP2 MUTATED CYFIP2 WILD-TYPE
  R0             11              121
  R1              0               10
  R2              0                1
  RX              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYFIP2 MUTATED                                  1     5
  CYFIP2 WILD-TYPE                                0    32
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYFIP2 MUTATED                           1     6
  CYFIP2 WILD-TYPE                         7   102
D45V10, multiclass
                                  clus
vv                                 CYFIP2 MUTATED CYFIP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         5               32
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         6              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                  cls
clus                 0   1
  CYFIP2 MUTATED     0  13
  CYFIP2 WILD-TYPE   4 130
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYFIP2 MUTATED      0   13
  CYFIP2 WILD-TYPE    4  130
                        clus
vv                       CYFIP2 MUTATED CYFIP2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             13              130
[1] 2 2
[1] FALSE

Clustering(46) Variable = PRAMEF1 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  PRAMEF1 MUTATED    6  3
  PRAMEF1 WILD-TYPE 84 63
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
                9               147 
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
                3                63 
$`PRAMEF1 MUTATED`
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
       53.33         2.60        79.40        66.31        75.65        49.15 
TCGA-DD-A39Y TCGA-EP-A12J TCGA-NI-A4U2 
        5.62        18.74        58.88 

$`PRAMEF1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        51.29        90.71        19.79        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V 
       12.85         8.71         4.44 

  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
             2.60              0.03 
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
             79.4             113.0 
  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE 
            53.33             13.64 
[1] "2.6 - 79.4 (53.3)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "2.4"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PRAMEF1 MUTATED         5        1         1          2          0          0
  PRAMEF1 WILD-TYPE      59       35         1         30          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  PRAMEF1 MUTATED          0         0         0
  PRAMEF1 WILD-TYPE        1         1         2
D46V3, multiclass
            clus
vv           PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  STAGE I                  5                59
  STAGE II                 1                35
  STAGE III                1                 1
  STAGE IIIA               2                30
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  PRAMEF1 MUTATED    5  1  3  0
  PRAMEF1 WILD-TYPE 62 39 40  9
D46V4, multiclass
    clus
vv   PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  T1               5                62
  T2               1                39
  T3               3                40
  T4               0                 9
[1] 4 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
  PRAMEF1 MUTATED    6  0
  PRAMEF1 WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF1 MUTATED      6    0
  PRAMEF1 WILD-TYPE   95    3
   clus
vv  PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  0               6                95
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  PRAMEF1 MUTATED     7   0   2
  PRAMEF1 WILD-TYPE 115   3  33
D46V6, multiclass
    clus
vv   PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  M0               7               115
  M1               0                 3
  MX               2                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                 0  1
  PRAMEF1 MUTATED    1  8
  PRAMEF1 WILD-TYPE 60 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF1 MUTATED      1    8
  PRAMEF1 WILD-TYPE   60   91
        clus
vv       PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  FEMALE               1                60
  MALE                 8                91
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PRAMEF1 MUTATED                         0                        9
  PRAMEF1 WILD-TYPE                       1                      148
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  PRAMEF1 MUTATED                                  0
  PRAMEF1 WILD-TYPE                                2
D46V8, multiclass
                                  clus
vv                                 PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       9               148
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PRAMEF1 MUTATED     9   0   0   0
  PRAMEF1 WILD-TYPE 123  10   1  12
D46V9, multiclass
    clus
vv   PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  R0               9               123
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRAMEF1 MUTATED                                  0     3
  PRAMEF1 WILD-TYPE                                1    34
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PRAMEF1 MUTATED                           2     3
  PRAMEF1 WILD-TYPE                         6   105
D46V10, multiclass
                                  clus
vv                                 PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                34
  BLACK OR AFRICAN AMERICAN                      2                 6
  WHITE                                          3               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                   cls
clus                  0   1
  PRAMEF1 MUTATED     0   8
  PRAMEF1 WILD-TYPE   4 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF1 MUTATED      0    8
  PRAMEF1 WILD-TYPE    4  135
                        clus
vv                       PRAMEF1 MUTATED PRAMEF1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               8               135
[1] 2 2
[1] FALSE

Clustering(47) Variable = MST1 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2             0  1
  MST1 MUTATED    4  4
  MST1 WILD-TYPE 86 62
  MST1 MUTATED MST1 WILD-TYPE 
             8            148 
  MST1 MUTATED MST1 WILD-TYPE 
             4             62 
$`MST1 MUTATED`
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-FV-A496 
       19.79        75.65        45.11         5.62        25.81         0.33 
TCGA-G3-A3CJ TCGA-NI-A4U2 
       19.53        58.88 

$`MST1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       66.31        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V 
       14.24        12.85         8.71         4.44 

  MST1 MUTATED MST1 WILD-TYPE 
          0.33           0.03 
  MST1 MUTATED MST1 WILD-TYPE 
         75.65         113.00 
  MST1 MUTATED MST1 WILD-TYPE 
         22.80          13.71 
[1] "0.3 - 75.7 (22.8)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "1.1"
D47V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MST1 MUTATED         6        1         0          1          0          0
  MST1 WILD-TYPE      58       35         2         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  MST1 MUTATED          0         0         0
  MST1 WILD-TYPE        1         1         2
D47V3, multiclass
            clus
vv           MST1 MUTATED MST1 WILD-TYPE
  STAGE I               6             58
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MST1 MUTATED    6  1  1  0
  MST1 WILD-TYPE 61 39 42  9
D47V4, multiclass
    clus
vv   MST1 MUTATED MST1 WILD-TYPE
  T1            6             61
  T2            1             39
  T3            1             42
  T4            0              9
[1] 4 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
  MST1 MUTATED    4  0
  MST1 WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      4    0
  MST1 WILD-TYPE   97    3
   clus
vv  MST1 MUTATED MST1 WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  MST1 MUTATED     7   0   1
  MST1 WILD-TYPE 115   3  34
D47V6, multiclass
    clus
vv   MST1 MUTATED MST1 WILD-TYPE
  M0            7            115
  M1            0              3
  MX            1             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"
D47V7, binary
                cls
clus              0  1
  MST1 MUTATED    2  6
  MST1 WILD-TYPE 59 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      2    6
  MST1 WILD-TYPE   59   93
        clus
vv       MST1 MUTATED MST1 WILD-TYPE
  FEMALE            2             59
  MALE              6             93
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MST1 MUTATED                         0                        8
  MST1 WILD-TYPE                       1                      149
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  MST1 MUTATED                                  0
  MST1 WILD-TYPE                                2
D47V8, multiclass
                                  clus
vv                                 MST1 MUTATED MST1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    8            149
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MST1 MUTATED     8   0   0   0
  MST1 WILD-TYPE 124  10   1  12
D47V9, multiclass
    clus
vv   MST1 MUTATED MST1 WILD-TYPE
  R0            8            124
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST1 MUTATED                                  1     1
  MST1 WILD-TYPE                                0    36
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MST1 MUTATED                           0     6
  MST1 WILD-TYPE                         8   102
D47V10, multiclass
                                  clus
vv                                 MST1 MUTATED MST1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       1             36
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       6            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                cls
clus               0   1
  MST1 MUTATED     0   8
  MST1 WILD-TYPE   4 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      0    8
  MST1 WILD-TYPE    4  135
                        clus
vv                       MST1 MUTATED MST1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            135
[1] 2 2
[1] FALSE

Clustering(48) Variable = ZC3H7A MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2               0  1
  ZC3H7A MUTATED    8  3
  ZC3H7A WILD-TYPE 82 63
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
              11              145 
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
               3               63 
$`ZC3H7A MUTATED`
TCGA-BC-A3KG TCGA-BC-A69I TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       22.36        12.72        66.31        75.65        12.95        45.11 
TCGA-DD-A39V TCGA-DD-A73G TCGA-G3-A25U TCGA-G3-A25Z TCGA-MI-A75C 
       21.14       100.96        53.79        21.53         9.57 

$`ZC3H7A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       44.42        13.84         0.26         9.50        14.60         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EH 
       21.76        51.29        90.71        79.40        19.79        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        29.16        18.35        13.64        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A459 
        9.30         7.56        10.98         1.45        27.72        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG 
        1.22        51.06        28.27        30.74        14.86        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
            9.57             0.03 
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
          100.96           113.00 
  ZC3H7A MUTATED ZC3H7A WILD-TYPE 
           22.36            13.64 
[1] "9.6 - 101.0 (22.4)" "0.0 - 113.0 (13.6)"
[1] "hr=" "2.7"
D48V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZC3H7A MUTATED         9        2         0          0          0          0
  ZC3H7A WILD-TYPE      55       34         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ZC3H7A MUTATED          0         0         0
  ZC3H7A WILD-TYPE        1         1         2
D48V3, multiclass
            clus
vv           ZC3H7A MUTATED ZC3H7A WILD-TYPE
  STAGE I                 9               55
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ZC3H7A MUTATED    9  2  0  0
  ZC3H7A WILD-TYPE 58 38 43  9
D48V4, multiclass
    clus
vv   ZC3H7A MUTATED ZC3H7A WILD-TYPE
  T1              9               58
  T2              2               38
  T3              0               43
  T4              0                9
[1] 4 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
  ZC3H7A MUTATED   10  0
  ZC3H7A WILD-TYPE 91  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7A MUTATED     10    0
  ZC3H7A WILD-TYPE   91    3
   clus
vv  ZC3H7A MUTATED ZC3H7A WILD-TYPE
  0             10               91
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  ZC3H7A MUTATED    11   0   0
  ZC3H7A WILD-TYPE 111   3  35
D48V6, multiclass
    clus
vv   ZC3H7A MUTATED ZC3H7A WILD-TYPE
  M0             11              111
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                  cls
clus                0  1
  ZC3H7A MUTATED    5  6
  ZC3H7A WILD-TYPE 56 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7A MUTATED      5    6
  ZC3H7A WILD-TYPE   56   93
        clus
vv       ZC3H7A MUTATED ZC3H7A WILD-TYPE
  FEMALE              5               56
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ZC3H7A MUTATED                         0                       11
  ZC3H7A WILD-TYPE                       1                      146
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ZC3H7A MUTATED                                  0
  ZC3H7A WILD-TYPE                                2
D48V8, multiclass
                                  clus
vv                                 ZC3H7A MUTATED ZC3H7A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     11              146
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZC3H7A MUTATED    11   0   0   0
  ZC3H7A WILD-TYPE 121  10   1  12
D48V9, multiclass
    clus
vv   ZC3H7A MUTATED ZC3H7A WILD-TYPE
  R0             11              121
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H7A MUTATED                                  0     2
  ZC3H7A WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZC3H7A MUTATED                           0     8
  ZC3H7A WILD-TYPE                         8   100
D48V10, multiclass
                                  clus
vv                                 ZC3H7A MUTATED ZC3H7A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         8              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                  cls
clus                 0   1
  ZC3H7A MUTATED     0   9
  ZC3H7A WILD-TYPE   4 134
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H7A MUTATED      0    9
  ZC3H7A WILD-TYPE    4  134
                        clus
vv                       ZC3H7A MUTATED ZC3H7A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              9              134
[1] 2 2
[1] FALSE

Clustering(49) Variable = MLL3 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2             0  1
  MLL3 MUTATED   14 13
  MLL3 WILD-TYPE 76 53
  MLL3 MUTATED MLL3 WILD-TYPE 
            27            129 
  MLL3 MUTATED MLL3 WILD-TYPE 
            13             53 
$`MLL3 MUTATED`
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Z TCGA-CC-A3M9 TCGA-DD-A116 
       27.52        27.52         2.99         1.12         0.10        53.33 
TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A39Y 
        2.60        51.29        79.40        75.65        45.11         5.62 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NL TCGA-DD-A73G TCGA-ED-A459 TCGA-EP-A12J 
       13.78        30.61        56.25       100.96        13.41        18.74 
TCGA-FV-A23B TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       32.45         0.33        60.36         1.22        51.06        53.79 
TCGA-G3-A25Y TCGA-LG-A6GG TCGA-MI-A75H 
       14.86         0.49        12.85 

$`MLL3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        10.13        46.78        25.32        23.34 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       69.57         5.03        44.42        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
        9.50        14.60        12.72         0.07         0.16         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         3.39         4.24         3.32         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        0.13        79.73        37.78        83.57       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF 
        0.46        21.76        90.71        66.31        19.79        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       10.98         1.45        27.72        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25V 
        8.12         6.38         0.13         0.03         0.39        28.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
        2.14        11.84        13.38         9.57         5.10        14.24 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  MLL3 MUTATED MLL3 WILD-TYPE 
          0.10           0.03 
  MLL3 MUTATED MLL3 WILD-TYPE 
        100.96         113.00 
  MLL3 MUTATED MLL3 WILD-TYPE 
         27.52          13.38 
[1] "0.1 - 101.0 (27.5)" "0.0 - 113.0 (13.4)"
[1] "hr=" "1.1"
D49V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MLL3 MUTATED        13        4         0          4          1          0
  MLL3 WILD-TYPE      51       32         2         28          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  MLL3 MUTATED          0         0         1
  MLL3 WILD-TYPE        1         1         1
D49V3, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I              13             51
  STAGE II              4             32
  STAGE III             0              2
  STAGE IIIA            4             28
  STAGE IIIB            1              4
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  MLL3 MUTATED   13  5  5  3
  MLL3 WILD-TYPE 54 35 38  6
D49V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1           13             54
  T2            5             35
  T3            5             38
  T4            3              6
[1] 4 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
  MLL3 MUTATED   18  0
  MLL3 WILD-TYPE 83  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     18    0
  MLL3 WILD-TYPE   83    3
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           18             83
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  MLL3 MUTATED    20   1   6
  MLL3 WILD-TYPE 102   2  29
D49V6, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  M0           20            102
  M1            1              2
  MX            6             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                cls
clus              0  1
  MLL3 MUTATED   10 17
  MLL3 WILD-TYPE 51 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     10   17
  MLL3 WILD-TYPE   51   82
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           10             51
  MALE             17             82
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MLL3 MUTATED                         0                       27
  MLL3 WILD-TYPE                       1                      130
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  MLL3 MUTATED                                  0
  MLL3 WILD-TYPE                                2
D49V8, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   27            130
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    22   5   0   0
  MLL3 WILD-TYPE 110   5   1  12
D49V9, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           22            110
  R1            5              5
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  0     8
  MLL3 WILD-TYPE                                1    29
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED                           2    16
  MLL3 WILD-TYPE                         6    92
D49V10, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       8             29
  BLACK OR AFRICAN AMERICAN                   2              6
  WHITE                                      16             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                cls
clus               0   1
  MLL3 MUTATED     0  26
  MLL3 WILD-TYPE   4 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      0   26
  MLL3 WILD-TYPE    4  117
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO           26            117
[1] 2 2
[1] FALSE

Clustering(50) Variable = HNRNPCL1 MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  HNRNPCL1 MUTATED    2  9
  HNRNPCL1 WILD-TYPE 88 57
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                11                145 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
                 9                 57 
$`HNRNPCL1 MUTATED`
TCGA-BC-A10T TCGA-CC-5260 TCGA-CC-5261 TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A 
       27.52         2.86         0.39        37.78        53.33         2.60 
TCGA-DD-A1EH TCGA-DD-A3A0 TCGA-DD-A4NN TCGA-ES-A2HS TCGA-FV-A2QR 
       49.15        25.81        29.56        22.85        19.10 

$`HNRNPCL1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         0.16         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 
        0.07         0.10         0.13        79.73        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        45.11         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       15.06        39.78        56.25        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       32.45        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
              0.39               0.03 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             53.33             113.00 
  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE 
             25.81              13.64 
[1] "0.4 - 53.3 (25.8)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "1.9"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  HNRNPCL1 MUTATED         5        2         1          1          0
  HNRNPCL1 WILD-TYPE      59       34         1         31          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  HNRNPCL1 MUTATED            1        0         0         0
  HNRNPCL1 WILD-TYPE          5        1         1         2
D50V3, multiclass
            clus
vv           HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  STAGE I                   5                 59
  STAGE II                  2                 34
  STAGE III                 1                  1
  STAGE IIIA                1                 31
  STAGE IIIB                0                  5
  STAGE IIIC                1                  5
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of 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    5  2  2  2
  HNRNPCL1 WILD-TYPE 62 38 41  7
D50V4, multiclass
    clus
vv   HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  T1                5                 62
  T2                2                 38
  T3                2                 41
  T4                2                  7
[1] 4 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
  HNRNPCL1 MUTATED    7  0
  HNRNPCL1 WILD-TYPE 94  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      7    0
  HNRNPCL1 WILD-TYPE   94    3
   clus
vv  HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  0                7                 94
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  HNRNPCL1 MUTATED     9   0   2
  HNRNPCL1 WILD-TYPE 113   3  33
D50V6, multiclass
    clus
vv   HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  M0                9                113
  M1                0                  3
  MX                2                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                    cls
clus                  0  1
  HNRNPCL1 MUTATED    2  9
  HNRNPCL1 WILD-TYPE 59 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      2    9
  HNRNPCL1 WILD-TYPE   59   90
        clus
vv       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  FEMALE                2                 59
  MALE                  9                 90
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HNRNPCL1 MUTATED                         0                       11
  HNRNPCL1 WILD-TYPE                       1                      146
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  HNRNPCL1 MUTATED                                  0
  HNRNPCL1 WILD-TYPE                                2
D50V8, multiclass
                                  clus
vv                                 HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                       11                146
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HNRNPCL1 MUTATED     7   1   0   3
  HNRNPCL1 WILD-TYPE 125   9   1   9
D50V9, multiclass
    clus
vv   HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  R0                7                125
  R1                1                  9
  R2                0                  1
  RX                3                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPCL1 MUTATED                                  0     3
  HNRNPCL1 WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HNRNPCL1 MUTATED                           2     6
  HNRNPCL1 WILD-TYPE                         6   102
D50V10, multiclass
                                  clus
vv                                 HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                 34
  BLACK OR AFRICAN AMERICAN                       2                  6
  WHITE                                           6                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                    cls
clus                   0   1
  HNRNPCL1 MUTATED     0  11
  HNRNPCL1 WILD-TYPE   4 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HNRNPCL1 MUTATED      0   11
  HNRNPCL1 WILD-TYPE    4  132
                        clus
vv                       HNRNPCL1 MUTATED HNRNPCL1 WILD-TYPE
  HISPANIC OR LATINO                    0                  4
  NOT HISPANIC OR LATINO               11                132
[1] 2 2
[1] FALSE

Clustering(51) Variable = TUBA3E MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2               0  1
  TUBA3E MUTATED    5  2
  TUBA3E WILD-TYPE 85 64
  TUBA3E MUTATED TUBA3E WILD-TYPE 
               7              149 
  TUBA3E MUTATED TUBA3E WILD-TYPE 
               2               64 
$`TUBA3E MUTATED`
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
       53.33         2.60        79.40        75.65        45.11        49.15 
TCGA-EP-A12J 
       18.74 

$`TUBA3E WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF 
       21.76        51.29        90.71        66.31        19.79        12.95 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  TUBA3E MUTATED TUBA3E WILD-TYPE 
            2.60             0.03 
  TUBA3E MUTATED TUBA3E WILD-TYPE 
            79.4            113.0 
  TUBA3E MUTATED TUBA3E WILD-TYPE 
           49.15            13.64 
[1] "2.6 - 79.4 (49.1)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "2.8"
D51V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TUBA3E MUTATED         4        1         1          1          0          0
  TUBA3E WILD-TYPE      60       35         1         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  TUBA3E MUTATED          0         0         0
  TUBA3E WILD-TYPE        1         1         2
D51V3, multiclass
            clus
vv           TUBA3E MUTATED TUBA3E WILD-TYPE
  STAGE I                 4               60
  STAGE II                1               35
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  TUBA3E MUTATED    4  1  2  0
  TUBA3E WILD-TYPE 63 39 41  9
D51V4, multiclass
    clus
vv   TUBA3E MUTATED TUBA3E WILD-TYPE
  T1              4               63
  T2              1               39
  T3              2               41
  T4              0                9
[1] 4 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
  TUBA3E MUTATED    6  0
  TUBA3E WILD-TYPE 95  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA3E MUTATED      6    0
  TUBA3E WILD-TYPE   95    3
   clus
vv  TUBA3E MUTATED TUBA3E WILD-TYPE
  0              6               95
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  TUBA3E MUTATED     6   0   1
  TUBA3E WILD-TYPE 116   3  34
D51V6, multiclass
    clus
vv   TUBA3E MUTATED TUBA3E WILD-TYPE
  M0              6              116
  M1              0                3
  MX              1               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"
D51V7, binary
                  cls
clus                0  1
  TUBA3E MUTATED    0  7
  TUBA3E WILD-TYPE 61 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA3E MUTATED      0    7
  TUBA3E WILD-TYPE   61   92
        clus
vv       TUBA3E MUTATED TUBA3E WILD-TYPE
  FEMALE              0               61
  MALE                7               92
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TUBA3E MUTATED                         0                        7
  TUBA3E WILD-TYPE                       1                      150
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  TUBA3E MUTATED                                  0
  TUBA3E WILD-TYPE                                2
D51V8, multiclass
                                  clus
vv                                 TUBA3E MUTATED TUBA3E WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      7              150
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TUBA3E MUTATED     7   0   0   0
  TUBA3E WILD-TYPE 125  10   1  12
D51V9, multiclass
    clus
vv   TUBA3E MUTATED TUBA3E WILD-TYPE
  R0              7              125
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBA3E MUTATED                                  0     2
  TUBA3E WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TUBA3E MUTATED                           2     3
  TUBA3E WILD-TYPE                         6   105
D51V10, multiclass
                                  clus
vv                                 TUBA3E MUTATED TUBA3E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     2                6
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                  cls
clus                 0   1
  TUBA3E MUTATED     0   7
  TUBA3E WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA3E MUTATED      0    7
  TUBA3E WILD-TYPE    4  136
                        clus
vv                       TUBA3E MUTATED TUBA3E WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(52) Variable = MUC21 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  MUC21 MUTATED    5  9
  MUC21 WILD-TYPE 85 57
  MUC21 MUTATED MUC21 WILD-TYPE 
             14             142 
  MUC21 MUTATED MUC21 WILD-TYPE 
              9              57 
$`MUC21 MUTATED`
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A3KF TCGA-DD-A114 
       10.13        46.78        27.52        27.52         0.26        37.78 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A4NS TCGA-ED-A627 
       53.33         2.60        12.95        49.15        80.75        13.91 
TCGA-EP-A12J TCGA-G3-A25S 
       18.74         1.22 

$`MUC21 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.91        37.32         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57         5.03        44.42        13.84        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       14.60        12.72         0.07         0.16         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.39         4.24         3.32         0.10         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.13        79.73        83.57       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       75.65        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A66X 
       27.72       100.96        13.41        12.69        15.85        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  MUC21 MUTATED MUC21 WILD-TYPE 
           0.26            0.03 
  MUC21 MUTATED MUC21 WILD-TYPE 
          80.75          113.00 
  MUC21 MUTATED MUC21 WILD-TYPE 
          23.13           13.71 
[1] "0.3 - 80.8 (23.1)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "1.4"
D52V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MUC21 MUTATED         7        1         1          2          0          0
  MUC21 WILD-TYPE      57       35         1         30          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  MUC21 MUTATED          0         0         0
  MUC21 WILD-TYPE        1         1         2
D52V3, multiclass
            clus
vv           MUC21 MUTATED MUC21 WILD-TYPE
  STAGE I                7              57
  STAGE II               1              35
  STAGE III              1               1
  STAGE IIIA             2              30
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  MUC21 MUTATED    7  2  5  1
  MUC21 WILD-TYPE 60 38 38  8
D52V4, multiclass
    clus
vv   MUC21 MUTATED MUC21 WILD-TYPE
  T1             7              60
  T2             2              38
  T3             5              38
  T4             1               8
[1] 4 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
  MUC21 MUTATED    7  0
  MUC21 WILD-TYPE 94  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      7    0
  MUC21 WILD-TYPE   94    3
   clus
vv  MUC21 MUTATED MUC21 WILD-TYPE
  0             7              94
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  MUC21 MUTATED    10   0   5
  MUC21 WILD-TYPE 112   3  30
D52V6, multiclass
    clus
vv   MUC21 MUTATED MUC21 WILD-TYPE
  M0            10             112
  M1             0               3
  MX             5              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                 cls
clus               0  1
  MUC21 MUTATED    5 10
  MUC21 WILD-TYPE 56 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      5   10
  MUC21 WILD-TYPE   56   89
        clus
vv       MUC21 MUTATED MUC21 WILD-TYPE
  FEMALE             5              56
  MALE              10              89
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MUC21 MUTATED                         0                       15
  MUC21 WILD-TYPE                       1                      142
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  MUC21 MUTATED                                  0
  MUC21 WILD-TYPE                                2
D52V8, multiclass
                                  clus
vv                                 MUC21 MUTATED MUC21 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    15             142
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MUC21 MUTATED    11   3   0   1
  MUC21 WILD-TYPE 121   7   1  11
D52V9, multiclass
    clus
vv   MUC21 MUTATED MUC21 WILD-TYPE
  R0            11             121
  R1             3               7
  R2             0               1
  RX             1              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC21 MUTATED                                  0     2
  MUC21 WILD-TYPE                                1    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC21 MUTATED                           3    10
  MUC21 WILD-TYPE                         5    98
D52V10, multiclass
                                  clus
vv                                 MUC21 MUTATED MUC21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    3               5
  WHITE                                       10              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                 cls
clus                0   1
  MUC21 MUTATED     0  14
  MUC21 WILD-TYPE   4 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC21 MUTATED      0   14
  MUC21 WILD-TYPE    4  129
                        clus
vv                       MUC21 MUTATED MUC21 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO            14             129
[1] 2 2
[1] FALSE

Clustering(53) Variable = HPS4 MUTATION ANALYSIS
D53V1, survival
                sevent
clus2             0  1
  HPS4 MUTATED    3  0
  HPS4 WILD-TYPE 87 66
  HPS4 MUTATED HPS4 WILD-TYPE 
             3            153 
  HPS4 MUTATED HPS4 WILD-TYPE 
             0             66 
$`HPS4 MUTATED`
TCGA-DD-A1ED TCGA-DD-A4NP TCGA-ED-A82E 
       75.65        93.67         0.20 

$`HPS4 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  HPS4 MUTATED HPS4 WILD-TYPE 
          0.20           0.03 
  HPS4 MUTATED HPS4 WILD-TYPE 
         93.67         113.00 
  HPS4 MUTATED HPS4 WILD-TYPE 
         75.65          13.84 
[1] "0.2 - 93.7 (75.7)"  "0.0 - 113.0 (13.8)"
[1] "hr="     "2.7e+07"
D53V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HPS4 MUTATED         2        0         0          1          0          0
  HPS4 WILD-TYPE      62       36         2         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  HPS4 MUTATED          0         0         0
  HPS4 WILD-TYPE        1         1         2
D53V3, multiclass
            clus
vv           HPS4 MUTATED HPS4 WILD-TYPE
  STAGE I               2             62
  STAGE II              0             36
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  HPS4 MUTATED    2  0  1  0
  HPS4 WILD-TYPE 65 40 42  9
D53V4, multiclass
    clus
vv   HPS4 MUTATED HPS4 WILD-TYPE
  T1            2             65
  T2            0             40
  T3            1             42
  T4            0              9
[1] 4 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
  HPS4 MUTATED    3  0
  HPS4 WILD-TYPE 98  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS4 MUTATED      3    0
  HPS4 WILD-TYPE   98    3
   clus
vv  HPS4 MUTATED HPS4 WILD-TYPE
  0            3             98
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  HPS4 MUTATED     3   0   0
  HPS4 WILD-TYPE 119   3  35
D53V6, multiclass
    clus
vv   HPS4 MUTATED HPS4 WILD-TYPE
  M0            3            119
  M1            0              3
  MX            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                cls
clus              0  1
  HPS4 MUTATED    1  2
  HPS4 WILD-TYPE 60 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS4 MUTATED      1    2
  HPS4 WILD-TYPE   60   97
        clus
vv       HPS4 MUTATED HPS4 WILD-TYPE
  FEMALE            1             60
  MALE              2             97
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HPS4 MUTATED                         0                        3
  HPS4 WILD-TYPE                       1                      154
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  HPS4 MUTATED                                  0
  HPS4 WILD-TYPE                                2
D53V8, multiclass
                                  clus
vv                                 HPS4 MUTATED HPS4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    3            154
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HPS4 MUTATED     3   0   0   0
  HPS4 WILD-TYPE 129  10   1  12
D53V9, multiclass
    clus
vv   HPS4 MUTATED HPS4 WILD-TYPE
  R0            3            129
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPS4 MUTATED                                  0     1
  HPS4 WILD-TYPE                                1    36
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPS4 MUTATED                           0     2
  HPS4 WILD-TYPE                         8   106
D53V10, multiclass
                                  clus
vv                                 HPS4 MUTATED HPS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             36
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       2            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                cls
clus               0   1
  HPS4 MUTATED     0   3
  HPS4 WILD-TYPE   4 140
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS4 MUTATED      0    3
  HPS4 WILD-TYPE    4  140
                        clus
vv                       HPS4 MUTATED HPS4 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            3            140
[1] 2 2
[1] FALSE

Clustering(54) Variable = OR2T4 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2              0  1
  OR2T4 MUTATED    5  7
  OR2T4 WILD-TYPE 85 59
  OR2T4 MUTATED OR2T4 WILD-TYPE 
             12             144 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              7              59 
$`OR2T4 MUTATED`
TCGA-BC-A10R TCGA-BC-A10T TCGA-CC-5261 TCGA-DD-A116 TCGA-DD-A1EF TCGA-DD-A1EH 
       10.13        27.52         0.39        53.33        12.95        49.15 
TCGA-ED-A7PZ TCGA-EP-A12J TCGA-G3-A25S TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-O8-A75V 
        0.20        18.74         1.22         2.14        13.38         4.44 

$`OR2T4 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.16         2.86         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG 
       90.71        79.40        66.31        19.79        75.65        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-LG-A6GG 
        1.84         1.02         2.66         4.01        11.84         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 

  OR2T4 MUTATED OR2T4 WILD-TYPE 
           0.20            0.03 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
          53.33          113.00 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
         11.540          14.155 
[1] "0.2 - 53.3 (11.5)"  "0.0 - 113.0 (14.2)"
[1] "hr=" "2.1"
D54V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR2T4 MUTATED         5        3         1          1          0          0
  OR2T4 WILD-TYPE      59       33         1         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  OR2T4 MUTATED          0         0         0
  OR2T4 WILD-TYPE        1         1         2
D54V3, multiclass
            clus
vv           OR2T4 MUTATED OR2T4 WILD-TYPE
  STAGE I                5              59
  STAGE II               3              33
  STAGE III              1               1
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  OR2T4 MUTATED    5  3  3  1
  OR2T4 WILD-TYPE 62 37 40  8
D54V4, multiclass
    clus
vv   OR2T4 MUTATED OR2T4 WILD-TYPE
  T1             5              62
  T2             3              37
  T3             3              40
  T4             1               8
[1] 4 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
  OR2T4 MUTATED    7  0
  OR2T4 WILD-TYPE 94  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      7    0
  OR2T4 WILD-TYPE   94    3
   clus
vv  OR2T4 MUTATED OR2T4 WILD-TYPE
  0             7              94
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  OR2T4 MUTATED     8   0   4
  OR2T4 WILD-TYPE 114   3  31
D54V6, multiclass
    clus
vv   OR2T4 MUTATED OR2T4 WILD-TYPE
  M0             8             114
  M1             0               3
  MX             4              31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                 cls
clus               0  1
  OR2T4 MUTATED    3  9
  OR2T4 WILD-TYPE 58 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      3    9
  OR2T4 WILD-TYPE   58   90
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  FEMALE             3              58
  MALE               9              90
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR2T4 MUTATED                         0                       12
  OR2T4 WILD-TYPE                       1                      145
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR2T4 MUTATED                                  0
  OR2T4 WILD-TYPE                                2
D54V8, multiclass
                                  clus
vv                                 OR2T4 MUTATED OR2T4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                    12             145
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2T4 MUTATED     8   3   0   1
  OR2T4 WILD-TYPE 124   7   1  11
D54V9, multiclass
    clus
vv   OR2T4 MUTATED OR2T4 WILD-TYPE
  R0             8             124
  R1             3               7
  R2             0               1
  RX             1              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2T4 MUTATED                                  0     3
  OR2T4 WILD-TYPE                                1    34
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2T4 MUTATED                           1     7
  OR2T4 WILD-TYPE                         7   101
D54V10, multiclass
                                  clus
vv                                 OR2T4 MUTATED OR2T4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3              34
  BLACK OR AFRICAN AMERICAN                    1               7
  WHITE                                        7             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                 cls
clus                0   1
  OR2T4 MUTATED     1   9
  OR2T4 WILD-TYPE   3 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      1    9
  OR2T4 WILD-TYPE    3  134
                        clus
vv                       OR2T4 MUTATED OR2T4 WILD-TYPE
  HISPANIC OR LATINO                 1               3
  NOT HISPANIC OR LATINO             9             134
[1] 2 2
[1] FALSE

Clustering(55) Variable = SPDYE1 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2               0  1
  SPDYE1 MUTATED    2  2
  SPDYE1 WILD-TYPE 88 64
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
               4              152 
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
               2               64 
$`SPDYE1 MUTATED`
TCGA-BC-A10S TCGA-BC-A10U TCGA-DD-A1ED TCGA-EP-A12J 
       46.78        27.52        75.65        18.74 

$`SPDYE1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
           18.74             0.03 
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
           75.65           113.00 
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
           37.15            13.71 
[1] "18.7 - 75.7 (37.1)" "0.0 - 113.0 (13.7)"
[1] "hr=" "1.5"
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SPDYE1 MUTATED         2        0         0          0          0          0
  SPDYE1 WILD-TYPE      62       36         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  SPDYE1 MUTATED          0         0         0
  SPDYE1 WILD-TYPE        1         1         2
D55V3, multiclass
[1] "Remove cluster labels:" "SPDYE1 MUTATED"        
clus
  SPDYE1 MUTATED SPDYE1 WILD-TYPE 
               2              147 
      TCGA-BC-4073       TCGA-BC-A10X       TCGA-BC-A10Z       TCGA-BC-A216 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-BC-A217       TCGA-BC-A3KF       TCGA-BC-A3KG       TCGA-BC-A5W4 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-BC-A69H       TCGA-BC-A69I       TCGA-BW-A5NQ       TCGA-CC-5258 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-CC-5259       TCGA-CC-5260       TCGA-CC-5261       TCGA-CC-5262 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-CC-5263       TCGA-CC-5264       TCGA-CC-A123       TCGA-CC-A1HT 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-CC-A3M9       TCGA-CC-A3MA       TCGA-CC-A3MB       TCGA-CC-A3MC 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A113       TCGA-DD-A114       TCGA-DD-A115       TCGA-DD-A116 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A118       TCGA-DD-A119       TCGA-DD-A11A       TCGA-DD-A11B 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A11C       TCGA-DD-A11D       TCGA-DD-A1E9       TCGA-DD-A1EA 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A1EB       TCGA-DD-A1EC       TCGA-DD-A1EF       TCGA-DD-A1EG 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A1EH       TCGA-DD-A1EI       TCGA-DD-A1EJ       TCGA-DD-A1EK 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A1EL       TCGA-DD-A39V       TCGA-DD-A39X       TCGA-DD-A39Y 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A39Z       TCGA-DD-A3A0       TCGA-DD-A3A1       TCGA-DD-A3A2 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A3A3       TCGA-DD-A3A4       TCGA-DD-A3A5       TCGA-DD-A3A6 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A3A7       TCGA-DD-A3A8       TCGA-DD-A3A9       TCGA-DD-A4NA 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A4NB       TCGA-DD-A4ND       TCGA-DD-A4NE       TCGA-DD-A4NF 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A4NG       TCGA-DD-A4NH       TCGA-DD-A4NI       TCGA-DD-A4NJ 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A4NK       TCGA-DD-A4NL       TCGA-DD-A4NN       TCGA-DD-A4NO 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A4NP       TCGA-DD-A4NQ       TCGA-DD-A4NR       TCGA-DD-A4NS 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A4NV       TCGA-DD-A73A       TCGA-DD-A73B       TCGA-DD-A73C 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-DD-A73D       TCGA-DD-A73E       TCGA-DD-A73F       TCGA-DD-A73G 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-ED-A459       TCGA-ED-A4XI       TCGA-ED-A5KG       TCGA-ED-A627 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-ED-A66X       TCGA-ED-A66Y       TCGA-ED-A7PX       TCGA-ED-A7PY 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-ED-A7PZ       TCGA-ED-A7XO       TCGA-ED-A7XP       TCGA-ED-A82E 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-EP-A26S       TCGA-EP-A2KA       TCGA-EP-A2KB       TCGA-EP-A2KC 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-EP-A3JL       TCGA-EP-A3RK       TCGA-ES-A2HS       TCGA-ES-A2HT 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-FV-A23B       TCGA-FV-A2QQ       TCGA-FV-A2QR       TCGA-FV-A3I0 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-FV-A3I1       TCGA-FV-A3R2       TCGA-FV-A3R3       TCGA-FV-A495 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-FV-A496       TCGA-FV-A4ZP       TCGA-FV-A4ZQ       TCGA-G3-A25S 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-G3-A25T       TCGA-G3-A25U       TCGA-G3-A25V       TCGA-G3-A25W 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-G3-A25Y       TCGA-G3-A25Z       TCGA-G3-A3CG       TCGA-G3-A3CH 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-G3-A3CI       TCGA-G3-A3CJ       TCGA-G3-A3CK       TCGA-G3-A5SI 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-G3-A5SJ       TCGA-G3-A5SK       TCGA-G3-A5SL       TCGA-G3-A5SM 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-G3-A6UC       TCGA-G3-A7M7       TCGA-G3-A7M9       TCGA-GJ-A6C0 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-HP-A5MZ       TCGA-K7-A6G5       TCGA-KR-A7K0       TCGA-KR-A7K2 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-KR-A7K7       TCGA-LG-A6GG       TCGA-MI-A75C       TCGA-MI-A75E 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
      TCGA-MI-A75G       TCGA-NI-A4U2       TCGA-O8-A75V 
"SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" "SPDYE1 WILD-TYPE" 
                  vv
clus               T1 T2 T3 T4
  SPDYE1 MUTATED    2  1  1  0
  SPDYE1 WILD-TYPE 65 39 42  9
D55V4, multiclass
    clus
vv   SPDYE1 MUTATED SPDYE1 WILD-TYPE
  T1              2               65
  T2              1               39
  T3              1               42
  T4              0                9
[1] 4 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
  SPDYE1 MUTATED     1   0
  SPDYE1 WILD-TYPE 100   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPDYE1 MUTATED      1    0
  SPDYE1 WILD-TYPE  100    3
   clus
vv  SPDYE1 MUTATED SPDYE1 WILD-TYPE
  0              1              100
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  SPDYE1 MUTATED     1   0   3
  SPDYE1 WILD-TYPE 121   3  32
D55V6, multiclass
    clus
vv   SPDYE1 MUTATED SPDYE1 WILD-TYPE
  M0              1              121
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                  cls
clus                0  1
  SPDYE1 MUTATED    0  4
  SPDYE1 WILD-TYPE 61 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPDYE1 MUTATED      0    4
  SPDYE1 WILD-TYPE   61   95
        clus
vv       SPDYE1 MUTATED SPDYE1 WILD-TYPE
  FEMALE              0               61
  MALE                4               95
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SPDYE1 MUTATED                         0                        4
  SPDYE1 WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  SPDYE1 MUTATED                                  0
  SPDYE1 WILD-TYPE                                2
D55V8, multiclass
                                  clus
vv                                 SPDYE1 MUTATED SPDYE1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPDYE1 MUTATED     3   1   0   0
  SPDYE1 WILD-TYPE 129   9   1  12
D55V9, multiclass
    clus
vv   SPDYE1 MUTATED SPDYE1 WILD-TYPE
  R0              3              129
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPDYE1 MUTATED                                  0     0
  SPDYE1 WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPDYE1 MUTATED                           1     3
  SPDYE1 WILD-TYPE                         7   105
D55V10, multiclass
                                  clus
vv                                 SPDYE1 MUTATED SPDYE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                  cls
clus                 0   1
  SPDYE1 MUTATED     0   4
  SPDYE1 WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPDYE1 MUTATED      0    4
  SPDYE1 WILD-TYPE    4  139
                        clus
vv                       SPDYE1 MUTATED SPDYE1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(56) Variable = COG2 MUTATION ANALYSIS
D56V1, survival
                sevent
clus2             0  1
  COG2 MUTATED    2  4
  COG2 WILD-TYPE 88 62
  COG2 MUTATED COG2 WILD-TYPE 
             6            150 
  COG2 MUTATED COG2 WILD-TYPE 
             4             62 
$`COG2 MUTATED`
TCGA-CC-5262 TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A25Z TCGA-G3-A3CJ 
        3.39        45.11         5.62        25.81        21.53        19.53 

$`COG2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       12.72         0.07         0.16         2.86         0.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  COG2 MUTATED COG2 WILD-TYPE 
          3.39           0.03 
  COG2 MUTATED COG2 WILD-TYPE 
         45.11         113.00 
  COG2 MUTATED COG2 WILD-TYPE 
         20.53          13.81 
[1] "3.4 - 45.1 (20.5)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.8"
D56V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  COG2 MUTATED         4        1         0          0          0          1
  COG2 WILD-TYPE      60       35         2         32          5          5
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  COG2 MUTATED          0         0         0
  COG2 WILD-TYPE        1         1         2
D56V3, multiclass
            clus
vv           COG2 MUTATED COG2 WILD-TYPE
  STAGE I               4             60
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            0             32
  STAGE IIIB            0              5
  STAGE IIIC            1              5
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  COG2 MUTATED    4  1  0  1
  COG2 WILD-TYPE 63 39 43  8
D56V4, multiclass
    clus
vv   COG2 MUTATED COG2 WILD-TYPE
  T1            4             63
  T2            1             39
  T3            0             43
  T4            1              8
[1] 4 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
  COG2 MUTATED    4  0
  COG2 WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      4    0
  COG2 WILD-TYPE   97    3
   clus
vv  COG2 MUTATED COG2 WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  COG2 MUTATED     6   0   0
  COG2 WILD-TYPE 116   3  35
D56V6, multiclass
    clus
vv   COG2 MUTATED COG2 WILD-TYPE
  M0            6            116
  M1            0              3
  MX            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                cls
clus              0  1
  COG2 MUTATED    0  6
  COG2 WILD-TYPE 61 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      0    6
  COG2 WILD-TYPE   61   93
        clus
vv       COG2 MUTATED COG2 WILD-TYPE
  FEMALE            0             61
  MALE              6             93
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  COG2 MUTATED                         0                        6
  COG2 WILD-TYPE                       1                      151
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  COG2 MUTATED                                  0
  COG2 WILD-TYPE                                2
D56V8, multiclass
                                  clus
vv                                 COG2 MUTATED COG2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    6            151
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  COG2 MUTATED     5   0   0   0
  COG2 WILD-TYPE 127  10   1  12
D56V9, multiclass
    clus
vv   COG2 MUTATED COG2 WILD-TYPE
  R0            5            127
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COG2 MUTATED                                  1     3
  COG2 WILD-TYPE                                0    34
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  COG2 MUTATED                           0     2
  COG2 WILD-TYPE                         8   106
D56V10, multiclass
                                  clus
vv                                 COG2 MUTATED COG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3             34
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       2            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                cls
clus               0   1
  COG2 MUTATED     0   6
  COG2 WILD-TYPE   4 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      0    6
  COG2 WILD-TYPE    4  137
                        clus
vv                       COG2 MUTATED COG2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            137
[1] 2 2
[1] FALSE

Clustering(57) Variable = SEC63 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  SEC63 MUTATED    5  5
  SEC63 WILD-TYPE 85 61
  SEC63 MUTATED SEC63 WILD-TYPE 
             10             146 
  SEC63 MUTATED SEC63 WILD-TYPE 
              5              61 
$`SEC63 MUTATED`
TCGA-CC-5258 TCGA-DD-A1EG TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV 
        0.07        45.11        21.14         5.62        25.81        66.35 
TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A3CJ TCGA-KR-A7K2 
        1.22        30.74        19.53        11.84 

$`SEC63 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        13.64        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       17.59        20.12       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
       30.61        33.14        32.52        73.38        21.70        14.07 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       14.63        14.24        18.44        15.06        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
       60.36         0.39        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
        1.84         1.02         2.66         4.01         2.14        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  SEC63 MUTATED SEC63 WILD-TYPE 
           0.07            0.03 
  SEC63 MUTATED SEC63 WILD-TYPE 
          66.35          113.00 
  SEC63 MUTATED SEC63 WILD-TYPE 
         20.335          13.810 
[1] "0.1 - 66.3 (20.3)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D57V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SEC63 MUTATED         5        3         0          1          1          0
  SEC63 WILD-TYPE      59       33         2         31          4          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SEC63 MUTATED          0         0         0
  SEC63 WILD-TYPE        1         1         2
D57V3, multiclass
            clus
vv           SEC63 MUTATED SEC63 WILD-TYPE
  STAGE I                5              59
  STAGE II               3              33
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             1               4
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of 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    5  3  2  0
  SEC63 WILD-TYPE 62 37 41  9
D57V4, multiclass
    clus
vv   SEC63 MUTATED SEC63 WILD-TYPE
  T1             5              62
  T2             3              37
  T3             2              41
  T4             0               9
[1] 4 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
  SEC63 MUTATED    7  0
  SEC63 WILD-TYPE 94  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      7    0
  SEC63 WILD-TYPE   94    3
   clus
vv  SEC63 MUTATED SEC63 WILD-TYPE
  0             7              94
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  SEC63 MUTATED    10   0   0
  SEC63 WILD-TYPE 112   3  35
D57V6, multiclass
    clus
vv   SEC63 MUTATED SEC63 WILD-TYPE
  M0            10             112
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                 cls
clus               0  1
  SEC63 MUTATED    1  9
  SEC63 WILD-TYPE 60 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      1    9
  SEC63 WILD-TYPE   60   90
        clus
vv       SEC63 MUTATED SEC63 WILD-TYPE
  FEMALE             1              60
  MALE               9              90
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SEC63 MUTATED                         0                        9
  SEC63 WILD-TYPE                       1                      148
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SEC63 MUTATED                                  1
  SEC63 WILD-TYPE                                1
D57V8, multiclass
                                  clus
vv                                 SEC63 MUTATED SEC63 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             148
  HEPATOCHOLANGIOCARCINOMA (MIXED)             1               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SEC63 MUTATED     8   1   0   1
  SEC63 WILD-TYPE 124   9   1  11
D57V9, multiclass
    clus
vv   SEC63 MUTATED SEC63 WILD-TYPE
  R0             8             124
  R1             1               9
  R2             0               1
  RX             1              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC63 MUTATED                                  1     2
  SEC63 WILD-TYPE                                0    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SEC63 MUTATED                           0     7
  SEC63 WILD-TYPE                         8   101
D57V10, multiclass
                                  clus
vv                                 SEC63 MUTATED SEC63 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        7             101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, binary
                 cls
clus                0   1
  SEC63 MUTATED     0   9
  SEC63 WILD-TYPE   4 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEC63 MUTATED      0    9
  SEC63 WILD-TYPE    4  134
                        clus
vv                       SEC63 MUTATED SEC63 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             9             134
[1] 2 2
[1] FALSE

Clustering(58) Variable = LILRA3 MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2               0  1
  LILRA3 MUTATED    2  2
  LILRA3 WILD-TYPE 88 64
  LILRA3 MUTATED LILRA3 WILD-TYPE 
               4              152 
  LILRA3 MUTATED LILRA3 WILD-TYPE 
               2               64 
$`LILRA3 MUTATED`
TCGA-BC-A10S TCGA-DD-A1ED TCGA-DD-A4NG TCGA-EP-A12J 
       46.78        75.65        14.63        18.74 

$`LILRA3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        21.70        14.07        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  LILRA3 MUTATED LILRA3 WILD-TYPE 
           14.63             0.03 
  LILRA3 MUTATED LILRA3 WILD-TYPE 
           75.65           113.00 
  LILRA3 MUTATED LILRA3 WILD-TYPE 
           32.76            13.71 
[1] "14.6 - 75.7 (32.8)" "0.0 - 113.0 (13.7)"
[1] "hr=" "1.3"
D58V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LILRA3 MUTATED         2        0         0          1          0          0
  LILRA3 WILD-TYPE      62       36         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  LILRA3 MUTATED          0         0         0
  LILRA3 WILD-TYPE        1         1         2
D58V3, multiclass
            clus
vv           LILRA3 MUTATED LILRA3 WILD-TYPE
  STAGE I                 2               62
  STAGE II                0               36
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  LILRA3 MUTATED    2  0  2  0
  LILRA3 WILD-TYPE 65 40 41  9
D58V4, multiclass
    clus
vv   LILRA3 MUTATED LILRA3 WILD-TYPE
  T1              2               65
  T2              0               40
  T3              2               41
  T4              0                9
[1] 4 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
  LILRA3 MUTATED     1   0
  LILRA3 WILD-TYPE 100   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA3 MUTATED      1    0
  LILRA3 WILD-TYPE  100    3
   clus
vv  LILRA3 MUTATED LILRA3 WILD-TYPE
  0              1              100
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  LILRA3 MUTATED     2   0   2
  LILRA3 WILD-TYPE 120   3  33
D58V6, multiclass
    clus
vv   LILRA3 MUTATED LILRA3 WILD-TYPE
  M0              2              120
  M1              0                3
  MX              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                  cls
clus                0  1
  LILRA3 MUTATED    0  4
  LILRA3 WILD-TYPE 61 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA3 MUTATED      0    4
  LILRA3 WILD-TYPE   61   95
        clus
vv       LILRA3 MUTATED LILRA3 WILD-TYPE
  FEMALE              0               61
  MALE                4               95
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LILRA3 MUTATED                         0                        4
  LILRA3 WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  LILRA3 MUTATED                                  0
  LILRA3 WILD-TYPE                                2
D58V8, multiclass
                                  clus
vv                                 LILRA3 MUTATED LILRA3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LILRA3 MUTATED     4   0   0   0
  LILRA3 WILD-TYPE 128  10   1  12
D58V9, multiclass
    clus
vv   LILRA3 MUTATED LILRA3 WILD-TYPE
  R0              4              128
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LILRA3 MUTATED                                  0     0
  LILRA3 WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LILRA3 MUTATED                           1     3
  LILRA3 WILD-TYPE                         7   105
D58V10, multiclass
                                  clus
vv                                 LILRA3 MUTATED LILRA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                  cls
clus                 0   1
  LILRA3 MUTATED     0   4
  LILRA3 WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRA3 MUTATED      0    4
  LILRA3 WILD-TYPE    4  139
                        clus
vv                       LILRA3 MUTATED LILRA3 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(59) Variable = CYP2A6 MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2               0  1
  CYP2A6 MUTATED    1  3
  CYP2A6 WILD-TYPE 89 63
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4              152 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               3               63 
$`CYP2A6 MUTATED`
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10X TCGA-DD-A11A 
       46.78        27.52        25.32         2.60 

$`CYP2A6 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10Y 
       27.91        37.32        10.13        27.52         2.99        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 
       22.36         9.50        14.60        12.72         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
            2.60             0.03 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
           46.78           113.00 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
           26.42            13.81 
[1] "2.6 - 46.8 (26.4)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.6"
D59V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CYP2A6 MUTATED         2        0         0          1          0          0
  CYP2A6 WILD-TYPE      62       36         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CYP2A6 MUTATED          0         0         0
  CYP2A6 WILD-TYPE        1         1         2
D59V3, multiclass
            clus
vv           CYP2A6 MUTATED CYP2A6 WILD-TYPE
  STAGE I                 2               62
  STAGE II                0               36
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CYP2A6 MUTATED    2  1  2  0
  CYP2A6 WILD-TYPE 65 39 41  9
D59V4, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  T1              2               65
  T2              1               39
  T3              2               41
  T4              0                9
[1] 4 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
  CYP2A6 MUTATED    2  0
  CYP2A6 WILD-TYPE 99  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      2    0
  CYP2A6 WILD-TYPE   99    3
   clus
vv  CYP2A6 MUTATED CYP2A6 WILD-TYPE
  0              2               99
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  CYP2A6 MUTATED     1   0   4
  CYP2A6 WILD-TYPE 121   3  31
D59V6, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  M0              1              121
  M1              0                3
  MX              4               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  4
  CYP2A6 WILD-TYPE 60 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    4
  CYP2A6 WILD-TYPE   60   95
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  FEMALE              1               60
  MALE                4               95
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CYP2A6 MUTATED                         0                        5
  CYP2A6 WILD-TYPE                       1                      152
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CYP2A6 MUTATED                                  0
  CYP2A6 WILD-TYPE                                2
D59V8, multiclass
                                  clus
vv                                 CYP2A6 MUTATED CYP2A6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      5              152
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP2A6 MUTATED     3   1   0   1
  CYP2A6 WILD-TYPE 129   9   1  11
D59V9, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  R0              3              129
  R1              1                9
  R2              0                1
  RX              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2A6 MUTATED                                  0     0
  CYP2A6 WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP2A6 MUTATED                           1     4
  CYP2A6 WILD-TYPE                         7   104
D59V10, multiclass
                                  clus
vv                                 CYP2A6 MUTATED CYP2A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         4              104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                  cls
clus                 0   1
  CYP2A6 MUTATED     0   5
  CYP2A6 WILD-TYPE   4 138
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      0    5
  CYP2A6 WILD-TYPE    4  138
                        clus
vv                       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              138
[1] 2 2
[1] FALSE

Clustering(60) Variable = ZC3H11A MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                0  1
  ZC3H11A MUTATED    2  1
  ZC3H11A WILD-TYPE 88 65
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                3               153 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
                1                65 
$`ZC3H11A MUTATED`
TCGA-BC-4073 TCGA-CC-5259 TCGA-G3-A25Y 
       27.91         0.16        14.86 

$`ZC3H11A WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       37.32        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        1.22        51.06        53.79        28.27        30.74        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
             0.16              0.03 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            27.91            113.00 
  ZC3H11A MUTATED ZC3H11A WILD-TYPE 
            14.86             13.84 
[1] "0.2 - 27.9 (14.9)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D60V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZC3H11A MUTATED         1        0         0          1          0          1
  ZC3H11A WILD-TYPE      63       36         2         31          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  ZC3H11A MUTATED          0         0         0
  ZC3H11A WILD-TYPE        1         1         2
D60V3, multiclass
            clus
vv           ZC3H11A MUTATED ZC3H11A WILD-TYPE
  STAGE I                  1                63
  STAGE II                 0                36
  STAGE III                0                 2
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               1                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of 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    1  0  1  1
  ZC3H11A WILD-TYPE 66 40 42  8
D60V4, multiclass
    clus
vv   ZC3H11A MUTATED ZC3H11A WILD-TYPE
  T1               1                66
  T2               0                40
  T3               1                42
  T4               1                 8
[1] 4 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
  ZC3H11A MUTATED    3  0
  ZC3H11A WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      3    0
  ZC3H11A WILD-TYPE   98    3
   clus
vv  ZC3H11A MUTATED ZC3H11A WILD-TYPE
  0               3                98
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  ZC3H11A MUTATED     2   0   1
  ZC3H11A WILD-TYPE 120   3  34
D60V6, multiclass
    clus
vv   ZC3H11A MUTATED ZC3H11A WILD-TYPE
  M0               2               120
  M1               0                 3
  MX               1                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"
D60V7, binary
                   cls
clus                 0  1
  ZC3H11A MUTATED    2  1
  ZC3H11A WILD-TYPE 59 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      2    1
  ZC3H11A WILD-TYPE   59   98
        clus
vv       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  FEMALE               2                59
  MALE                 1                98
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ZC3H11A MUTATED                         0                        3
  ZC3H11A WILD-TYPE                       1                      154
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  ZC3H11A MUTATED                                  0
  ZC3H11A WILD-TYPE                                2
D60V8, multiclass
                                  clus
vv                                 ZC3H11A MUTATED ZC3H11A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       3               154
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZC3H11A MUTATED     2   1   0   0
  ZC3H11A WILD-TYPE 130   9   1  12
D60V9, multiclass
    clus
vv   ZC3H11A MUTATED ZC3H11A WILD-TYPE
  R0               2               130
  R1               1                 9
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H11A MUTATED                                  0     2
  ZC3H11A WILD-TYPE                                1    35
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZC3H11A MUTATED                           0     1
  ZC3H11A WILD-TYPE                         8   107
D60V10, multiclass
                                  clus
vv                                 ZC3H11A MUTATED ZC3H11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                35
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          1               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                   cls
clus                  0   1
  ZC3H11A MUTATED     0   3
  ZC3H11A WILD-TYPE   4 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H11A MUTATED      0    3
  ZC3H11A WILD-TYPE    4  140
                        clus
vv                       ZC3H11A MUTATED ZC3H11A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               140
[1] 2 2
[1] FALSE

Clustering(61) Variable = LCE4A MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2              0  1
  LCE4A MUTATED    2  7
  LCE4A WILD-TYPE 88 59
  LCE4A MUTATED LCE4A WILD-TYPE 
              9             147 
  LCE4A MUTATED LCE4A WILD-TYPE 
              7              59 
$`LCE4A MUTATED`
TCGA-CC-A3MA TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
        0.07         7.33        45.11        55.69        19.76        25.81 
TCGA-FV-A2QR TCGA-G3-A3CJ TCGA-GJ-A6C0 
       19.10        19.53         1.02 

$`LCE4A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.10         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14         5.62         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        32.45        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.86        21.53        22.13        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        5.98         1.84         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  LCE4A MUTATED LCE4A WILD-TYPE 
           0.07            0.03 
  LCE4A MUTATED LCE4A WILD-TYPE 
          55.69          113.00 
  LCE4A MUTATED LCE4A WILD-TYPE 
          19.53           13.78 
[1] "0.1 - 55.7 (19.5)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.1"
D61V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LCE4A MUTATED         4        3         0          1          0          0
  LCE4A WILD-TYPE      60       33         2         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  LCE4A MUTATED          1         0         0
  LCE4A WILD-TYPE        0         1         2
D61V3, multiclass
            clus
vv           LCE4A MUTATED LCE4A WILD-TYPE
  STAGE I                4              60
  STAGE II               3              33
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               1               0
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  LCE4A MUTATED    4  3  2  0
  LCE4A WILD-TYPE 63 37 41  9
D61V4, multiclass
    clus
vv   LCE4A MUTATED LCE4A WILD-TYPE
  T1             4              63
  T2             3              37
  T3             2              41
  T4             0               9
[1] 4 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
  LCE4A MUTATED    5  0
  LCE4A WILD-TYPE 96  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE4A MUTATED      5    0
  LCE4A WILD-TYPE   96    3
   clus
vv  LCE4A MUTATED LCE4A WILD-TYPE
  0             5              96
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  LCE4A MUTATED     7   1   1
  LCE4A WILD-TYPE 115   2  34
D61V6, multiclass
    clus
vv   LCE4A MUTATED LCE4A WILD-TYPE
  M0             7             115
  M1             1               2
  MX             1              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"
D61V7, binary
                 cls
clus               0  1
  LCE4A MUTATED    3  6
  LCE4A WILD-TYPE 58 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE4A MUTATED      3    6
  LCE4A WILD-TYPE   58   93
        clus
vv       LCE4A MUTATED LCE4A WILD-TYPE
  FEMALE             3              58
  MALE               6              93
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LCE4A MUTATED                         0                        9
  LCE4A WILD-TYPE                       1                      148
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  LCE4A MUTATED                                  0
  LCE4A WILD-TYPE                                2
D61V8, multiclass
                                  clus
vv                                 LCE4A MUTATED LCE4A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             148
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LCE4A MUTATED     6   0   1   2
  LCE4A WILD-TYPE 126  10   0  10
D61V9, multiclass
    clus
vv   LCE4A MUTATED LCE4A WILD-TYPE
  R0             6             126
  R1             0              10
  R2             1               0
  RX             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCE4A MUTATED                                  1     2
  LCE4A WILD-TYPE                                0    35
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LCE4A MUTATED                           0     5
  LCE4A WILD-TYPE                         8   103
D61V10, multiclass
                                  clus
vv                                 LCE4A MUTATED LCE4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2              35
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        5             103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                 cls
clus                0   1
  LCE4A MUTATED     0   8
  LCE4A WILD-TYPE   4 135
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE4A MUTATED      0    8
  LCE4A WILD-TYPE    4  135
                        clus
vv                       LCE4A MUTATED LCE4A WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             8             135
[1] 2 2
[1] FALSE

Clustering(62) Variable = ATXN3 MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2              0  1
  ATXN3 MUTATED    3  1
  ATXN3 WILD-TYPE 87 65
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              4             152 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
              1              65 
$`ATXN3 MUTATED`
TCGA-BC-A112 TCGA-DD-A1ED TCGA-FV-A496 TCGA-G3-A25T 
        5.03        75.65         0.33        51.06 

$`ATXN3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        6.38         0.13         0.03        60.36         0.39         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  ATXN3 MUTATED ATXN3 WILD-TYPE 
           0.33            0.03 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
          75.65          113.00 
  ATXN3 MUTATED ATXN3 WILD-TYPE 
         28.045          13.875 
[1] "0.3 - 75.7 (28.0)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "2.2"
D62V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ATXN3 MUTATED         2        0         0          1          0          0
  ATXN3 WILD-TYPE      62       36         2         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  ATXN3 MUTATED          0         0         0
  ATXN3 WILD-TYPE        1         1         2
D62V3, multiclass
            clus
vv           ATXN3 MUTATED ATXN3 WILD-TYPE
  STAGE I                2              62
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  ATXN3 MUTATED    2  0  2  0
  ATXN3 WILD-TYPE 65 40 41  9
D62V4, multiclass
    clus
vv   ATXN3 MUTATED ATXN3 WILD-TYPE
  T1             2              65
  T2             0              40
  T3             2              41
  T4             0               9
[1] 4 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
  ATXN3 MUTATED    2  0
  ATXN3 WILD-TYPE 99  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      2    0
  ATXN3 WILD-TYPE   99    3
   clus
vv  ATXN3 MUTATED ATXN3 WILD-TYPE
  0             2              99
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  ATXN3 MUTATED     3   0   1
  ATXN3 WILD-TYPE 119   3  34
D62V6, multiclass
    clus
vv   ATXN3 MUTATED ATXN3 WILD-TYPE
  M0             3             119
  M1             0               3
  MX             1              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"
D62V7, binary
                 cls
clus               0  1
  ATXN3 MUTATED    2  2
  ATXN3 WILD-TYPE 59 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      2    2
  ATXN3 WILD-TYPE   59   97
        clus
vv       ATXN3 MUTATED ATXN3 WILD-TYPE
  FEMALE             2              59
  MALE               2              97
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ATXN3 MUTATED                         0                        4
  ATXN3 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  ATXN3 MUTATED                                  0
  ATXN3 WILD-TYPE                                2
D62V8, multiclass
                                  clus
vv                                 ATXN3 MUTATED ATXN3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATXN3 MUTATED     4   0   0   0
  ATXN3 WILD-TYPE 128  10   1  12
D62V9, multiclass
    clus
vv   ATXN3 MUTATED ATXN3 WILD-TYPE
  R0             4             128
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATXN3 MUTATED                                  0     0
  ATXN3 WILD-TYPE                                1    37
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATXN3 MUTATED                           0     4
  ATXN3 WILD-TYPE                         8   104
D62V10, multiclass
                                  clus
vv                                 ATXN3 MUTATED ATXN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              37
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        4             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                 cls
clus                0   1
  ATXN3 MUTATED     0   4
  ATXN3 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN3 MUTATED      0    4
  ATXN3 WILD-TYPE    4  139
                        clus
vv                       ATXN3 MUTATED ATXN3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(63) Variable = GTF2IRD2B MUTATION ANALYSIS
D63V1, survival
                     sevent
clus2                  0  1
  GTF2IRD2B MUTATED    2  3
  GTF2IRD2B WILD-TYPE 88 63
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
                  5                 151 
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
                  3                  63 
$`GTF2IRD2B MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-ED-A7PZ TCGA-G3-A3CJ 
       45.11         5.62        25.81         0.20        19.53 

$`GTF2IRD2B WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
               0.20                0.03 
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
              45.11              113.00 
  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE 
              19.53               13.84 
[1] "0.2 - 45.1 (19.5)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.7"
D63V2, continuous
                     vv
clus                  STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  GTF2IRD2B MUTATED         3        2         0          0          0
  GTF2IRD2B WILD-TYPE      61       34         2         32          5
                     vv
clus                  STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  GTF2IRD2B MUTATED            0        0         0         0
  GTF2IRD2B WILD-TYPE          6        1         1         2
D63V3, multiclass
            clus
vv           GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  STAGE I                    3                  61
  STAGE II                   2                  34
  STAGE III                  0                   2
  STAGE IIIA                 0                  32
  STAGE IIIB                 0                   5
  STAGE IIIC                 0                   6
  STAGE IV                   0                   1
  STAGE IVA                  0                   1
  STAGE IVB                  0                   2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3 T4
  GTF2IRD2B MUTATED    3  2  0  0
  GTF2IRD2B WILD-TYPE 64 38 43  9
D63V4, multiclass
    clus
vv   GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  T1                 3                  64
  T2                 2                  38
  T3                 0                  43
  T4                 0                   9
[1] 4 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
  GTF2IRD2B MUTATED    2  0
  GTF2IRD2B WILD-TYPE 99  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  GTF2IRD2B MUTATED      2    0
  GTF2IRD2B WILD-TYPE   99    3
   clus
vv  GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  0                 2                  99
  1                 0                   3
[1] 2 2
[1] FALSE
                     vv
clus                   M0  M1  MX
  GTF2IRD2B MUTATED     5   0   0
  GTF2IRD2B WILD-TYPE 117   3  35
D63V6, multiclass
    clus
vv   GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  M0                 5                 117
  M1                 0                   3
  MX                 0                  35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                     cls
clus                   0  1
  GTF2IRD2B MUTATED    0  5
  GTF2IRD2B WILD-TYPE 61 94
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  GTF2IRD2B MUTATED      0    5
  GTF2IRD2B WILD-TYPE   61   94
        clus
vv       GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  FEMALE                 0                  61
  MALE                   5                  94
[1] 2 2
[1] FALSE
                     vv
clus                  FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GTF2IRD2B MUTATED                         0                        5
  GTF2IRD2B WILD-TYPE                       1                      152
                     vv
clus                  HEPATOCHOLANGIOCARCINOMA (MIXED)
  GTF2IRD2B MUTATED                                  0
  GTF2IRD2B WILD-TYPE                                2
D63V8, multiclass
                                  clus
vv                                 GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                          0                   1
  HEPATOCELLULAR CARCINOMA                         5                 152
  HEPATOCHOLANGIOCARCINOMA (MIXED)                 0                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  GTF2IRD2B MUTATED     5   0   0   0
  GTF2IRD2B WILD-TYPE 127  10   1  12
D63V9, multiclass
    clus
vv   GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  R0                 5                 127
  R1                 0                  10
  R2                 0                   1
  RX                 0                  12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2IRD2B MUTATED                                  1     2
  GTF2IRD2B WILD-TYPE                                0    35
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  GTF2IRD2B MUTATED                           0     2
  GTF2IRD2B WILD-TYPE                         8   106
D63V10, multiclass
                                  clus
vv                                 GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            2                  35
  BLACK OR AFRICAN AMERICAN                        0                   8
  WHITE                                            2                 106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                     cls
clus                    0   1
  GTF2IRD2B MUTATED     0   5
  GTF2IRD2B WILD-TYPE   4 138
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  GTF2IRD2B MUTATED      0    5
  GTF2IRD2B WILD-TYPE    4  138
                        clus
vv                       GTF2IRD2B MUTATED GTF2IRD2B WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 5                 138
[1] 2 2
[1] FALSE

Clustering(64) Variable = QRICH2 MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2               0  1
  QRICH2 MUTATED   11  6
  QRICH2 WILD-TYPE 79 60
  QRICH2 MUTATED QRICH2 WILD-TYPE 
              17              139 
  QRICH2 MUTATED QRICH2 WILD-TYPE 
               6               60 
$`QRICH2 MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA 
       46.78         2.99        37.78        53.33         2.60        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A39Y TCGA-DD-A4NI TCGA-ED-A4XI TCGA-EP-A26S 
       66.31        75.65         5.62        18.44        12.69        19.99 
TCGA-G3-A25W TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A7M9 TCGA-MI-A75C 
       30.74         5.92        19.53         1.84         9.57 

$`QRICH2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        79.73        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        14.07        14.63        14.24        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        13.41        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        22.13        25.64        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        0.49         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  QRICH2 MUTATED QRICH2 WILD-TYPE 
            1.84             0.03 
  QRICH2 MUTATED QRICH2 WILD-TYPE 
            79.4            113.0 
  QRICH2 MUTATED QRICH2 WILD-TYPE 
           19.53            13.78 
[1] "1.8 - 79.4 (19.5)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D64V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  QRICH2 MUTATED         7        5         0          1          2          0
  QRICH2 WILD-TYPE      57       31         2         31          3          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  QRICH2 MUTATED          0         0         0
  QRICH2 WILD-TYPE        1         1         2
D64V3, multiclass
            clus
vv           QRICH2 MUTATED QRICH2 WILD-TYPE
  STAGE I                 7               57
  STAGE II                5               31
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              2                3
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  QRICH2 MUTATED    7  5  4  1
  QRICH2 WILD-TYPE 60 35 39  8
D64V4, multiclass
    clus
vv   QRICH2 MUTATED QRICH2 WILD-TYPE
  T1              7               60
  T2              5               35
  T3              4               39
  T4              1                8
[1] 4 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
  QRICH2 MUTATED   11  0
  QRICH2 WILD-TYPE 90  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH2 MUTATED     11    0
  QRICH2 WILD-TYPE   90    3
   clus
vv  QRICH2 MUTATED QRICH2 WILD-TYPE
  0             11               90
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  QRICH2 MUTATED    13   0   4
  QRICH2 WILD-TYPE 109   3  31
D64V6, multiclass
    clus
vv   QRICH2 MUTATED QRICH2 WILD-TYPE
  M0             13              109
  M1              0                3
  MX              4               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                  cls
clus                0  1
  QRICH2 MUTATED    2 15
  QRICH2 WILD-TYPE 59 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH2 MUTATED      2   15
  QRICH2 WILD-TYPE   59   84
        clus
vv       QRICH2 MUTATED QRICH2 WILD-TYPE
  FEMALE              2               59
  MALE               15               84
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  QRICH2 MUTATED                         0                       17
  QRICH2 WILD-TYPE                       1                      140
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  QRICH2 MUTATED                                  0
  QRICH2 WILD-TYPE                                2
D64V8, multiclass
                                  clus
vv                                 QRICH2 MUTATED QRICH2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     17              140
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  QRICH2 MUTATED    15   1   0   0
  QRICH2 WILD-TYPE 117   9   1  12
D64V9, multiclass
    clus
vv   QRICH2 MUTATED QRICH2 WILD-TYPE
  R0             15              117
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  QRICH2 MUTATED                                  1     5
  QRICH2 WILD-TYPE                                0    32
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  QRICH2 MUTATED                           2     8
  QRICH2 WILD-TYPE                         6   100
D64V10, multiclass
                                  clus
vv                                 QRICH2 MUTATED QRICH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         5               32
  BLACK OR AFRICAN AMERICAN                     2                6
  WHITE                                         8              100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, binary
                  cls
clus                 0   1
  QRICH2 MUTATED     0  16
  QRICH2 WILD-TYPE   4 127
[1] "tbl2"
                  cls
clus               [,1] [,2]
  QRICH2 MUTATED      0   16
  QRICH2 WILD-TYPE    4  127
                        clus
vv                       QRICH2 MUTATED QRICH2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             16              127
[1] 2 2
[1] FALSE

Clustering(65) Variable = PLAU MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  PLAU MUTATED    2  4
  PLAU WILD-TYPE 88 62
  PLAU MUTATED PLAU WILD-TYPE 
             6            150 
  PLAU MUTATED PLAU WILD-TYPE 
             4             62 
$`PLAU MUTATED`
TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-G3-A25V TCGA-G3-A3CJ 
       45.11        25.81        11.74        10.98        28.27        19.53 

$`PLAU WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       19.99         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  PLAU MUTATED PLAU WILD-TYPE 
         10.98           0.03 
  PLAU MUTATED PLAU WILD-TYPE 
         45.11         113.00 
  PLAU MUTATED PLAU WILD-TYPE 
         22.67          13.81 
[1] "11.0 - 45.1 (22.7)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1.6"
D65V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PLAU MUTATED         4        1         0          1          0          0
  PLAU WILD-TYPE      60       35         2         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PLAU MUTATED          0         0         0
  PLAU WILD-TYPE        1         1         2
D65V3, multiclass
            clus
vv           PLAU MUTATED PLAU WILD-TYPE
  STAGE I               4             60
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PLAU MUTATED    4  1  1  0
  PLAU WILD-TYPE 63 39 42  9
D65V4, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  T1            4             63
  T2            1             39
  T3            1             42
  T4            0              9
[1] 4 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
  PLAU MUTATED    3  0
  PLAU WILD-TYPE 98  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      3    0
  PLAU WILD-TYPE   98    3
   clus
vv  PLAU MUTATED PLAU WILD-TYPE
  0            3             98
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  PLAU MUTATED     4   0   2
  PLAU WILD-TYPE 118   3  33
D65V6, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  M0            4            118
  M1            0              3
  MX            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                cls
clus              0  1
  PLAU MUTATED    2  4
  PLAU WILD-TYPE 59 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      2    4
  PLAU WILD-TYPE   59   95
        clus
vv       PLAU MUTATED PLAU WILD-TYPE
  FEMALE            2             59
  MALE              4             95
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PLAU MUTATED                         0                        6
  PLAU WILD-TYPE                       1                      151
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PLAU MUTATED                                  0
  PLAU WILD-TYPE                                2
D65V8, multiclass
                                  clus
vv                                 PLAU MUTATED PLAU WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    6            151
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLAU MUTATED     6   0   0   0
  PLAU WILD-TYPE 126  10   1  12
D65V9, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  R0            6            126
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLAU MUTATED                                  1     0
  PLAU WILD-TYPE                                0    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLAU MUTATED                           0     5
  PLAU WILD-TYPE                         8   103
D65V10, multiclass
                                  clus
vv                                 PLAU MUTATED PLAU WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       5            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, binary
                cls
clus               0   1
  PLAU MUTATED     0   6
  PLAU WILD-TYPE   4 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      0    6
  PLAU WILD-TYPE    4  137
                        clus
vv                       PLAU MUTATED PLAU WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            6            137
[1] 2 2
[1] FALSE

Clustering(66) Variable = MAPKAPK2 MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  MAPKAPK2 MUTATED    3  1
  MAPKAPK2 WILD-TYPE 87 65
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
                 4                152 
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
                 1                 65 
$`MAPKAPK2 MUTATED`
TCGA-DD-A4NV TCGA-DD-A73B TCGA-ED-A66Y TCGA-EP-A26S 
       66.35         9.30         0.23        19.99 

$`MAPKAPK2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A 
       73.81        93.67        12.26         0.30        80.75        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        18.74        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
              0.23               0.03 
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
             66.35             113.00 
  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE 
            14.645             13.875 
[1] "0.2 - 66.3 (14.6)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.6"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  MAPKAPK2 MUTATED         2        0         0          2          0
  MAPKAPK2 WILD-TYPE      62       36         2         30          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  MAPKAPK2 MUTATED            0        0         0         0
  MAPKAPK2 WILD-TYPE          6        1         1         2
D66V3, multiclass
            clus
vv           MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  STAGE I                   2                 62
  STAGE II                  0                 36
  STAGE III                 0                  2
  STAGE IIIA                2                 30
  STAGE IIIB                0                  5
  STAGE IIIC                0                  6
  STAGE IV                  0                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  MAPKAPK2 MUTATED    2  0  2  0
  MAPKAPK2 WILD-TYPE 65 40 41  9
D66V4, multiclass
    clus
vv   MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  T1                2                 65
  T2                0                 40
  T3                2                 41
  T4                0                  9
[1] 4 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
  MAPKAPK2 MUTATED    4  0
  MAPKAPK2 WILD-TYPE 97  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MAPKAPK2 MUTATED      4    0
  MAPKAPK2 WILD-TYPE   97    3
   clus
vv  MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  0                4                 97
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  MAPKAPK2 MUTATED     3   0   1
  MAPKAPK2 WILD-TYPE 119   3  34
D66V6, multiclass
    clus
vv   MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  M0                3                119
  M1                0                  3
  MX                1                 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"
D66V7, binary
                    cls
clus                  0  1
  MAPKAPK2 MUTATED    2  2
  MAPKAPK2 WILD-TYPE 59 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MAPKAPK2 MUTATED      2    2
  MAPKAPK2 WILD-TYPE   59   97
        clus
vv       MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  FEMALE                2                 59
  MALE                  2                 97
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MAPKAPK2 MUTATED                         0                        4
  MAPKAPK2 WILD-TYPE                       1                      153
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  MAPKAPK2 MUTATED                                  0
  MAPKAPK2 WILD-TYPE                                2
D66V8, multiclass
                                  clus
vv                                 MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                        4                153
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  MAPKAPK2 MUTATED     3   0   0   0
  MAPKAPK2 WILD-TYPE 129  10   1  12
D66V9, multiclass
    clus
vv   MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  R0                3                129
  R1                0                 10
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPKAPK2 MUTATED                                  0     1
  MAPKAPK2 WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  MAPKAPK2 MUTATED                           0     3
  MAPKAPK2 WILD-TYPE                         8   105
D66V10, multiclass
                                  clus
vv                                 MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 36
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           3                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, binary
                    cls
clus                   0   1
  MAPKAPK2 MUTATED     1   3
  MAPKAPK2 WILD-TYPE   3 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MAPKAPK2 MUTATED      1    3
  MAPKAPK2 WILD-TYPE    3  140
                        clus
vv                       MAPKAPK2 MUTATED MAPKAPK2 WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                3                140
[1] 2 2
[1] FALSE

Clustering(67) Variable = NAP1L1 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2               0  1
  NAP1L1 MUTATED    1  4
  NAP1L1 WILD-TYPE 89 62
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               5              151 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               4               62 
$`NAP1L1 MUTATED`
TCGA-DD-A116 TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A25W 
       53.33        45.11         5.62        25.81        30.74 

$`NAP1L1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
            5.62             0.03 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
           53.33           113.00 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
           30.74            13.78 
[1] "5.6 - 53.3 (30.7)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.4"
D67V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NAP1L1 MUTATED         3        0         0          1          1          0
  NAP1L1 WILD-TYPE      61       36         2         31          4          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  NAP1L1 MUTATED          0         0         0
  NAP1L1 WILD-TYPE        1         1         2
D67V3, multiclass
            clus
vv           NAP1L1 MUTATED NAP1L1 WILD-TYPE
  STAGE I                 3               61
  STAGE II                0               36
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              1                4
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  NAP1L1 MUTATED    3  0  2  0
  NAP1L1 WILD-TYPE 64 40 41  9
D67V4, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  T1              3               64
  T2              0               40
  T3              2               41
  T4              0                9
[1] 4 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
  NAP1L1 MUTATED    3  0
  NAP1L1 WILD-TYPE 98  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      3    0
  NAP1L1 WILD-TYPE   98    3
   clus
vv  NAP1L1 MUTATED NAP1L1 WILD-TYPE
  0              3               98
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  NAP1L1 MUTATED     5   0   0
  NAP1L1 WILD-TYPE 117   3  35
D67V6, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  M0              5              117
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                  cls
clus                0  1
  NAP1L1 MUTATED    1  4
  NAP1L1 WILD-TYPE 60 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      1    4
  NAP1L1 WILD-TYPE   60   95
        clus
vv       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  FEMALE              1               60
  MALE                4               95
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NAP1L1 MUTATED                         0                        5
  NAP1L1 WILD-TYPE                       1                      152
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  NAP1L1 MUTATED                                  0
  NAP1L1 WILD-TYPE                                2
D67V8, multiclass
                                  clus
vv                                 NAP1L1 MUTATED NAP1L1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      5              152
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NAP1L1 MUTATED     5   0   0   0
  NAP1L1 WILD-TYPE 127  10   1  12
D67V9, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  R0              5              127
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L1 MUTATED                                  0     2
  NAP1L1 WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L1 MUTATED                           0     3
  NAP1L1 WILD-TYPE                         8   105
D67V10, multiclass
                                  clus
vv                                 NAP1L1 MUTATED NAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     0   5
  NAP1L1 WILD-TYPE   4 138
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      0    5
  NAP1L1 WILD-TYPE    4  138
                        clus
vv                       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              138
[1] 2 2
[1] FALSE

Clustering(68) Variable = FAM118A MUTATION ANALYSIS
D68V1, survival
                   sevent
clus2                0  1
  FAM118A MUTATED    1  3
  FAM118A WILD-TYPE 89 63
  FAM118A MUTATED FAM118A WILD-TYPE 
                4               152 
  FAM118A MUTATED FAM118A WILD-TYPE 
                3                63 
$`FAM118A MUTATED`
TCGA-BC-A10S TCGA-CC-5261 TCGA-DD-A1ED TCGA-FV-A23B 
       46.78         0.39        75.65        32.45 

$`FAM118A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         0.16         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  FAM118A MUTATED FAM118A WILD-TYPE 
             0.39              0.03 
  FAM118A MUTATED FAM118A WILD-TYPE 
            75.65            113.00 
  FAM118A MUTATED FAM118A WILD-TYPE 
           39.615            13.810 
[1] "0.4 - 75.7 (39.6)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D68V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM118A MUTATED         1        2         0          0          0          0
  FAM118A WILD-TYPE      63       34         2         32          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  FAM118A MUTATED          0         0         0
  FAM118A WILD-TYPE        1         1         2
D68V3, multiclass
            clus
vv           FAM118A MUTATED FAM118A WILD-TYPE
  STAGE I                  1                63
  STAGE II                 2                34
  STAGE III                0                 2
  STAGE IIIA               0                32
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  FAM118A MUTATED    1  2  1  0
  FAM118A WILD-TYPE 66 38 42  9
D68V4, multiclass
    clus
vv   FAM118A MUTATED FAM118A WILD-TYPE
  T1               1                66
  T2               2                38
  T3               1                42
  T4               0                 9
[1] 4 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
  FAM118A MUTATED    3  0
  FAM118A WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM118A MUTATED      3    0
  FAM118A WILD-TYPE   98    3
   clus
vv  FAM118A MUTATED FAM118A WILD-TYPE
  0               3                98
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  FAM118A MUTATED     3   0   1
  FAM118A WILD-TYPE 119   3  34
D68V6, multiclass
    clus
vv   FAM118A MUTATED FAM118A WILD-TYPE
  M0               3               119
  M1               0                 3
  MX               1                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"
D68V7, binary
                   cls
clus                 0  1
  FAM118A MUTATED    1  3
  FAM118A WILD-TYPE 60 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM118A MUTATED      1    3
  FAM118A WILD-TYPE   60   96
        clus
vv       FAM118A MUTATED FAM118A WILD-TYPE
  FEMALE               1                60
  MALE                 3                96
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FAM118A MUTATED                         0                        4
  FAM118A WILD-TYPE                       1                      153
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  FAM118A MUTATED                                  0
  FAM118A WILD-TYPE                                2
D68V8, multiclass
                                  clus
vv                                 FAM118A MUTATED FAM118A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       4               153
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM118A MUTATED     3   0   0   1
  FAM118A WILD-TYPE 129  10   1  11
D68V9, multiclass
    clus
vv   FAM118A MUTATED FAM118A WILD-TYPE
  R0               3               129
  R1               0                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM118A MUTATED                                  0     1
  FAM118A WILD-TYPE                                1    36
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM118A MUTATED                           0     3
  FAM118A WILD-TYPE                         8   105
D68V10, multiclass
                                  clus
vv                                 FAM118A MUTATED FAM118A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                36
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          3               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, binary
                   cls
clus                  0   1
  FAM118A MUTATED     0   4
  FAM118A WILD-TYPE   4 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM118A MUTATED      0    4
  FAM118A WILD-TYPE    4  139
                        clus
vv                       FAM118A MUTATED FAM118A WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               4               139
[1] 2 2
[1] FALSE

Clustering(69) Variable = SLC7A6OS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  SLC7A6OS MUTATED    0  4
  SLC7A6OS WILD-TYPE 90 62
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
                 4                152 
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
                 4                 62 
$`SLC7A6OS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-DD-A39Y TCGA-DD-A4NQ 
       46.78         2.99         5.62        12.26 

$`SLC7A6OS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
        0.26        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR 
       39.78        56.25        29.56        73.81        93.67         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
              2.99               0.03 
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
             46.78             113.00 
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
              8.94              13.99 
[1] "3.0 - 46.8 (8.9)"   "0.0 - 113.0 (14.0)"
[1] "hr=" "3.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  SLC7A6OS MUTATED         1        1         0          0          0
  SLC7A6OS WILD-TYPE      63       35         2         32          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  SLC7A6OS MUTATED            0        0         0         0
  SLC7A6OS WILD-TYPE          6        1         1         2
D69V3, multiclass
[1] "Remove cluster labels:" "SLC7A6OS MUTATED"      
clus
  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE 
                 2                147 
        TCGA-BC-4073         TCGA-BC-A10X         TCGA-BC-A10Z 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-BC-A5W4         TCGA-BC-A69H 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-BC-A69I         TCGA-BW-A5NQ         TCGA-CC-5258 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-CC-5259         TCGA-CC-5260         TCGA-CC-5261 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-5264 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-CC-A123         TCGA-CC-A1HT         TCGA-CC-A3M9 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A1EF         TCGA-DD-A1EG         TCGA-DD-A1EH 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EK 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39V         TCGA-DD-A39X 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A39Z         TCGA-DD-A3A0         TCGA-DD-A3A1 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A3A2         TCGA-DD-A3A3         TCGA-DD-A3A4 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A3A5         TCGA-DD-A3A6         TCGA-DD-A3A7 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A3A8         TCGA-DD-A3A9         TCGA-DD-A4NA 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NB         TCGA-DD-A4ND         TCGA-DD-A4NE 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NF         TCGA-DD-A4NG         TCGA-DD-A4NH 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NI         TCGA-DD-A4NJ         TCGA-DD-A4NK 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NL         TCGA-DD-A4NN         TCGA-DD-A4NO 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NP         TCGA-DD-A4NR         TCGA-DD-A4NS 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A4NV         TCGA-DD-A73A         TCGA-DD-A73B 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A73C         TCGA-DD-A73D         TCGA-DD-A73E 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-DD-A73F         TCGA-DD-A73G         TCGA-ED-A459 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-ED-A4XI         TCGA-ED-A5KG         TCGA-ED-A627 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-ED-A66X         TCGA-ED-A66Y         TCGA-ED-A7PX 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-ED-A7PY         TCGA-ED-A7PZ         TCGA-ED-A7XO 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-ED-A7XP         TCGA-ED-A82E         TCGA-EP-A12J 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-EP-A3RK 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-FV-A2QQ         TCGA-FV-A2QR         TCGA-FV-A3I0 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-FV-A3I1         TCGA-FV-A3R2         TCGA-FV-A3R3 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-FV-A495         TCGA-FV-A496         TCGA-FV-A4ZP 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-FV-A4ZQ         TCGA-G3-A25S         TCGA-G3-A25T 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A3CK         TCGA-G3-A5SI         TCGA-G3-A5SJ 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A5SK         TCGA-G3-A5SL         TCGA-G3-A5SM 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-G3-A6UC         TCGA-G3-A7M7         TCGA-G3-A7M9 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-GJ-A6C0         TCGA-HP-A5MZ         TCGA-K7-A6G5 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-KR-A7K0         TCGA-KR-A7K2         TCGA-KR-A7K7 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-LG-A6GG         TCGA-MI-A75C         TCGA-MI-A75E 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
        TCGA-MI-A75G         TCGA-NI-A4U2         TCGA-O8-A75V 
"SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" "SLC7A6OS WILD-TYPE" 
                    vv
clus                 T1 T2 T3 T4
  SLC7A6OS MUTATED    1  1  1  1
  SLC7A6OS WILD-TYPE 66 39 42  8
D69V4, multiclass
    clus
vv   SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  T1                1                 66
  T2                1                 39
  T3                1                 42
  T4                1                  8
[1] 4 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
  SLC7A6OS MUTATED     1   0
  SLC7A6OS WILD-TYPE 100   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC7A6OS MUTATED      1    0
  SLC7A6OS WILD-TYPE  100    3
   clus
vv  SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  0                1                100
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  SLC7A6OS MUTATED     2   0   2
  SLC7A6OS WILD-TYPE 120   3  33
D69V6, multiclass
    clus
vv   SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  M0                2                120
  M1                0                  3
  MX                2                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                  0  1
  SLC7A6OS MUTATED    0  4
  SLC7A6OS WILD-TYPE 61 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC7A6OS MUTATED      0    4
  SLC7A6OS WILD-TYPE   61   95
        clus
vv       SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  FEMALE                0                 61
  MALE                  4                 95
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SLC7A6OS MUTATED                         0                        4
  SLC7A6OS WILD-TYPE                       1                      153
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  SLC7A6OS MUTATED                                  0
  SLC7A6OS WILD-TYPE                                2
D69V8, multiclass
                                  clus
vv                                 SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                        4                153
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC7A6OS MUTATED     3   1   0   0
  SLC7A6OS WILD-TYPE 129   9   1  12
D69V9, multiclass
    clus
vv   SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  R0                3                129
  R1                1                  9
  R2                0                  1
  RX                0                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC7A6OS MUTATED                                  0     2
  SLC7A6OS WILD-TYPE                                1    35
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC7A6OS MUTATED                           0     2
  SLC7A6OS WILD-TYPE                         8   106
D69V10, multiclass
                                  clus
vv                                 SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                 35
  BLACK OR AFRICAN AMERICAN                       0                  8
  WHITE                                           2                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, binary
                    cls
clus                   0   1
  SLC7A6OS MUTATED     1   3
  SLC7A6OS WILD-TYPE   3 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC7A6OS MUTATED      1    3
  SLC7A6OS WILD-TYPE    3  140
                        clus
vv                       SLC7A6OS MUTATED SLC7A6OS WILD-TYPE
  HISPANIC OR LATINO                    1                  3
  NOT HISPANIC OR LATINO                3                140
[1] 2 2
[1] FALSE

Clustering(70) Variable = NBPF10 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2               0  1
  NBPF10 MUTATED    7  2
  NBPF10 WILD-TYPE 83 64
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               9              147 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               2               64 
$`NBPF10 MUTATED`
TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A69H TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
        5.03         0.26        14.60        66.31        75.65        49.15 
TCGA-ED-A4XI TCGA-EP-A12J TCGA-EP-A2KA 
       12.69        18.74        11.74 

$`NBPF10 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 
       13.84        22.36         9.50        12.72         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
       51.29        90.71        79.40        19.79        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
      100.96        13.41        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            0.26             0.03 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           75.65           113.00 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           14.60            13.84 
[1] "0.3 - 75.7 (14.6)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.2"
D70V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NBPF10 MUTATED         4        2         1          1          0          0
  NBPF10 WILD-TYPE      60       34         1         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  NBPF10 MUTATED          0         0         0
  NBPF10 WILD-TYPE        1         1         2
D70V3, multiclass
            clus
vv           NBPF10 MUTATED NBPF10 WILD-TYPE
  STAGE I                 4               60
  STAGE II                2               34
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of 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    4  2  3  0
  NBPF10 WILD-TYPE 63 38 40  9
D70V4, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  T1              4               63
  T2              2               38
  T3              3               40
  T4              0                9
[1] 4 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
  NBPF10 MUTATED    4  0
  NBPF10 WILD-TYPE 97  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      4    0
  NBPF10 WILD-TYPE   97    3
   clus
vv  NBPF10 MUTATED NBPF10 WILD-TYPE
  0              4               97
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  NBPF10 MUTATED     6   0   3
  NBPF10 WILD-TYPE 116   3  32
D70V6, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  M0              6              116
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                  cls
clus                0  1
  NBPF10 MUTATED    3  6
  NBPF10 WILD-TYPE 58 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      3    6
  NBPF10 WILD-TYPE   58   93
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  FEMALE              3               58
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NBPF10 MUTATED                         0                        9
  NBPF10 WILD-TYPE                       1                      148
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  NBPF10 MUTATED                                  0
  NBPF10 WILD-TYPE                                2
D70V8, multiclass
                                  clus
vv                                 NBPF10 MUTATED NBPF10 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      9              148
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NBPF10 MUTATED     9   0   0   0
  NBPF10 WILD-TYPE 123  10   1  12
D70V9, multiclass
    clus
vv   NBPF10 MUTATED NBPF10 WILD-TYPE
  R0              9              123
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF10 MUTATED                                  0     1
  NBPF10 WILD-TYPE                                1    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED                           1     6
  NBPF10 WILD-TYPE                         7   102
D70V10, multiclass
                                  clus
vv                                 NBPF10 MUTATED NBPF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         6              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, binary
                  cls
clus                 0   1
  NBPF10 MUTATED     0   7
  NBPF10 WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      0    7
  NBPF10 WILD-TYPE    4  136
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(71) Variable = ZXDC MUTATION ANALYSIS
D71V1, survival
                sevent
clus2             0  1
  ZXDC MUTATED    5  1
  ZXDC WILD-TYPE 85 65
  ZXDC MUTATED ZXDC WILD-TYPE 
             6            150 
  ZXDC MUTATED ZXDC WILD-TYPE 
             1             65 
$`ZXDC MUTATED`
TCGA-BC-A10S TCGA-BC-A69I TCGA-DD-A73E TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75G 
       46.78        12.72         1.45         0.49         9.57        14.24 

$`ZXDC WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       13.84         0.26        22.36         9.50        14.60         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
        7.56        10.98        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       13.38         5.10        12.85         8.71        58.88         4.44 

  ZXDC MUTATED ZXDC WILD-TYPE 
          0.49           0.03 
  ZXDC MUTATED ZXDC WILD-TYPE 
         46.78         113.00 
  ZXDC MUTATED ZXDC WILD-TYPE 
        11.145         13.990 
[1] "0.5 - 46.8 (11.1)"  "0.0 - 113.0 (14.0)"
[1] "hr=" "1.6"
D71V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZXDC MUTATED         3        2         0          0          0          0
  ZXDC WILD-TYPE      61       34         2         32          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  ZXDC MUTATED          0         0         0
  ZXDC WILD-TYPE        1         1         2
D71V3, multiclass
            clus
vv           ZXDC MUTATED ZXDC WILD-TYPE
  STAGE I               3             61
  STAGE II              2             34
  STAGE III             0              2
  STAGE IIIA            0             32
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  ZXDC MUTATED    3  2  1  0
  ZXDC WILD-TYPE 64 38 42  9
D71V4, multiclass
    clus
vv   ZXDC MUTATED ZXDC WILD-TYPE
  T1            3             64
  T2            2             38
  T3            1             42
  T4            0              9
[1] 4 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
  ZXDC MUTATED    4  0
  ZXDC WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZXDC MUTATED      4    0
  ZXDC WILD-TYPE   97    3
   clus
vv  ZXDC MUTATED ZXDC WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  ZXDC MUTATED     5   0   1
  ZXDC WILD-TYPE 117   3  34
D71V6, multiclass
    clus
vv   ZXDC MUTATED ZXDC WILD-TYPE
  M0            5            117
  M1            0              3
  MX            1             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"
D71V7, binary
                cls
clus              0  1
  ZXDC MUTATED    1  5
  ZXDC WILD-TYPE 60 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZXDC MUTATED      1    5
  ZXDC WILD-TYPE   60   94
        clus
vv       ZXDC MUTATED ZXDC WILD-TYPE
  FEMALE            1             60
  MALE              5             94
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ZXDC MUTATED                         0                        6
  ZXDC WILD-TYPE                       1                      151
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  ZXDC MUTATED                                  0
  ZXDC WILD-TYPE                                2
D71V8, multiclass
                                  clus
vv                                 ZXDC MUTATED ZXDC WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    6            151
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZXDC MUTATED     6   0   0   0
  ZXDC WILD-TYPE 126  10   1  12
D71V9, multiclass
    clus
vv   ZXDC MUTATED ZXDC WILD-TYPE
  R0            6            126
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZXDC MUTATED                                  0     0
  ZXDC WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZXDC MUTATED                           0     6
  ZXDC WILD-TYPE                         8   102
D71V10, multiclass
                                  clus
vv                                 ZXDC MUTATED ZXDC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       6            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, binary
                cls
clus               0   1
  ZXDC MUTATED     0   5
  ZXDC WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZXDC MUTATED      0    5
  ZXDC WILD-TYPE    4  138
                        clus
vv                       ZXDC MUTATED ZXDC WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(72) Variable = TAS2R30 MUTATION ANALYSIS
D72V1, survival
                   sevent
clus2                0  1
  TAS2R30 MUTATED    6  2
  TAS2R30 WILD-TYPE 84 64
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
                8               148 
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
                2                64 
$`TAS2R30 MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A3A3 
       46.78        13.84         0.07        75.65        49.15        17.59 
TCGA-FV-A495 TCGA-G3-A25T 
        0.03        51.06 

$`TAS2R30 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5259 
        0.26        22.36         9.50        14.60        12.72         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF 
       51.29        90.71        79.40        66.31        19.79        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         6.38         0.13         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
             0.03              0.07 
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
            75.65            113.00 
  TAS2R30 MUTATED TAS2R30 WILD-TYPE 
           32.185            13.710 
[1] "0.0 - 75.7 (32.2)"  "0.1 - 113.0 (13.7)"
[1] "hr=" "2.2"
D72V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TAS2R30 MUTATED         2        3         1          1          0          0
  TAS2R30 WILD-TYPE      62       33         1         31          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  TAS2R30 MUTATED          0         0         0
  TAS2R30 WILD-TYPE        1         1         2
D72V3, multiclass
            clus
vv           TAS2R30 MUTATED TAS2R30 WILD-TYPE
  STAGE I                  2                62
  STAGE II                 3                33
  STAGE III                1                 1
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  TAS2R30 MUTATED    2  3  3  0
  TAS2R30 WILD-TYPE 65 37 40  9
D72V4, multiclass
    clus
vv   TAS2R30 MUTATED TAS2R30 WILD-TYPE
  T1               2                65
  T2               3                37
  T3               3                40
  T4               0                 9
[1] 4 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
  TAS2R30 MUTATED    5  0
  TAS2R30 WILD-TYPE 96  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R30 MUTATED      5    0
  TAS2R30 WILD-TYPE   96    3
   clus
vv  TAS2R30 MUTATED TAS2R30 WILD-TYPE
  0               5                96
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  TAS2R30 MUTATED     7   0   1
  TAS2R30 WILD-TYPE 115   3  34
D72V6, multiclass
    clus
vv   TAS2R30 MUTATED TAS2R30 WILD-TYPE
  M0               7               115
  M1               0                 3
  MX               1                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"
D72V7, binary
                   cls
clus                 0  1
  TAS2R30 MUTATED    3  5
  TAS2R30 WILD-TYPE 58 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R30 MUTATED      3    5
  TAS2R30 WILD-TYPE   58   94
        clus
vv       TAS2R30 MUTATED TAS2R30 WILD-TYPE
  FEMALE               3                58
  MALE                 5                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TAS2R30 MUTATED                         0                        8
  TAS2R30 WILD-TYPE                       1                      149
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  TAS2R30 MUTATED                                  0
  TAS2R30 WILD-TYPE                                2
D72V8, multiclass
                                  clus
vv                                 TAS2R30 MUTATED TAS2R30 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       8               149
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TAS2R30 MUTATED     7   0   0   1
  TAS2R30 WILD-TYPE 125  10   1  11
D72V9, multiclass
    clus
vv   TAS2R30 MUTATED TAS2R30 WILD-TYPE
  R0               7               125
  R1               0                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAS2R30 MUTATED                                  0     2
  TAS2R30 WILD-TYPE                                1    35
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TAS2R30 MUTATED                           0     6
  TAS2R30 WILD-TYPE                         8   102
D72V10, multiclass
                                  clus
vv                                 TAS2R30 MUTATED TAS2R30 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                35
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          6               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, binary
                   cls
clus                  0   1
  TAS2R30 MUTATED     0   7
  TAS2R30 WILD-TYPE   4 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAS2R30 MUTATED      0    7
  TAS2R30 WILD-TYPE    4  136
                        clus
vv                       TAS2R30 MUTATED TAS2R30 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               136
[1] 2 2
[1] FALSE

Clustering(73) Variable = KRTAP10-2 MUTATION ANALYSIS
D73V1, survival
                     sevent
clus2                  0  1
  KRTAP10-2 MUTATED    3  3
  KRTAP10-2 WILD-TYPE 87 63
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
                  6                 150 
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
                  3                  63 
$`KRTAP10-2 MUTATED`
TCGA-BC-A3KF TCGA-DD-A1ED TCGA-DD-A1EG TCGA-FV-A23B TCGA-G3-A3CJ TCGA-G3-A7M9 
        0.26        75.65        45.11        32.45        19.53         1.84 

$`KRTAP10-2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.99         4.37         7.76         5.98         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
               0.26                0.03 
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
              75.65              113.00 
  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE 
              25.99               13.81 
[1] "0.3 - 75.7 (26.0)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1"  
D73V2, continuous
                     vv
clus                  STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  KRTAP10-2 MUTATED         3        2         0          0          1
  KRTAP10-2 WILD-TYPE      61       34         2         32          4
                     vv
clus                  STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  KRTAP10-2 MUTATED            0        0         0         0
  KRTAP10-2 WILD-TYPE          6        1         1         2
D73V3, multiclass
            clus
vv           KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  STAGE I                    3                  61
  STAGE II                   2                  34
  STAGE III                  0                   2
  STAGE IIIA                 0                  32
  STAGE IIIB                 1                   4
  STAGE IIIC                 0                   6
  STAGE IV                   0                   1
  STAGE IVA                  0                   1
  STAGE IVB                  0                   2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3 T4
  KRTAP10-2 MUTATED    3  2  1  0
  KRTAP10-2 WILD-TYPE 64 38 42  9
D73V4, multiclass
    clus
vv   KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  T1                 3                  64
  T2                 2                  38
  T3                 1                  42
  T4                 0                   9
[1] 4 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
  KRTAP10-2 MUTATED    4  0
  KRTAP10-2 WILD-TYPE 97  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-2 MUTATED      4    0
  KRTAP10-2 WILD-TYPE   97    3
   clus
vv  KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  0                 4                  97
  1                 0                   3
[1] 2 2
[1] FALSE
                     vv
clus                   M0  M1  MX
  KRTAP10-2 MUTATED     5   0   1
  KRTAP10-2 WILD-TYPE 117   3  34
D73V6, multiclass
    clus
vv   KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  M0                 5                 117
  M1                 0                   3
  MX                 1                  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"
D73V7, binary
                     cls
clus                   0  1
  KRTAP10-2 MUTATED    2  4
  KRTAP10-2 WILD-TYPE 59 95
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-2 MUTATED      2    4
  KRTAP10-2 WILD-TYPE   59   95
        clus
vv       KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  FEMALE                 2                  59
  MALE                   4                  95
[1] 2 2
[1] FALSE
                     vv
clus                  FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRTAP10-2 MUTATED                         0                        6
  KRTAP10-2 WILD-TYPE                       1                      151
                     vv
clus                  HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRTAP10-2 MUTATED                                  0
  KRTAP10-2 WILD-TYPE                                2
D73V8, multiclass
                                  clus
vv                                 KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                          0                   1
  HEPATOCELLULAR CARCINOMA                         6                 151
  HEPATOCHOLANGIOCARCINOMA (MIXED)                 0                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP10-2 MUTATED     6   0   0   0
  KRTAP10-2 WILD-TYPE 126  10   1  12
D73V9, multiclass
    clus
vv   KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  R0                 6                 126
  R1                 0                  10
  R2                 0                   1
  RX                 0                  12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP10-2 MUTATED                                  1     0
  KRTAP10-2 WILD-TYPE                                0    37
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-2 MUTATED                           0     5
  KRTAP10-2 WILD-TYPE                         8   103
D73V10, multiclass
                                  clus
vv                                 KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            0                  37
  BLACK OR AFRICAN AMERICAN                        0                   8
  WHITE                                            5                 103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, binary
                     cls
clus                    0   1
  KRTAP10-2 MUTATED     0   5
  KRTAP10-2 WILD-TYPE   4 138
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-2 MUTATED      0    5
  KRTAP10-2 WILD-TYPE    4  138
                        clus
vv                       KRTAP10-2 MUTATED KRTAP10-2 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 5                 138
[1] 2 2
[1] FALSE

Clustering(74) Variable = PPA2 MUTATION ANALYSIS
D74V1, survival
                sevent
clus2             0  1
  PPA2 MUTATED    4  0
  PPA2 WILD-TYPE 86 66
  PPA2 MUTATED PPA2 WILD-TYPE 
             4            152 
  PPA2 MUTATED PPA2 WILD-TYPE 
             0             66 
$`PPA2 MUTATED`
TCGA-BC-A69I TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1EH 
       12.72         2.60        66.31        49.15 

$`PPA2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  PPA2 MUTATED PPA2 WILD-TYPE 
          2.60           0.03 
  PPA2 MUTATED PPA2 WILD-TYPE 
         66.31         113.00 
  PPA2 MUTATED PPA2 WILD-TYPE 
        30.935         13.875 
[1] "2.6 - 66.3 (30.9)"  "0.0 - 113.0 (13.9)"
[1] "hr="     "2.6e+07"
D74V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PPA2 MUTATED         3        0         1          0          0          0
  PPA2 WILD-TYPE      61       36         1         32          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PPA2 MUTATED          0         0         0
  PPA2 WILD-TYPE        1         1         2
D74V3, multiclass
            clus
vv           PPA2 MUTATED PPA2 WILD-TYPE
  STAGE I               3             61
  STAGE II              0             36
  STAGE III             1              1
  STAGE IIIA            0             32
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PPA2 MUTATED    3  0  1  0
  PPA2 WILD-TYPE 64 40 42  9
D74V4, multiclass
    clus
vv   PPA2 MUTATED PPA2 WILD-TYPE
  T1            3             64
  T2            0             40
  T3            1             42
  T4            0              9
[1] 4 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
  PPA2 MUTATED    4  0
  PPA2 WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPA2 MUTATED      4    0
  PPA2 WILD-TYPE   97    3
   clus
vv  PPA2 MUTATED PPA2 WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  PPA2 MUTATED     4   0   0
  PPA2 WILD-TYPE 118   3  35
D74V6, multiclass
    clus
vv   PPA2 MUTATED PPA2 WILD-TYPE
  M0            4            118
  M1            0              3
  MX            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                cls
clus              0  1
  PPA2 MUTATED    1  3
  PPA2 WILD-TYPE 60 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPA2 MUTATED      1    3
  PPA2 WILD-TYPE   60   96
        clus
vv       PPA2 MUTATED PPA2 WILD-TYPE
  FEMALE            1             60
  MALE              3             96
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PPA2 MUTATED                         0                        4
  PPA2 WILD-TYPE                       1                      153
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PPA2 MUTATED                                  0
  PPA2 WILD-TYPE                                2
D74V8, multiclass
                                  clus
vv                                 PPA2 MUTATED PPA2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    4            153
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PPA2 MUTATED     4   0   0   0
  PPA2 WILD-TYPE 128  10   1  12
D74V9, multiclass
    clus
vv   PPA2 MUTATED PPA2 WILD-TYPE
  R0            4            128
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPA2 MUTATED                                  0     0
  PPA2 WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PPA2 MUTATED                           1     2
  PPA2 WILD-TYPE                         7   106
D74V10, multiclass
                                  clus
vv                                 PPA2 MUTATED PPA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   1              7
  WHITE                                       2            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                cls
clus               0   1
  PPA2 MUTATED     0   2
  PPA2 WILD-TYPE   4 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPA2 MUTATED      0    2
  PPA2 WILD-TYPE    4  141
                        clus
vv                       PPA2 MUTATED PPA2 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            2            141
[1] 2 2
[1] FALSE

Clustering(75) Variable = SEPT2 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2              0  1
  SEPT2 MUTATED    1  4
  SEPT2 WILD-TYPE 89 62
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              5             151 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              4              62 
$`SEPT2 MUTATED`
TCGA-CC-5263 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A3A0 TCGA-G3-A3CJ 
        4.24         7.33        51.29        25.81        19.53 

$`SEPT2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       13.64        21.14        55.69         5.62        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  SEPT2 MUTATED SEPT2 WILD-TYPE 
           4.24            0.03 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          51.29          113.00 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          19.53           13.84 
[1] "4.2 - 51.3 (19.5)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.1"
D75V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SEPT2 MUTATED         2        1         0          2          0          0
  SEPT2 WILD-TYPE      62       35         2         30          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SEPT2 MUTATED          1         0         0
  SEPT2 WILD-TYPE        0         1         2
D75V3, multiclass
            clus
vv           SEPT2 MUTATED SEPT2 WILD-TYPE
  STAGE I                2              62
  STAGE II               1              35
  STAGE III              0               2
  STAGE IIIA             2              30
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               1               0
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  SEPT2 MUTATED    2  1  3  0
  SEPT2 WILD-TYPE 65 39 40  9
D75V4, multiclass
    clus
vv   SEPT2 MUTATED SEPT2 WILD-TYPE
  T1             2              65
  T2             1              39
  T3             3              40
  T4             0               9
[1] 4 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
  SEPT2 MUTATED    5  0
  SEPT2 WILD-TYPE 96  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      5    0
  SEPT2 WILD-TYPE   96    3
   clus
vv  SEPT2 MUTATED SEPT2 WILD-TYPE
  0             5              96
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  SEPT2 MUTATED     5   1   0
  SEPT2 WILD-TYPE 117   2  35
D75V6, multiclass
    clus
vv   SEPT2 MUTATED SEPT2 WILD-TYPE
  M0             5             117
  M1             1               2
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                 cls
clus               0  1
  SEPT2 MUTATED    1  5
  SEPT2 WILD-TYPE 60 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      1    5
  SEPT2 WILD-TYPE   60   94
        clus
vv       SEPT2 MUTATED SEPT2 WILD-TYPE
  FEMALE             1              60
  MALE               5              94
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SEPT2 MUTATED                         0                        6
  SEPT2 WILD-TYPE                       1                      151
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SEPT2 MUTATED                                  0
  SEPT2 WILD-TYPE                                2
D75V8, multiclass
                                  clus
vv                                 SEPT2 MUTATED SEPT2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     6             151
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SEPT2 MUTATED     3   0   1   2
  SEPT2 WILD-TYPE 129  10   0  10
D75V9, multiclass
    clus
vv   SEPT2 MUTATED SEPT2 WILD-TYPE
  R0             3             129
  R1             0              10
  R2             1               0
  RX             2              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEPT2 MUTATED                                  1     3
  SEPT2 WILD-TYPE                                0    34
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SEPT2 MUTATED                           0     2
  SEPT2 WILD-TYPE                         8   106
D75V10, multiclass
                                  clus
vv                                 SEPT2 MUTATED SEPT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        3              34
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        2             106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, binary
                 cls
clus                0   1
  SEPT2 MUTATED     0   6
  SEPT2 WILD-TYPE   4 137
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      0    6
  SEPT2 WILD-TYPE    4  137
                        clus
vv                       SEPT2 MUTATED SEPT2 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             6             137
[1] 2 2
[1] FALSE

Clustering(76) Variable = DRD3 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2             0  1
  DRD3 MUTATED    0  5
  DRD3 WILD-TYPE 90 61
  DRD3 MUTATED DRD3 WILD-TYPE 
             5            151 
  DRD3 MUTATED DRD3 WILD-TYPE 
             5             61 
$`DRD3 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-FV-A2QR TCGA-G3-A25S 
       45.11         5.62        25.81        19.10         1.22 

$`DRD3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       14.40        32.45        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  DRD3 MUTATED DRD3 WILD-TYPE 
          1.22           0.03 
  DRD3 MUTATED DRD3 WILD-TYPE 
         45.11         113.00 
  DRD3 MUTATED DRD3 WILD-TYPE 
         19.10          13.84 
[1] "1.2 - 45.1 (19.1)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.9"
D76V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DRD3 MUTATED         5        0         0          0          0          0
  DRD3 WILD-TYPE      59       36         2         32          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  DRD3 MUTATED          0         0         0
  DRD3 WILD-TYPE        1         1         2
D76V3, multiclass
            clus
vv           DRD3 MUTATED DRD3 WILD-TYPE
  STAGE I               5             59
  STAGE II              0             36
  STAGE III             0              2
  STAGE IIIA            0             32
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  DRD3 MUTATED    5  0  0  0
  DRD3 WILD-TYPE 62 40 43  9
D76V4, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  T1            5             62
  T2            0             40
  T3            0             43
  T4            0              9
[1] 4 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
  DRD3 MUTATED    3  0
  DRD3 WILD-TYPE 98  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      3    0
  DRD3 WILD-TYPE   98    3
   clus
vv  DRD3 MUTATED DRD3 WILD-TYPE
  0            3             98
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  DRD3 MUTATED     5   0   0
  DRD3 WILD-TYPE 117   3  35
D76V6, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  M0            5            117
  M1            0              3
  MX            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                cls
clus              0  1
  DRD3 MUTATED    0  5
  DRD3 WILD-TYPE 61 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      0    5
  DRD3 WILD-TYPE   61   94
        clus
vv       DRD3 MUTATED DRD3 WILD-TYPE
  FEMALE            0             61
  MALE              5             94
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DRD3 MUTATED                         0                        5
  DRD3 WILD-TYPE                       1                      152
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DRD3 MUTATED                                  0
  DRD3 WILD-TYPE                                2
D76V8, multiclass
                                  clus
vv                                 DRD3 MUTATED DRD3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    5            152
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DRD3 MUTATED     3   1   0   1
  DRD3 WILD-TYPE 129   9   1  11
D76V9, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  R0            3            129
  R1            1              9
  R2            0              1
  RX            1             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DRD3 MUTATED                                  0     1
  DRD3 WILD-TYPE                                1    36
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DRD3 MUTATED                           0     4
  DRD3 WILD-TYPE                         8   104
D76V10, multiclass
                                  clus
vv                                 DRD3 MUTATED DRD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             36
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       4            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, binary
                cls
clus               0   1
  DRD3 MUTATED     0   5
  DRD3 WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      0    5
  DRD3 WILD-TYPE    4  138
                        clus
vv                       DRD3 MUTATED DRD3 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(77) Variable = PSRC1 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2              0  1
  PSRC1 MUTATED    1  3
  PSRC1 WILD-TYPE 89 63
  PSRC1 MUTATED PSRC1 WILD-TYPE 
              4             152 
  PSRC1 MUTATED PSRC1 WILD-TYPE 
              3              63 
$`PSRC1 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A25W 
       45.11         5.62        25.81        30.74 

$`PSRC1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       29.16        18.35        13.64        21.14        55.69        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        53.79        28.27        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  PSRC1 MUTATED PSRC1 WILD-TYPE 
           5.62            0.03 
  PSRC1 MUTATED PSRC1 WILD-TYPE 
          45.11          113.00 
  PSRC1 MUTATED PSRC1 WILD-TYPE 
         28.275          13.810 
[1] "5.6 - 45.1 (28.3)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D77V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PSRC1 MUTATED         3        0         0          0          1          0
  PSRC1 WILD-TYPE      61       36         2         32          4          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PSRC1 MUTATED          0         0         0
  PSRC1 WILD-TYPE        1         1         2
D77V3, multiclass
            clus
vv           PSRC1 MUTATED PSRC1 WILD-TYPE
  STAGE I                3              61
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             1               4
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  PSRC1 MUTATED    3  0  1  0
  PSRC1 WILD-TYPE 64 40 42  9
D77V4, multiclass
    clus
vv   PSRC1 MUTATED PSRC1 WILD-TYPE
  T1             3              64
  T2             0              40
  T3             1              42
  T4             0               9
[1] 4 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
  PSRC1 MUTATED    2  0
  PSRC1 WILD-TYPE 99  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSRC1 MUTATED      2    0
  PSRC1 WILD-TYPE   99    3
   clus
vv  PSRC1 MUTATED PSRC1 WILD-TYPE
  0             2              99
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  PSRC1 MUTATED     4   0   0
  PSRC1 WILD-TYPE 118   3  35
D77V6, multiclass
    clus
vv   PSRC1 MUTATED PSRC1 WILD-TYPE
  M0             4             118
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                 cls
clus               0  1
  PSRC1 MUTATED    1  3
  PSRC1 WILD-TYPE 60 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSRC1 MUTATED      1    3
  PSRC1 WILD-TYPE   60   96
        clus
vv       PSRC1 MUTATED PSRC1 WILD-TYPE
  FEMALE             1              60
  MALE               3              96
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PSRC1 MUTATED                         0                        4
  PSRC1 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PSRC1 MUTATED                                  0
  PSRC1 WILD-TYPE                                2
D77V8, multiclass
                                  clus
vv                                 PSRC1 MUTATED PSRC1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSRC1 MUTATED     4   0   0   0
  PSRC1 WILD-TYPE 128  10   1  12
D77V9, multiclass
    clus
vv   PSRC1 MUTATED PSRC1 WILD-TYPE
  R0             4             128
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSRC1 MUTATED                                  0     1
  PSRC1 WILD-TYPE                                1    36
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSRC1 MUTATED                           0     3
  PSRC1 WILD-TYPE                         8   105
D77V10, multiclass
                                  clus
vv                                 PSRC1 MUTATED PSRC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              36
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        3             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, binary
                 cls
clus                0   1
  PSRC1 MUTATED     0   4
  PSRC1 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSRC1 MUTATED      0    4
  PSRC1 WILD-TYPE    4  139
                        clus
vv                       PSRC1 MUTATED PSRC1 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(78) Variable = KRTAP10-9 MUTATION ANALYSIS
D78V1, survival
                     sevent
clus2                  0  1
  KRTAP10-9 MUTATED    3  0
  KRTAP10-9 WILD-TYPE 87 66
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  3                 153 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  0                  66 
$`KRTAP10-9 MUTATED`
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-EP-A12J 
       66.31        75.65        18.74 

$`KRTAP10-9 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        14.07        14.63        14.24        18.44 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       15.06        39.78        56.25        29.56        73.81        93.67 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        66.35        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S 
        0.20         0.20         0.20         0.20         0.20        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
              18.74                0.03 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
              75.65              113.00 
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
              66.31               13.78 
[1] "18.7 - 75.7 (66.3)" "0.0 - 113.0 (13.8)"
[1] "hr="     "2.6e+07"
D78V2, continuous
                     vv
clus                  STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  KRTAP10-9 MUTATED         3        0         0          0          0
  KRTAP10-9 WILD-TYPE      61       36         2         32          5
                     vv
clus                  STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  KRTAP10-9 MUTATED            0        0         0         0
  KRTAP10-9 WILD-TYPE          6        1         1         2
D78V3, multiclass
            clus
vv           KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  STAGE I                    3                  61
  STAGE II                   0                  36
  STAGE III                  0                   2
  STAGE IIIA                 0                  32
  STAGE IIIB                 0                   5
  STAGE IIIC                 0                   6
  STAGE IV                   0                   1
  STAGE IVA                  0                   1
  STAGE IVB                  0                   2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T1 T2 T3 T4
  KRTAP10-9 MUTATED    3  0  0  0
  KRTAP10-9 WILD-TYPE 64 40 43  9
D78V4, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  T1                 3                  64
  T2                 0                  40
  T3                 0                  43
  T4                 0                   9
[1] 4 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
  KRTAP10-9 MUTATED    2  0
  KRTAP10-9 WILD-TYPE 99  3
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      2    0
  KRTAP10-9 WILD-TYPE   99    3
   clus
vv  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  0                 2                  99
  1                 0                   3
[1] 2 2
[1] FALSE
                     vv
clus                   M0  M1  MX
  KRTAP10-9 MUTATED     2   0   1
  KRTAP10-9 WILD-TYPE 120   3  34
D78V6, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  M0                 2                 120
  M1                 0                   3
  MX                 1                  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"
D78V7, binary
                     cls
clus                   0  1
  KRTAP10-9 MUTATED    1  2
  KRTAP10-9 WILD-TYPE 60 97
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      1    2
  KRTAP10-9 WILD-TYPE   60   97
        clus
vv       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  FEMALE                 1                  60
  MALE                   2                  97
[1] 2 2
[1] FALSE
                     vv
clus                  FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRTAP10-9 MUTATED                         0                        3
  KRTAP10-9 WILD-TYPE                       1                      154
                     vv
clus                  HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRTAP10-9 MUTATED                                  0
  KRTAP10-9 WILD-TYPE                                2
D78V8, multiclass
                                  clus
vv                                 KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                          0                   1
  HEPATOCELLULAR CARCINOMA                         3                 154
  HEPATOCHOLANGIOCARCINOMA (MIXED)                 0                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP10-9 MUTATED     3   0   0   0
  KRTAP10-9 WILD-TYPE 129  10   1  12
D78V9, multiclass
    clus
vv   KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  R0                 3                 129
  R1                 0                  10
  R2                 0                   1
  RX                 0                  12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP10-9 MUTATED                                  0     0
  KRTAP10-9 WILD-TYPE                                1    37
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-9 MUTATED                           1     1
  KRTAP10-9 WILD-TYPE                         7   107
D78V10, multiclass
[1] "Remove cluster labels:" "KRTAP10-9 MUTATED"     
clus
  KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE 
                  2                 152 
         TCGA-BC-4073          TCGA-BC-A10Q          TCGA-BC-A10R 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A10S          TCGA-BC-A10T          TCGA-BC-A10U 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A10W          TCGA-BC-A10X          TCGA-BC-A10Y 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A10Z          TCGA-BC-A110          TCGA-BC-A112 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A216          TCGA-BC-A217          TCGA-BC-A3KF 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A3KG          TCGA-BC-A5W4          TCGA-BC-A69H 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-BC-A69I          TCGA-BW-A5NQ          TCGA-CC-5258 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-CC-5259          TCGA-CC-5260          TCGA-CC-5261 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-CC-5262          TCGA-CC-5263          TCGA-CC-5264 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-CC-A123          TCGA-CC-A1HT          TCGA-CC-A3M9 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-CC-A3MA          TCGA-CC-A3MB          TCGA-CC-A3MC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A113          TCGA-DD-A114          TCGA-DD-A115 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A116          TCGA-DD-A118          TCGA-DD-A119 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A11A          TCGA-DD-A11B          TCGA-DD-A11C 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A11D          TCGA-DD-A1E9          TCGA-DD-A1EA 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A1EC          TCGA-DD-A1EF          TCGA-DD-A1EG 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A1EH          TCGA-DD-A1EI          TCGA-DD-A1EJ 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A1EK          TCGA-DD-A1EL          TCGA-DD-A39V 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A39X          TCGA-DD-A39Y          TCGA-DD-A3A0 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A3A2          TCGA-DD-A3A3          TCGA-DD-A3A4 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A3A5          TCGA-DD-A3A6          TCGA-DD-A3A8 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A3A9          TCGA-DD-A4NA          TCGA-DD-A4NB 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4ND          TCGA-DD-A4NE          TCGA-DD-A4NF 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4NG          TCGA-DD-A4NH          TCGA-DD-A4NI 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4NJ          TCGA-DD-A4NK          TCGA-DD-A4NL 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4NN          TCGA-DD-A4NO          TCGA-DD-A4NP 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4NQ          TCGA-DD-A4NR          TCGA-DD-A4NS 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A4NV          TCGA-DD-A73A          TCGA-DD-A73B 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A73C          TCGA-DD-A73D          TCGA-DD-A73E 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-DD-A73F          TCGA-DD-A73G          TCGA-ED-A459 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-ED-A4XI          TCGA-ED-A5KG          TCGA-ED-A627 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-ED-A66X          TCGA-ED-A66Y          TCGA-ED-A7PX 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-ED-A7PY          TCGA-ED-A7PZ          TCGA-ED-A7XO 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-ED-A7XP          TCGA-ED-A82E          TCGA-EP-A26S 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-EP-A2KA          TCGA-EP-A2KB          TCGA-EP-A2KC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-EP-A3JL          TCGA-EP-A3RK          TCGA-ES-A2HS 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-ES-A2HT          TCGA-FV-A23B          TCGA-FV-A2QQ 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-FV-A2QR          TCGA-FV-A3I0          TCGA-FV-A3I1 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-FV-A3R2          TCGA-FV-A3R3          TCGA-FV-A495 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-FV-A496          TCGA-FV-A4ZP          TCGA-FV-A4ZQ 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A25S          TCGA-G3-A25T          TCGA-G3-A25U 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A25V          TCGA-G3-A25W          TCGA-G3-A25Y 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A25Z          TCGA-G3-A3CG          TCGA-G3-A3CH 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A3CI          TCGA-G3-A3CJ          TCGA-G3-A3CK 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A5SI          TCGA-G3-A5SJ          TCGA-G3-A5SK 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A5SL          TCGA-G3-A5SM          TCGA-G3-A6UC 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-G3-A7M7          TCGA-G3-A7M9          TCGA-GJ-A6C0 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-K7-A6G5          TCGA-KR-A7K0          TCGA-KR-A7K2 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-KR-A7K7          TCGA-LG-A6GG          TCGA-MI-A75C 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-MI-A75E          TCGA-MI-A75G          TCGA-MI-A75H 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
         TCGA-MI-A75I          TCGA-NI-A4U2 
"KRTAP10-9 WILD-TYPE" "KRTAP10-9 WILD-TYPE" 
D78V11, binary
                     cls
clus                    0   1
  KRTAP10-9 MUTATED     0   2
  KRTAP10-9 WILD-TYPE   4 141
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP10-9 MUTATED      0    2
  KRTAP10-9 WILD-TYPE    4  141
                        clus
vv                       KRTAP10-9 MUTATED KRTAP10-9 WILD-TYPE
  HISPANIC OR LATINO                     0                   4
  NOT HISPANIC OR LATINO                 2                 141
[1] 2 2
[1] FALSE

Clustering(79) Variable = SPATA12 MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                0  1
  SPATA12 MUTATED    4  2
  SPATA12 WILD-TYPE 86 64
  SPATA12 MUTATED SPATA12 WILD-TYPE 
                6               150 
  SPATA12 MUTATED SPATA12 WILD-TYPE 
                2                64 
$`SPATA12 MUTATED`
TCGA-CC-5262 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EH TCGA-G3-A25U TCGA-G3-A3CJ 
        3.39        21.76        12.95        49.15        53.79        19.53 

$`SPATA12 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       12.72         0.07         0.16         2.86         0.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       75.65        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  SPATA12 MUTATED SPATA12 WILD-TYPE 
             3.39              0.03 
  SPATA12 MUTATED SPATA12 WILD-TYPE 
            53.79            113.00 
  SPATA12 MUTATED SPATA12 WILD-TYPE 
           20.645            13.810 
[1] "3.4 - 53.8 (20.6)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D79V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SPATA12 MUTATED         3        1         1          0          0          1
  SPATA12 WILD-TYPE      61       35         1         32          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  SPATA12 MUTATED          0         0         0
  SPATA12 WILD-TYPE        1         1         2
D79V3, multiclass
            clus
vv           SPATA12 MUTATED SPATA12 WILD-TYPE
  STAGE I                  3                61
  STAGE II                 1                35
  STAGE III                1                 1
  STAGE IIIA               0                32
  STAGE IIIB               0                 5
  STAGE IIIC               1                 5
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  SPATA12 MUTATED    3  1  1  1
  SPATA12 WILD-TYPE 64 39 42  8
D79V4, multiclass
    clus
vv   SPATA12 MUTATED SPATA12 WILD-TYPE
  T1               3                64
  T2               1                39
  T3               1                42
  T4               1                 8
[1] 4 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
  SPATA12 MUTATED    6  0
  SPATA12 WILD-TYPE 95  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA12 MUTATED      6    0
  SPATA12 WILD-TYPE   95    3
   clus
vv  SPATA12 MUTATED SPATA12 WILD-TYPE
  0               6                95
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  SPATA12 MUTATED     6   0   0
  SPATA12 WILD-TYPE 116   3  35
D79V6, multiclass
    clus
vv   SPATA12 MUTATED SPATA12 WILD-TYPE
  M0               6               116
  M1               0                 3
  MX               0                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                   cls
clus                 0  1
  SPATA12 MUTATED    2  4
  SPATA12 WILD-TYPE 59 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA12 MUTATED      2    4
  SPATA12 WILD-TYPE   59   95
        clus
vv       SPATA12 MUTATED SPATA12 WILD-TYPE
  FEMALE               2                59
  MALE                 4                95
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SPATA12 MUTATED                         0                        6
  SPATA12 WILD-TYPE                       1                      151
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  SPATA12 MUTATED                                  0
  SPATA12 WILD-TYPE                                2
D79V8, multiclass
                                  clus
vv                                 SPATA12 MUTATED SPATA12 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       6               151
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPATA12 MUTATED     4   0   0   1
  SPATA12 WILD-TYPE 128  10   1  11
D79V9, multiclass
    clus
vv   SPATA12 MUTATED SPATA12 WILD-TYPE
  R0               4               128
  R1               0                10
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPATA12 MUTATED                                  1     2
  SPATA12 WILD-TYPE                                0    35
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPATA12 MUTATED                           0     3
  SPATA12 WILD-TYPE                         8   105
D79V10, multiclass
                                  clus
vv                                 SPATA12 MUTATED SPATA12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                35
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          3               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, binary
                   cls
clus                  0   1
  SPATA12 MUTATED     0   6
  SPATA12 WILD-TYPE   4 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA12 MUTATED      0    6
  SPATA12 WILD-TYPE    4  137
                        clus
vv                       SPATA12 MUTATED SPATA12 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               6               137
[1] 2 2
[1] FALSE

Clustering(80) Variable = GPR112 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2               0  1
  GPR112 MUTATED    5  9
  GPR112 WILD-TYPE 85 57
  GPR112 MUTATED GPR112 WILD-TYPE 
              14              142 
  GPR112 MUTATED GPR112 WILD-TYPE 
               9               57 
$`GPR112 MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A69I TCGA-CC-5261 TCGA-DD-A116 TCGA-DD-A11C 
       46.78         2.99        12.72         0.39        53.33        21.76 
TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-ED-A7XO TCGA-EP-A2KA 
       12.95         5.62        19.76         7.66         0.20        11.74 
TCGA-G3-A25T TCGA-G3-A25U 
       51.06        53.79 

$`GPR112 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 
        0.26        22.36         9.50        14.60         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         3.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 
       29.16        18.35        13.64        21.14        55.69        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
       60.36         0.39         1.22        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  GPR112 MUTATED GPR112 WILD-TYPE 
            0.20             0.03 
  GPR112 MUTATED GPR112 WILD-TYPE 
           53.79           113.00 
  GPR112 MUTATED GPR112 WILD-TYPE 
          12.835           13.990 
[1] "0.2 - 53.8 (12.8)"  "0.0 - 113.0 (14.0)"
[1] "hr=" "1.8"
D80V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GPR112 MUTATED         5        2         0          5          0          0
  GPR112 WILD-TYPE      59       34         2         27          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  GPR112 MUTATED          0         0         0
  GPR112 WILD-TYPE        1         1         2
D80V3, multiclass
            clus
vv           GPR112 MUTATED GPR112 WILD-TYPE
  STAGE I                 5               59
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              5               27
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  GPR112 MUTATED    5  2  6  1
  GPR112 WILD-TYPE 62 38 37  8
D80V4, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  T1              5               62
  T2              2               38
  T3              6               37
  T4              1                8
[1] 4 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
  GPR112 MUTATED    9  0
  GPR112 WILD-TYPE 92  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED      9    0
  GPR112 WILD-TYPE   92    3
   clus
vv  GPR112 MUTATED GPR112 WILD-TYPE
  0              9               92
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  GPR112 MUTATED    11   0   3
  GPR112 WILD-TYPE 111   3  32
D80V6, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  M0             11              111
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                  cls
clus                0  1
  GPR112 MUTATED    5  9
  GPR112 WILD-TYPE 56 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED      5    9
  GPR112 WILD-TYPE   56   90
        clus
vv       GPR112 MUTATED GPR112 WILD-TYPE
  FEMALE              5               56
  MALE                9               90
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GPR112 MUTATED                         0                       14
  GPR112 WILD-TYPE                       1                      143
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  GPR112 MUTATED                                  0
  GPR112 WILD-TYPE                                2
D80V8, multiclass
                                  clus
vv                                 GPR112 MUTATED GPR112 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     14              143
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR112 MUTATED    11   1   0   2
  GPR112 WILD-TYPE 121   9   1  10
D80V9, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  R0             11              121
  R1              1                9
  R2              0                1
  RX              2               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR112 MUTATED                                  0     6
  GPR112 WILD-TYPE                                1    31
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR112 MUTATED                           0     6
  GPR112 WILD-TYPE                         8   102
D80V10, multiclass
                                  clus
vv                                 GPR112 MUTATED GPR112 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         6               31
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         6              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, binary
                  cls
clus                 0   1
  GPR112 MUTATED     0  11
  GPR112 WILD-TYPE   4 132
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED      0   11
  GPR112 WILD-TYPE    4  132
                        clus
vv                       GPR112 MUTATED GPR112 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO             11              132
[1] 2 2
[1] FALSE

Clustering(81) Variable = CLTCL1 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2               0  1
  CLTCL1 MUTATED    5 10
  CLTCL1 WILD-TYPE 85 56
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              15              141 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              10               56 
$`CLTCL1 MUTATED`
TCGA-CC-5260 TCGA-CC-A1HT TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A39Y 
        2.86         3.32        79.40        75.65        45.11         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A4NE TCGA-DD-A4NK TCGA-EP-A12J TCGA-EP-A2KB 
       19.76        25.81        21.70        39.78        18.74        10.98 
TCGA-FV-A23B TCGA-G3-A25Z TCGA-G3-A3CJ 
       32.45        21.53        19.53 

$`CLTCL1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
       12.72         0.07         0.16         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF 
       21.76        51.29        90.71        66.31        19.79        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20         0.20        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        22.85        14.40        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
            2.86             0.03 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
            79.4            113.0 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
           21.53            13.41 
[1] "2.9 - 79.4 (21.5)"  "0.0 - 113.0 (13.4)"
[1] "hr=" "1.4"
D81V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CLTCL1 MUTATED         7        4         0          3          0          1
  CLTCL1 WILD-TYPE      57       32         2         29          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CLTCL1 MUTATED          0         0         0
  CLTCL1 WILD-TYPE        1         1         2
D81V3, multiclass
            clus
vv           CLTCL1 MUTATED CLTCL1 WILD-TYPE
  STAGE I                 7               57
  STAGE II                4               32
  STAGE III               0                2
  STAGE IIIA              3               29
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CLTCL1 MUTATED    7  4  3  1
  CLTCL1 WILD-TYPE 60 36 40  8
D81V4, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  T1              7               60
  T2              4               36
  T3              3               40
  T4              1                8
[1] 4 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
  CLTCL1 MUTATED   10  0
  CLTCL1 WILD-TYPE 91  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     10    0
  CLTCL1 WILD-TYPE   91    3
   clus
vv  CLTCL1 MUTATED CLTCL1 WILD-TYPE
  0             10               91
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  CLTCL1 MUTATED    13   0   2
  CLTCL1 WILD-TYPE 109   3  33
D81V6, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  M0             13              109
  M1              0                3
  MX              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                  cls
clus                0  1
  CLTCL1 MUTATED    6  9
  CLTCL1 WILD-TYPE 55 90
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED      6    9
  CLTCL1 WILD-TYPE   55   90
        clus
vv       CLTCL1 MUTATED CLTCL1 WILD-TYPE
  FEMALE              6               55
  MALE                9               90
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CLTCL1 MUTATED                         0                       15
  CLTCL1 WILD-TYPE                       1                      142
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CLTCL1 MUTATED                                  0
  CLTCL1 WILD-TYPE                                2
D81V8, multiclass
                                  clus
vv                                 CLTCL1 MUTATED CLTCL1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     15              142
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLTCL1 MUTATED    13   0   0   1
  CLTCL1 WILD-TYPE 119  10   1  11
D81V9, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  R0             13              119
  R1              0               10
  R2              0                1
  RX              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLTCL1 MUTATED                                  1     5
  CLTCL1 WILD-TYPE                                0    32
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLTCL1 MUTATED                           1     7
  CLTCL1 WILD-TYPE                         7   101
D81V10, multiclass
                                  clus
vv                                 CLTCL1 MUTATED CLTCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         5               32
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         7              101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED     1  13
  CLTCL1 WILD-TYPE   3 130
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED      1   13
  CLTCL1 WILD-TYPE    3  130
                        clus
vv                       CLTCL1 MUTATED CLTCL1 WILD-TYPE
  HISPANIC OR LATINO                  1                3
  NOT HISPANIC OR LATINO             13              130
[1] 2 2
[1] FALSE

Clustering(82) Variable = OR2A14 MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2               0  1
  OR2A14 MUTATED    1  3
  OR2A14 WILD-TYPE 89 63
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               4              152 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
               3               63 
$`OR2A14 MUTATED`
TCGA-BC-A10Z TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-G3-A3CJ 
        1.12        19.76        25.81        19.53 

$`OR2A14 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  OR2A14 MUTATED OR2A14 WILD-TYPE 
            1.12             0.03 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
           25.81           113.00 
  OR2A14 MUTATED OR2A14 WILD-TYPE 
          19.645           13.810 
[1] "1.1 - 25.8 (19.6)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.4"
D82V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR2A14 MUTATED         2        2         0          0          0          0
  OR2A14 WILD-TYPE      62       34         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  OR2A14 MUTATED          0         0         0
  OR2A14 WILD-TYPE        1         1         2
D82V3, multiclass
            clus
vv           OR2A14 MUTATED OR2A14 WILD-TYPE
  STAGE I                 2               62
  STAGE II                2               34
  STAGE III               0                2
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  OR2A14 MUTATED    2  2  0  0
  OR2A14 WILD-TYPE 65 38 43  9
D82V4, multiclass
    clus
vv   OR2A14 MUTATED OR2A14 WILD-TYPE
  T1              2               65
  T2              2               38
  T3              0               43
  T4              0                9
[1] 4 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
  OR2A14 MUTATED    2  0
  OR2A14 WILD-TYPE 99  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      2    0
  OR2A14 WILD-TYPE   99    3
   clus
vv  OR2A14 MUTATED OR2A14 WILD-TYPE
  0              2               99
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  OR2A14 MUTATED     3   0   1
  OR2A14 WILD-TYPE 119   3  34
D82V6, multiclass
    clus
vv   OR2A14 MUTATED OR2A14 WILD-TYPE
  M0              3              119
  M1              0                3
  MX              1               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"
D82V7, binary
                  cls
clus                0  1
  OR2A14 MUTATED    2  2
  OR2A14 WILD-TYPE 59 97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      2    2
  OR2A14 WILD-TYPE   59   97
        clus
vv       OR2A14 MUTATED OR2A14 WILD-TYPE
  FEMALE              2               59
  MALE                2               97
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR2A14 MUTATED                         0                        4
  OR2A14 WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR2A14 MUTATED                                  0
  OR2A14 WILD-TYPE                                2
D82V8, multiclass
                                  clus
vv                                 OR2A14 MUTATED OR2A14 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR2A14 MUTATED     4   0   0   0
  OR2A14 WILD-TYPE 128  10   1  12
D82V9, multiclass
    clus
vv   OR2A14 MUTATED OR2A14 WILD-TYPE
  R0              4              128
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2A14 MUTATED                                  1     0
  OR2A14 WILD-TYPE                                0    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2A14 MUTATED                           0     2
  OR2A14 WILD-TYPE                         8   106
D82V10, multiclass
                                  clus
vv                                 OR2A14 MUTATED OR2A14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         2              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, binary
                  cls
clus                 0   1
  OR2A14 MUTATED     0   3
  OR2A14 WILD-TYPE   4 140
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2A14 MUTATED      0    3
  OR2A14 WILD-TYPE    4  140
                        clus
vv                       OR2A14 MUTATED OR2A14 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3              140
[1] 2 2
[1] FALSE

Clustering(83) Variable = OR4C16 MUTATION ANALYSIS
D83V1, survival
                  sevent
clus2               0  1
  OR4C16 MUTATED    5  2
  OR4C16 WILD-TYPE 85 64
  OR4C16 MUTATED OR4C16 WILD-TYPE 
               7              149 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
               2               64 
$`OR4C16 MUTATED`
TCGA-BC-A69I TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NP TCGA-G3-A25T 
       12.72        75.65        45.11         5.62        93.67        51.06 
TCGA-G3-A3CJ 
       19.53 

$`OR4C16 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        12.95        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14        55.69        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  OR4C16 MUTATED OR4C16 WILD-TYPE 
            5.62             0.03 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
           93.67           113.00 
  OR4C16 MUTATED OR4C16 WILD-TYPE 
           45.11            13.78 
[1] "5.6 - 93.7 (45.1)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "2.7"
D83V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR4C16 MUTATED         5        1         0          1          0          0
  OR4C16 WILD-TYPE      59       35         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  OR4C16 MUTATED          0         0         0
  OR4C16 WILD-TYPE        1         1         2
D83V3, multiclass
            clus
vv           OR4C16 MUTATED OR4C16 WILD-TYPE
  STAGE I                 5               59
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  OR4C16 MUTATED    5  1  1  0
  OR4C16 WILD-TYPE 62 39 42  9
D83V4, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  T1              5               62
  T2              1               39
  T3              1               42
  T4              0                9
[1] 4 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
  OR4C16 MUTATED    6  0
  OR4C16 WILD-TYPE 95  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED      6    0
  OR4C16 WILD-TYPE   95    3
   clus
vv  OR4C16 MUTATED OR4C16 WILD-TYPE
  0              6               95
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  OR4C16 MUTATED     7   0   0
  OR4C16 WILD-TYPE 115   3  35
D83V6, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  M0              7              115
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                  cls
clus                0  1
  OR4C16 MUTATED    1  6
  OR4C16 WILD-TYPE 60 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED      1    6
  OR4C16 WILD-TYPE   60   93
        clus
vv       OR4C16 MUTATED OR4C16 WILD-TYPE
  FEMALE              1               60
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR4C16 MUTATED                         0                        7
  OR4C16 WILD-TYPE                       1                      150
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR4C16 MUTATED                                  0
  OR4C16 WILD-TYPE                                2
D83V8, multiclass
                                  clus
vv                                 OR4C16 MUTATED OR4C16 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      7              150
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR4C16 MUTATED     7   0   0   0
  OR4C16 WILD-TYPE 125  10   1  12
D83V9, multiclass
    clus
vv   OR4C16 MUTATED OR4C16 WILD-TYPE
  R0              7              125
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4C16 MUTATED                                  1     1
  OR4C16 WILD-TYPE                                0    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4C16 MUTATED                           0     5
  OR4C16 WILD-TYPE                         8   103
D83V10, multiclass
                                  clus
vv                                 OR4C16 MUTATED OR4C16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         5              103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V11, binary
                  cls
clus                 0   1
  OR4C16 MUTATED     0   6
  OR4C16 WILD-TYPE   4 137
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C16 MUTATED      0    6
  OR4C16 WILD-TYPE    4  137
                        clus
vv                       OR4C16 MUTATED OR4C16 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              137
[1] 2 2
[1] FALSE

Clustering(84) Variable = GBP1 MUTATION ANALYSIS
D84V1, survival
                sevent
clus2             0  1
  GBP1 MUTATED    3  3
  GBP1 WILD-TYPE 87 63
  GBP1 MUTATED GBP1 WILD-TYPE 
             6            150 
  GBP1 MUTATED GBP1 WILD-TYPE 
             3             63 
$`GBP1 MUTATED`
TCGA-BC-A10S TCGA-CC-5261 TCGA-DD-A11B TCGA-DD-A1ED TCGA-G3-A25V TCGA-G3-A5SJ 
       46.78         0.39         0.46        75.65        28.27        11.97 

$`GBP1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         0.16         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       83.57        53.33       113.00         7.33         2.60        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF 
       51.29        90.71        79.40        66.31        19.79        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  GBP1 MUTATED GBP1 WILD-TYPE 
          0.39           0.03 
  GBP1 MUTATED GBP1 WILD-TYPE 
         75.65         113.00 
  GBP1 MUTATED GBP1 WILD-TYPE 
        20.120         13.875 
[1] "0.4 - 75.7 (20.1)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.1"
D84V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GBP1 MUTATED         5        1         0          0          0          0
  GBP1 WILD-TYPE      59       35         2         32          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  GBP1 MUTATED          0         0         0
  GBP1 WILD-TYPE        1         1         2
D84V3, multiclass
            clus
vv           GBP1 MUTATED GBP1 WILD-TYPE
  STAGE I               5             59
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            0             32
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  GBP1 MUTATED    5  1  1  0
  GBP1 WILD-TYPE 62 39 42  9
D84V4, multiclass
    clus
vv   GBP1 MUTATED GBP1 WILD-TYPE
  T1            5             62
  T2            1             39
  T3            1             42
  T4            0              9
[1] 4 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
  GBP1 MUTATED    4  0
  GBP1 WILD-TYPE 97  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP1 MUTATED      4    0
  GBP1 WILD-TYPE   97    3
   clus
vv  GBP1 MUTATED GBP1 WILD-TYPE
  0            4             97
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  GBP1 MUTATED     5   0   2
  GBP1 WILD-TYPE 117   3  33
D84V6, multiclass
    clus
vv   GBP1 MUTATED GBP1 WILD-TYPE
  M0            5            117
  M1            0              3
  MX            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                cls
clus              0  1
  GBP1 MUTATED    0  7
  GBP1 WILD-TYPE 61 92
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP1 MUTATED      0    7
  GBP1 WILD-TYPE   61   92
        clus
vv       GBP1 MUTATED GBP1 WILD-TYPE
  FEMALE            0             61
  MALE              7             92
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GBP1 MUTATED                         0                        7
  GBP1 WILD-TYPE                       1                      150
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  GBP1 MUTATED                                  0
  GBP1 WILD-TYPE                                2
D84V8, multiclass
                                  clus
vv                                 GBP1 MUTATED GBP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    7            150
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GBP1 MUTATED     4   0   0   3
  GBP1 WILD-TYPE 128  10   1   9
D84V9, multiclass
    clus
vv   GBP1 MUTATED GBP1 WILD-TYPE
  R0            4            128
  R1            0             10
  R2            0              1
  RX            3              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GBP1 MUTATED                                  0     1
  GBP1 WILD-TYPE                                1    36
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GBP1 MUTATED                           0     6
  GBP1 WILD-TYPE                         8   102
D84V10, multiclass
                                  clus
vv                                 GBP1 MUTATED GBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             36
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       6            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V11, binary
                cls
clus               0   1
  GBP1 MUTATED     0   7
  GBP1 WILD-TYPE   4 136
[1] "tbl2"
                cls
clus             [,1] [,2]
  GBP1 MUTATED      0    7
  GBP1 WILD-TYPE    4  136
                        clus
vv                       GBP1 MUTATED GBP1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            7            136
[1] 2 2
[1] FALSE

Clustering(85) Variable = OR6B3 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2              0  1
  OR6B3 MUTATED    3  1
  OR6B3 WILD-TYPE 87 65
  OR6B3 MUTATED OR6B3 WILD-TYPE 
              4             152 
  OR6B3 MUTATED OR6B3 WILD-TYPE 
              1              65 
$`OR6B3 MUTATED`
TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EF TCGA-EP-A12J 
        2.60        79.40        12.95        18.74 

$`OR6B3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  OR6B3 MUTATED OR6B3 WILD-TYPE 
           2.60            0.03 
  OR6B3 MUTATED OR6B3 WILD-TYPE 
           79.4           113.0 
  OR6B3 MUTATED OR6B3 WILD-TYPE 
         15.845          13.875 
[1] "2.6 - 79.4 (15.8)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.8"
D85V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR6B3 MUTATED         3        1         0          0          0          0
  OR6B3 WILD-TYPE      61       35         2         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  OR6B3 MUTATED          0         0         0
  OR6B3 WILD-TYPE        1         1         2
D85V3, multiclass
            clus
vv           OR6B3 MUTATED OR6B3 WILD-TYPE
  STAGE I                3              61
  STAGE II               1              35
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  OR6B3 MUTATED    3  1  0  0
  OR6B3 WILD-TYPE 64 39 43  9
D85V4, multiclass
    clus
vv   OR6B3 MUTATED OR6B3 WILD-TYPE
  T1             3              64
  T2             1              39
  T3             0              43
  T4             0               9
[1] 4 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
  OR6B3 MUTATED    3  0
  OR6B3 WILD-TYPE 98  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6B3 MUTATED      3    0
  OR6B3 WILD-TYPE   98    3
   clus
vv  OR6B3 MUTATED OR6B3 WILD-TYPE
  0             3              98
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  OR6B3 MUTATED     3   0   1
  OR6B3 WILD-TYPE 119   3  34
D85V6, multiclass
    clus
vv   OR6B3 MUTATED OR6B3 WILD-TYPE
  M0             3             119
  M1             0               3
  MX             1              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"
D85V7, binary
                 cls
clus               0  1
  OR6B3 MUTATED    1  3
  OR6B3 WILD-TYPE 60 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6B3 MUTATED      1    3
  OR6B3 WILD-TYPE   60   96
        clus
vv       OR6B3 MUTATED OR6B3 WILD-TYPE
  FEMALE             1              60
  MALE               3              96
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR6B3 MUTATED                         0                        4
  OR6B3 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR6B3 MUTATED                                  0
  OR6B3 WILD-TYPE                                2
D85V8, multiclass
                                  clus
vv                                 OR6B3 MUTATED OR6B3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR6B3 MUTATED     4   0   0   0
  OR6B3 WILD-TYPE 128  10   1  12
D85V9, multiclass
    clus
vv   OR6B3 MUTATED OR6B3 WILD-TYPE
  R0             4             128
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6B3 MUTATED                                  0     1
  OR6B3 WILD-TYPE                                1    36
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6B3 MUTATED                           2     1
  OR6B3 WILD-TYPE                         6   107
D85V10, multiclass
                                  clus
vv                                 OR6B3 MUTATED OR6B3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              36
  BLACK OR AFRICAN AMERICAN                    2               6
  WHITE                                        1             107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V11, binary
                 cls
clus                0   1
  OR6B3 MUTATED     0   4
  OR6B3 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6B3 MUTATED      0    4
  OR6B3 WILD-TYPE    4  139
                        clus
vv                       OR6B3 MUTATED OR6B3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(86) Variable = OR2T27 MUTATION ANALYSIS
D86V1, survival
                  sevent
clus2               0  1
  OR2T27 MUTATED    6  3
  OR2T27 WILD-TYPE 84 63
  OR2T27 MUTATED OR2T27 WILD-TYPE 
               9              147 
  OR2T27 MUTATED OR2T27 WILD-TYPE 
               3               63 
$`OR2T27 MUTATED`
TCGA-BC-A10U TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EH TCGA-DD-A39Y 
       27.52         2.60        79.40        66.31        49.15         5.62 
TCGA-DD-A3A0 TCGA-EP-A12J TCGA-EP-A26S 
       25.81        18.74        19.99 

$`OR2T27 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       27.91        37.32        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       21.76        51.29        90.71        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         6.02        29.16        18.35        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  OR2T27 MUTATED OR2T27 WILD-TYPE 
            2.60             0.03 
  OR2T27 MUTATED OR2T27 WILD-TYPE 
            79.4            113.0 
  OR2T27 MUTATED OR2T27 WILD-TYPE 
           25.81            13.64 
[1] "2.6 - 79.4 (25.8)"  "0.0 - 113.0 (13.6)"
[1] "hr=" "1.7"
D86V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR2T27 MUTATED         6        1         1          0          0          0
  OR2T27 WILD-TYPE      58       35         1         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  OR2T27 MUTATED          0         0         0
  OR2T27 WILD-TYPE        1         1         2
D86V3, multiclass
            clus
vv           OR2T27 MUTATED OR2T27 WILD-TYPE
  STAGE I                 6               58
  STAGE II                1               35
  STAGE III               1                1
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  OR2T27 MUTATED    6  2  1  0
  OR2T27 WILD-TYPE 61 38 42  9
D86V4, multiclass
    clus
vv   OR2T27 MUTATED OR2T27 WILD-TYPE
  T1              6               61
  T2              2               38
  T3              1               42
  T4              0                9
[1] 4 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
  OR2T27 MUTATED    5  0
  OR2T27 WILD-TYPE 96  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T27 MUTATED      5    0
  OR2T27 WILD-TYPE   96    3
   clus
vv  OR2T27 MUTATED OR2T27 WILD-TYPE
  0              5               96
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  OR2T27 MUTATED     6   0   3
  OR2T27 WILD-TYPE 116   3  32
D86V6, multiclass
    clus
vv   OR2T27 MUTATED OR2T27 WILD-TYPE
  M0              6              116
  M1              0                3
  MX              3               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                  cls
clus                0  1
  OR2T27 MUTATED    1  8
  OR2T27 WILD-TYPE 60 91
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T27 MUTATED      1    8
  OR2T27 WILD-TYPE   60   91
        clus
vv       OR2T27 MUTATED OR2T27 WILD-TYPE
  FEMALE              1               60
  MALE                8               91
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR2T27 MUTATED                         0                        9
  OR2T27 WILD-TYPE                       1                      148
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR2T27 MUTATED                                  0
  OR2T27 WILD-TYPE                                2
D86V8, multiclass
                                  clus
vv                                 OR2T27 MUTATED OR2T27 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      9              148
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR2T27 MUTATED     7   1   0   0
  OR2T27 WILD-TYPE 125   9   1  12
D86V9, multiclass
    clus
vv   OR2T27 MUTATED OR2T27 WILD-TYPE
  R0              7              125
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2T27 MUTATED                                  0     2
  OR2T27 WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2T27 MUTATED                           2     4
  OR2T27 WILD-TYPE                         6   104
D86V10, multiclass
                                  clus
vv                                 OR2T27 MUTATED OR2T27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     2                6
  WHITE                                         4              104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V11, binary
                  cls
clus                 0   1
  OR2T27 MUTATED     0   8
  OR2T27 WILD-TYPE   4 135
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T27 MUTATED      0    8
  OR2T27 WILD-TYPE    4  135
                        clus
vv                       OR2T27 MUTATED OR2T27 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              8              135
[1] 2 2
[1] FALSE

Clustering(87) Variable = RAET1E MUTATION ANALYSIS
D87V1, survival
                  sevent
clus2               0  1
  RAET1E MUTATED    2  3
  RAET1E WILD-TYPE 88 63
  RAET1E MUTATED RAET1E WILD-TYPE 
               5              151 
  RAET1E MUTATED RAET1E WILD-TYPE 
               3               63 
$`RAET1E MUTATED`
TCGA-BC-A10S TCGA-BC-A69I TCGA-DD-A1ED TCGA-DD-A1EL TCGA-G3-A25S 
       46.78        12.72        75.65        13.64         1.22 

$`RAET1E WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       13.84         0.26        22.36         9.50        14.60         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         0.39        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  RAET1E MUTATED RAET1E WILD-TYPE 
            1.22             0.03 
  RAET1E MUTATED RAET1E WILD-TYPE 
           75.65           113.00 
  RAET1E MUTATED RAET1E WILD-TYPE 
           13.64            13.91 
[1] "1.2 - 75.7 (13.6)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "1.2"
D87V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RAET1E MUTATED         3        1         0          0          0          0
  RAET1E WILD-TYPE      61       35         2         32          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  RAET1E MUTATED          0         0         0
  RAET1E WILD-TYPE        1         1         2
D87V3, multiclass
            clus
vv           RAET1E MUTATED RAET1E WILD-TYPE
  STAGE I                 3               61
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              0               32
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  RAET1E MUTATED    3  1  1  0
  RAET1E WILD-TYPE 64 39 42  9
D87V4, multiclass
    clus
vv   RAET1E MUTATED RAET1E WILD-TYPE
  T1              3               64
  T2              1               39
  T3              1               42
  T4              0                9
[1] 4 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
  RAET1E MUTATED    4  0
  RAET1E WILD-TYPE 97  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAET1E MUTATED      4    0
  RAET1E WILD-TYPE   97    3
   clus
vv  RAET1E MUTATED RAET1E WILD-TYPE
  0              4               97
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  RAET1E MUTATED     4   0   1
  RAET1E WILD-TYPE 118   3  34
D87V6, multiclass
    clus
vv   RAET1E MUTATED RAET1E WILD-TYPE
  M0              4              118
  M1              0                3
  MX              1               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"
D87V7, binary
                  cls
clus                0  1
  RAET1E MUTATED    0  5
  RAET1E WILD-TYPE 61 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAET1E MUTATED      0    5
  RAET1E WILD-TYPE   61   94
        clus
vv       RAET1E MUTATED RAET1E WILD-TYPE
  FEMALE              0               61
  MALE                5               94
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RAET1E MUTATED                         0                        5
  RAET1E WILD-TYPE                       1                      152
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  RAET1E MUTATED                                  0
  RAET1E WILD-TYPE                                2
D87V8, multiclass
                                  clus
vv                                 RAET1E MUTATED RAET1E WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      5              152
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RAET1E MUTATED     4   1   0   0
  RAET1E WILD-TYPE 128   9   1  12
D87V9, multiclass
    clus
vv   RAET1E MUTATED RAET1E WILD-TYPE
  R0              4              128
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAET1E MUTATED                                  0     0
  RAET1E WILD-TYPE                                1    37
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RAET1E MUTATED                           1     4
  RAET1E WILD-TYPE                         7   104
D87V10, multiclass
                                  clus
vv                                 RAET1E MUTATED RAET1E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               37
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         4              104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V11, binary
                  cls
clus                 0   1
  RAET1E MUTATED     0   4
  RAET1E WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAET1E MUTATED      0    4
  RAET1E WILD-TYPE    4  139
                        clus
vv                       RAET1E MUTATED RAET1E WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(88) Variable = SHROOM1 MUTATION ANALYSIS
D88V1, survival
                   sevent
clus2                0  1
  SHROOM1 MUTATED    1  2
  SHROOM1 WILD-TYPE 89 64
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
                3               153 
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
                2                64 
$`SHROOM1 MUTATED`
TCGA-DD-A1EG TCGA-EP-A2KB TCGA-G3-A3CJ 
       45.11        10.98        19.53 

$`SHROOM1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        32.45        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       13.38         0.49         9.57         5.10        14.24        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        8.71        58.88         4.44 

  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
            10.98              0.03 
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
            45.11            113.00 
  SHROOM1 MUTATED SHROOM1 WILD-TYPE 
            19.53             13.84 
[1] "11.0 - 45.1 (19.5)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1.5"
D88V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SHROOM1 MUTATED         2        1         0          0          0          0
  SHROOM1 WILD-TYPE      62       35         2         32          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  SHROOM1 MUTATED          0         0         0
  SHROOM1 WILD-TYPE        1         1         2
D88V3, multiclass
            clus
vv           SHROOM1 MUTATED SHROOM1 WILD-TYPE
  STAGE I                  2                62
  STAGE II                 1                35
  STAGE III                0                 2
  STAGE IIIA               0                32
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  SHROOM1 MUTATED    2  1  0  0
  SHROOM1 WILD-TYPE 65 39 43  9
D88V4, multiclass
    clus
vv   SHROOM1 MUTATED SHROOM1 WILD-TYPE
  T1               2                65
  T2               1                39
  T3               0                43
  T4               0                 9
[1] 4 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
  SHROOM1 MUTATED    2  0
  SHROOM1 WILD-TYPE 99  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM1 MUTATED      2    0
  SHROOM1 WILD-TYPE   99    3
   clus
vv  SHROOM1 MUTATED SHROOM1 WILD-TYPE
  0               2                99
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  SHROOM1 MUTATED     2   0   1
  SHROOM1 WILD-TYPE 120   3  34
D88V6, multiclass
    clus
vv   SHROOM1 MUTATED SHROOM1 WILD-TYPE
  M0               2               120
  M1               0                 3
  MX               1                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"
D88V7, binary
                   cls
clus                 0  1
  SHROOM1 MUTATED    1  2
  SHROOM1 WILD-TYPE 60 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM1 MUTATED      1    2
  SHROOM1 WILD-TYPE   60   97
        clus
vv       SHROOM1 MUTATED SHROOM1 WILD-TYPE
  FEMALE               1                60
  MALE                 2                97
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SHROOM1 MUTATED                         0                        3
  SHROOM1 WILD-TYPE                       1                      154
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  SHROOM1 MUTATED                                  0
  SHROOM1 WILD-TYPE                                2
D88V8, multiclass
                                  clus
vv                                 SHROOM1 MUTATED SHROOM1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       3               154
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SHROOM1 MUTATED     3   0   0   0
  SHROOM1 WILD-TYPE 129  10   1  12
D88V9, multiclass
    clus
vv   SHROOM1 MUTATED SHROOM1 WILD-TYPE
  R0               3               129
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SHROOM1 MUTATED                                  1     0
  SHROOM1 WILD-TYPE                                0    37
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SHROOM1 MUTATED                           0     2
  SHROOM1 WILD-TYPE                         8   106
D88V10, multiclass
                                  clus
vv                                 SHROOM1 MUTATED SHROOM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                37
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          2               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V11, binary
                   cls
clus                  0   1
  SHROOM1 MUTATED     0   3
  SHROOM1 WILD-TYPE   4 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM1 MUTATED      0    3
  SHROOM1 WILD-TYPE    4  140
                        clus
vv                       SHROOM1 MUTATED SHROOM1 WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               3               140
[1] 2 2
[1] FALSE

Clustering(89) Variable = OR52I2 MUTATION ANALYSIS
D89V1, survival
                  sevent
clus2               0  1
  OR52I2 MUTATED    4  2
  OR52I2 WILD-TYPE 86 64
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               6              150 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
               2               64 
$`OR52I2 MUTATED`
TCGA-DD-A116 TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-EP-A12J TCGA-G3-A25S 
       53.33        66.31        75.65        49.15        18.74         1.22 

$`OR52I2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20         0.20        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  OR52I2 MUTATED OR52I2 WILD-TYPE 
            1.22             0.03 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
           75.65           113.00 
  OR52I2 MUTATED OR52I2 WILD-TYPE 
           51.24            13.71 
[1] "1.2 - 75.7 (51.2)"  "0.0 - 113.0 (13.7)"
[1] "hr=" "2.3"
D89V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR52I2 MUTATED         4        0         1          1          0          0
  OR52I2 WILD-TYPE      60       36         1         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  OR52I2 MUTATED          0         0         0
  OR52I2 WILD-TYPE        1         1         2
D89V3, multiclass
            clus
vv           OR52I2 MUTATED OR52I2 WILD-TYPE
  STAGE I                 4               60
  STAGE II                0               36
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  OR52I2 MUTATED    4  0  2  0
  OR52I2 WILD-TYPE 63 40 41  9
D89V4, multiclass
    clus
vv   OR52I2 MUTATED OR52I2 WILD-TYPE
  T1              4               63
  T2              0               40
  T3              2               41
  T4              0                9
[1] 4 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
  OR52I2 MUTATED    5  0
  OR52I2 WILD-TYPE 96  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      5    0
  OR52I2 WILD-TYPE   96    3
   clus
vv  OR52I2 MUTATED OR52I2 WILD-TYPE
  0              5               96
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  OR52I2 MUTATED     5   0   1
  OR52I2 WILD-TYPE 117   3  34
D89V6, multiclass
    clus
vv   OR52I2 MUTATED OR52I2 WILD-TYPE
  M0              5              117
  M1              0                3
  MX              1               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"
D89V7, binary
                  cls
clus                0  1
  OR52I2 MUTATED    1  5
  OR52I2 WILD-TYPE 60 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      1    5
  OR52I2 WILD-TYPE   60   94
        clus
vv       OR52I2 MUTATED OR52I2 WILD-TYPE
  FEMALE              1               60
  MALE                5               94
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR52I2 MUTATED                         0                        6
  OR52I2 WILD-TYPE                       1                      151
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR52I2 MUTATED                                  0
  OR52I2 WILD-TYPE                                2
D89V8, multiclass
                                  clus
vv                                 OR52I2 MUTATED OR52I2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      6              151
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR52I2 MUTATED     5   1   0   0
  OR52I2 WILD-TYPE 127   9   1  12
D89V9, multiclass
    clus
vv   OR52I2 MUTATED OR52I2 WILD-TYPE
  R0              5              127
  R1              1                9
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR52I2 MUTATED                                  0     1
  OR52I2 WILD-TYPE                                1    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR52I2 MUTATED                           1     3
  OR52I2 WILD-TYPE                         7   105
D89V10, multiclass
                                  clus
vv                                 OR52I2 MUTATED OR52I2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         3              105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V11, binary
                  cls
clus                 0   1
  OR52I2 MUTATED     0   5
  OR52I2 WILD-TYPE   4 138
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52I2 MUTATED      0    5
  OR52I2 WILD-TYPE    4  138
                        clus
vv                       OR52I2 MUTATED OR52I2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              5              138
[1] 2 2
[1] FALSE

Clustering(90) Variable = OR13C2 MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2               0  1
  OR13C2 MUTATED    2  2
  OR13C2 WILD-TYPE 88 64
  OR13C2 MUTATED OR13C2 WILD-TYPE 
               4              152 
  OR13C2 MUTATED OR13C2 WILD-TYPE 
               2               64 
$`OR13C2 MUTATED`
TCGA-DD-A116 TCGA-DD-A1EF TCGA-DD-A1EH TCGA-EP-A12J 
       53.33        12.95        49.15        18.74 

$`OR13C2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        75.65        45.11         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20         0.20        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  OR13C2 MUTATED OR13C2 WILD-TYPE 
           12.95             0.03 
  OR13C2 MUTATED OR13C2 WILD-TYPE 
           53.33           113.00 
  OR13C2 MUTATED OR13C2 WILD-TYPE 
          33.945           13.810 
[1] "12.9 - 53.3 (33.9)" "0.0 - 113.0 (13.8)"
[1] "hr=" "1.2"
D90V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  OR13C2 MUTATED         2        0         1          1          0          0
  OR13C2 WILD-TYPE      62       36         1         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  OR13C2 MUTATED          0         0         0
  OR13C2 WILD-TYPE        1         1         2
D90V3, multiclass
            clus
vv           OR13C2 MUTATED OR13C2 WILD-TYPE
  STAGE I                 2               62
  STAGE II                0               36
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  OR13C2 MUTATED    2  0  2  0
  OR13C2 WILD-TYPE 65 40 41  9
D90V4, multiclass
    clus
vv   OR13C2 MUTATED OR13C2 WILD-TYPE
  T1              2               65
  T2              0               40
  T3              2               41
  T4              0                9
[1] 4 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
  OR13C2 MUTATED    3  0
  OR13C2 WILD-TYPE 98  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C2 MUTATED      3    0
  OR13C2 WILD-TYPE   98    3
   clus
vv  OR13C2 MUTATED OR13C2 WILD-TYPE
  0              3               98
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  OR13C2 MUTATED     3   0   1
  OR13C2 WILD-TYPE 119   3  34
D90V6, multiclass
    clus
vv   OR13C2 MUTATED OR13C2 WILD-TYPE
  M0              3              119
  M1              0                3
  MX              1               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"
D90V7, binary
                  cls
clus                0  1
  OR13C2 MUTATED    1  3
  OR13C2 WILD-TYPE 60 96
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C2 MUTATED      1    3
  OR13C2 WILD-TYPE   60   96
        clus
vv       OR13C2 MUTATED OR13C2 WILD-TYPE
  FEMALE              1               60
  MALE                3               96
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  OR13C2 MUTATED                         0                        4
  OR13C2 WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  OR13C2 MUTATED                                  0
  OR13C2 WILD-TYPE                                2
D90V8, multiclass
                                  clus
vv                                 OR13C2 MUTATED OR13C2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR13C2 MUTATED     4   0   0   0
  OR13C2 WILD-TYPE 128  10   1  12
D90V9, multiclass
    clus
vv   OR13C2 MUTATED OR13C2 WILD-TYPE
  R0              4              128
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR13C2 MUTATED                                  0     1
  OR13C2 WILD-TYPE                                1    36
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR13C2 MUTATED                           1     2
  OR13C2 WILD-TYPE                         7   106
D90V10, multiclass
                                  clus
vv                                 OR13C2 MUTATED OR13C2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               36
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         2              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V11, binary
                  cls
clus                 0   1
  OR13C2 MUTATED     0   4
  OR13C2 WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C2 MUTATED      0    4
  OR13C2 WILD-TYPE    4  139
                        clus
vv                       OR13C2 MUTATED OR13C2 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(91) Variable = LIPC MUTATION ANALYSIS
D91V1, survival
                sevent
clus2             0  1
  LIPC MUTATED    2  3
  LIPC WILD-TYPE 88 63
  LIPC MUTATED LIPC WILD-TYPE 
             5            151 
  LIPC MUTATED LIPC WILD-TYPE 
             3             63 
$`LIPC MUTATED`
TCGA-BC-A10S TCGA-DD-A118 TCGA-DD-A4NH TCGA-ES-A2HS TCGA-FV-A23B 
       46.78       113.00        14.24        22.85        32.45 

$`LIPC WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        21.70        14.07        14.63        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        30.74        14.86        21.53        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97         9.93 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
        7.99         4.37         7.76         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.66         4.01         2.14        11.84        13.38         0.49 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57         5.10        14.24        12.85         8.71        58.88 
TCGA-O8-A75V 
        4.44 

  LIPC MUTATED LIPC WILD-TYPE 
         14.24           0.03 
  LIPC MUTATED LIPC WILD-TYPE 
        113.00         107.11 
  LIPC MUTATED LIPC WILD-TYPE 
         32.45          13.64 
[1] "14.2 - 113.0 (32.5)" "0.0 - 107.1 (13.6)" 
[1] "hr=" "1.6"
D91V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LIPC MUTATED         1        2         0          0          1          0
  LIPC WILD-TYPE      63       34         2         32          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  LIPC MUTATED          0         0         0
  LIPC WILD-TYPE        1         1         2
D91V3, multiclass
            clus
vv           LIPC MUTATED LIPC WILD-TYPE
  STAGE I               1             63
  STAGE II              2             34
  STAGE III             0              2
  STAGE IIIA            0             32
  STAGE IIIB            1              4
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  LIPC MUTATED    1  2  2  0
  LIPC WILD-TYPE 66 38 41  9
D91V4, multiclass
    clus
vv   LIPC MUTATED LIPC WILD-TYPE
  T1            1             66
  T2            2             38
  T3            2             41
  T4            0              9
[1] 4 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
  LIPC MUTATED    3  0
  LIPC WILD-TYPE 98  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPC MUTATED      3    0
  LIPC WILD-TYPE   98    3
   clus
vv  LIPC MUTATED LIPC WILD-TYPE
  0            3             98
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  LIPC MUTATED     3   0   2
  LIPC WILD-TYPE 119   3  33
D91V6, multiclass
    clus
vv   LIPC MUTATED LIPC WILD-TYPE
  M0            3            119
  M1            0              3
  MX            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                cls
clus              0  1
  LIPC MUTATED    3  2
  LIPC WILD-TYPE 58 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPC MUTATED      3    2
  LIPC WILD-TYPE   58   97
        clus
vv       LIPC MUTATED LIPC WILD-TYPE
  FEMALE            3             58
  MALE              2             97
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LIPC MUTATED                         0                        5
  LIPC WILD-TYPE                       1                      152
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  LIPC MUTATED                                  0
  LIPC WILD-TYPE                                2
D91V8, multiclass
                                  clus
vv                                 LIPC MUTATED LIPC WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    5            152
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LIPC MUTATED     5   0   0   0
  LIPC WILD-TYPE 127  10   1  12
D91V9, multiclass
    clus
vv   LIPC MUTATED LIPC WILD-TYPE
  R0            5            127
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIPC MUTATED                                  0     0
  LIPC WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIPC MUTATED                           0     5
  LIPC WILD-TYPE                         8   103
D91V10, multiclass
                                  clus
vv                                 LIPC MUTATED LIPC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   0              8
  WHITE                                       5            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V11, binary
                cls
clus               0   1
  LIPC MUTATED     0   5
  LIPC WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPC MUTATED      0    5
  LIPC WILD-TYPE    4  138
                        clus
vv                       LIPC MUTATED LIPC WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(92) Variable = FAM22F MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2               0  1
  FAM22F MUTATED    1  3
  FAM22F WILD-TYPE 89 63
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              152 
  FAM22F MUTATED FAM22F WILD-TYPE 
               3               63 
$`FAM22F MUTATED`
TCGA-BC-A10R TCGA-CC-A3MA TCGA-DD-A119 TCGA-DD-A39X 
       10.13         0.07         7.33        55.69 

$`FAM22F WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33       113.00         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        21.14         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        66.35        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  FAM22F MUTATED FAM22F WILD-TYPE 
            0.07             0.03 
  FAM22F MUTATED FAM22F WILD-TYPE 
           55.69           113.00 
  FAM22F MUTATED FAM22F WILD-TYPE 
            8.73            13.99 
[1] "0.1 - 55.7 (8.7)"   "0.0 - 113.0 (14.0)"
[1] "hr=" "2.3"
D92V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM22F MUTATED         1        0         0          1          0          0
  FAM22F WILD-TYPE      63       36         2         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  FAM22F MUTATED          1         0         0
  FAM22F WILD-TYPE        0         1         2
D92V3, multiclass
            clus
vv           FAM22F MUTATED FAM22F WILD-TYPE
  STAGE I                 1               63
  STAGE II                0               36
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                1                0
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  FAM22F MUTATED    1  0  3  0
  FAM22F WILD-TYPE 66 40 40  9
D92V4, multiclass
    clus
vv   FAM22F MUTATED FAM22F WILD-TYPE
  T1              1               66
  T2              0               40
  T3              3               40
  T4              0                9
[1] 4 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
  FAM22F MUTATED    2  0
  FAM22F WILD-TYPE 99  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      2    0
  FAM22F WILD-TYPE   99    3
   clus
vv  FAM22F MUTATED FAM22F WILD-TYPE
  0              2               99
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  FAM22F MUTATED     2   1   1
  FAM22F WILD-TYPE 120   2  34
D92V6, multiclass
    clus
vv   FAM22F MUTATED FAM22F WILD-TYPE
  M0              2              120
  M1              1                2
  MX              1               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"
D92V7, binary
                  cls
clus                0  1
  FAM22F MUTATED    2  2
  FAM22F WILD-TYPE 59 97
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      2    2
  FAM22F WILD-TYPE   59   97
        clus
vv       FAM22F MUTATED FAM22F WILD-TYPE
  FEMALE              2               59
  MALE                2               97
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FAM22F MUTATED                         0                        4
  FAM22F WILD-TYPE                       1                      153
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  FAM22F MUTATED                                  0
  FAM22F WILD-TYPE                                2
D92V8, multiclass
                                  clus
vv                                 FAM22F MUTATED FAM22F WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      4              153
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM22F MUTATED     3   0   1   0
  FAM22F WILD-TYPE 129  10   0  12
D92V9, multiclass
    clus
vv   FAM22F MUTATED FAM22F WILD-TYPE
  R0              3              129
  R1              0               10
  R2              1                0
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM22F MUTATED                                  0     2
  FAM22F WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM22F MUTATED                           0     2
  FAM22F WILD-TYPE                         8   106
D92V10, multiclass
                                  clus
vv                                 FAM22F MUTATED FAM22F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         2              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V11, binary
                  cls
clus                 0   1
  FAM22F MUTATED     0   4
  FAM22F WILD-TYPE   4 139
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      0    4
  FAM22F WILD-TYPE    4  139
                        clus
vv                       FAM22F MUTATED FAM22F WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              4              139
[1] 2 2
[1] FALSE

Clustering(93) Variable = GLRX3 MUTATION ANALYSIS
D93V1, survival
                 sevent
clus2              0  1
  GLRX3 MUTATED    4  0
  GLRX3 WILD-TYPE 86 66
  GLRX3 MUTATED GLRX3 WILD-TYPE 
              4             152 
  GLRX3 MUTATED GLRX3 WILD-TYPE 
              0              66 
$`GLRX3 MUTATED`
TCGA-BC-A69I TCGA-DD-A1ED TCGA-DD-A4NF TCGA-G3-A25U 
       12.72        75.65        14.07        53.79 

$`GLRX3 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       73.38        21.70        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       51.06        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        0.49         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  GLRX3 MUTATED GLRX3 WILD-TYPE 
          12.72            0.03 
  GLRX3 MUTATED GLRX3 WILD-TYPE 
          75.65          113.00 
  GLRX3 MUTATED GLRX3 WILD-TYPE 
          33.93           13.81 
[1] "12.7 - 75.7 (33.9)" "0.0 - 113.0 (13.8)"
[1] "hr="     "2.6e+07"
D93V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GLRX3 MUTATED         4        0         0          0          0          0
  GLRX3 WILD-TYPE      60       36         2         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  GLRX3 MUTATED          0         0         0
  GLRX3 WILD-TYPE        1         1         2
D93V3, multiclass
            clus
vv           GLRX3 MUTATED GLRX3 WILD-TYPE
  STAGE I                4              60
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  GLRX3 MUTATED    4  0  0  0
  GLRX3 WILD-TYPE 63 40 43  9
D93V4, multiclass
    clus
vv   GLRX3 MUTATED GLRX3 WILD-TYPE
  T1             4              63
  T2             0              40
  T3             0              43
  T4             0               9
[1] 4 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
  GLRX3 MUTATED    4  0
  GLRX3 WILD-TYPE 97  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRX3 MUTATED      4    0
  GLRX3 WILD-TYPE   97    3
   clus
vv  GLRX3 MUTATED GLRX3 WILD-TYPE
  0             4              97
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  GLRX3 MUTATED     4   0   0
  GLRX3 WILD-TYPE 118   3  35
D93V6, multiclass
    clus
vv   GLRX3 MUTATED GLRX3 WILD-TYPE
  M0             4             118
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
                 cls
clus               0  1
  GLRX3 MUTATED    1  3
  GLRX3 WILD-TYPE 60 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRX3 MUTATED      1    3
  GLRX3 WILD-TYPE   60   96
        clus
vv       GLRX3 MUTATED GLRX3 WILD-TYPE
  FEMALE             1              60
  MALE               3              96
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GLRX3 MUTATED                         0                        4
  GLRX3 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  GLRX3 MUTATED                                  0
  GLRX3 WILD-TYPE                                2
D93V8, multiclass
                                  clus
vv                                 GLRX3 MUTATED GLRX3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GLRX3 MUTATED     4   0   0   0
  GLRX3 WILD-TYPE 128  10   1  12
D93V9, multiclass
    clus
vv   GLRX3 MUTATED GLRX3 WILD-TYPE
  R0             4             128
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLRX3 MUTATED                                  0     1
  GLRX3 WILD-TYPE                                1    36
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLRX3 MUTATED                           0     3
  GLRX3 WILD-TYPE                         8   105
D93V10, multiclass
                                  clus
vv                                 GLRX3 MUTATED GLRX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              36
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        3             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V11, binary
                 cls
clus                0   1
  GLRX3 MUTATED     0   3
  GLRX3 WILD-TYPE   4 140
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRX3 MUTATED      0    3
  GLRX3 WILD-TYPE    4  140
                        clus
vv                       GLRX3 MUTATED GLRX3 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             3             140
[1] 2 2
[1] FALSE

Clustering(94) Variable = HOXA4 MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2              0  1
  HOXA4 MUTATED    4  1
  HOXA4 WILD-TYPE 86 65
  HOXA4 MUTATED HOXA4 WILD-TYPE 
              5             151 
  HOXA4 MUTATED HOXA4 WILD-TYPE 
              1              65 
$`HOXA4 MUTATED`
TCGA-BC-A10R TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-A73F TCGA-MI-A75I 
       10.13        66.35         1.45        27.72         8.71 

$`HOXA4 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       93.67        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        7.56        10.98       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
        9.93         7.99         4.37         7.76         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.02         2.66         4.01         2.14        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 
        0.49         9.57         5.10        14.24        12.85        58.88 
TCGA-O8-A75V 
        4.44 

  HOXA4 MUTATED HOXA4 WILD-TYPE 
           1.45            0.03 
  HOXA4 MUTATED HOXA4 WILD-TYPE 
          66.35          113.00 
  HOXA4 MUTATED HOXA4 WILD-TYPE 
          10.13           13.91 
[1] "1.4 - 66.3 (10.1)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "2"  
D94V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HOXA4 MUTATED         2        0         0          1          0          0
  HOXA4 WILD-TYPE      62       36         2         31          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  HOXA4 MUTATED          0         0         0
  HOXA4 WILD-TYPE        1         1         2
D94V3, multiclass
            clus
vv           HOXA4 MUTATED HOXA4 WILD-TYPE
  STAGE I                2              62
  STAGE II               0              36
  STAGE III              0               2
  STAGE IIIA             1              31
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  HOXA4 MUTATED    2  1  2  0
  HOXA4 WILD-TYPE 65 39 41  9
D94V4, multiclass
    clus
vv   HOXA4 MUTATED HOXA4 WILD-TYPE
  T1             2              65
  T2             1              39
  T3             2              41
  T4             0               9
[1] 4 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
  HOXA4 MUTATED    3  0
  HOXA4 WILD-TYPE 98  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA4 MUTATED      3    0
  HOXA4 WILD-TYPE   98    3
   clus
vv  HOXA4 MUTATED HOXA4 WILD-TYPE
  0             3              98
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  HOXA4 MUTATED     3   0   2
  HOXA4 WILD-TYPE 119   3  33
D94V6, multiclass
    clus
vv   HOXA4 MUTATED HOXA4 WILD-TYPE
  M0             3             119
  M1             0               3
  MX             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                 cls
clus               0  1
  HOXA4 MUTATED    2  3
  HOXA4 WILD-TYPE 59 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA4 MUTATED      2    3
  HOXA4 WILD-TYPE   59   96
        clus
vv       HOXA4 MUTATED HOXA4 WILD-TYPE
  FEMALE             2              59
  MALE               3              96
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HOXA4 MUTATED                         0                        5
  HOXA4 WILD-TYPE                       1                      152
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  HOXA4 MUTATED                                  0
  HOXA4 WILD-TYPE                                2
D94V8, multiclass
                                  clus
vv                                 HOXA4 MUTATED HOXA4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     5             152
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOXA4 MUTATED     5   0   0   0
  HOXA4 WILD-TYPE 127  10   1  12
D94V9, multiclass
    clus
vv   HOXA4 MUTATED HOXA4 WILD-TYPE
  R0             5             127
  R1             0              10
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOXA4 MUTATED                                  0     0
  HOXA4 WILD-TYPE                                1    37
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOXA4 MUTATED                           1     4
  HOXA4 WILD-TYPE                         7   104
D94V10, multiclass
                                  clus
vv                                 HOXA4 MUTATED HOXA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              37
  BLACK OR AFRICAN AMERICAN                    1               7
  WHITE                                        4             104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V11, binary
                 cls
clus                0   1
  HOXA4 MUTATED     0   5
  HOXA4 WILD-TYPE   4 138
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXA4 MUTATED      0    5
  HOXA4 WILD-TYPE    4  138
                        clus
vv                       HOXA4 MUTATED HOXA4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             5             138
[1] 2 2
[1] FALSE

Clustering(95) Variable = DENND4B MUTATION ANALYSIS
D95V1, survival
                   sevent
clus2                0  1
  DENND4B MUTATED    1  7
  DENND4B WILD-TYPE 89 59
  DENND4B MUTATED DENND4B WILD-TYPE 
                8               148 
  DENND4B MUTATED DENND4B WILD-TYPE 
                7                59 
$`DENND4B MUTATED`
TCGA-BC-A3KF TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS 
        0.26        45.11        25.81        11.74        10.98        22.85 
TCGA-FV-A2QR TCGA-G3-A25S 
       19.10         1.22 

$`DENND4B WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42        13.84        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        14.07        14.63        14.24        18.44        15.06 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81        93.67        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        66.35        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        0.62         9.96        11.93        14.40        32.45        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  DENND4B MUTATED DENND4B WILD-TYPE 
             0.26              0.03 
  DENND4B MUTATED DENND4B WILD-TYPE 
            45.11            113.00 
  DENND4B MUTATED DENND4B WILD-TYPE 
           15.420            13.875 
[1] "0.3 - 45.1 (15.4)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "3"  
D95V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DENND4B MUTATED         7        0         0          1          0          0
  DENND4B WILD-TYPE      57       36         2         31          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  DENND4B MUTATED          0         0         0
  DENND4B WILD-TYPE        1         1         2
D95V3, multiclass
            clus
vv           DENND4B MUTATED DENND4B WILD-TYPE
  STAGE I                  7                57
  STAGE II                 0                36
  STAGE III                0                 2
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  DENND4B MUTATED    7  0  1  0
  DENND4B WILD-TYPE 60 40 42  9
D95V4, multiclass
    clus
vv   DENND4B MUTATED DENND4B WILD-TYPE
  T1               7                60
  T2               0                40
  T3               1                42
  T4               0                 9
[1] 4 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
  DENND4B MUTATED    3  0
  DENND4B WILD-TYPE 98  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      3    0
  DENND4B WILD-TYPE   98    3
   clus
vv  DENND4B MUTATED DENND4B WILD-TYPE
  0               3                98
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  DENND4B MUTATED     5   0   3
  DENND4B WILD-TYPE 117   3  32
D95V6, multiclass
    clus
vv   DENND4B MUTATED DENND4B WILD-TYPE
  M0               5               117
  M1               0                 3
  MX               3                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
                   cls
clus                 0  1
  DENND4B MUTATED    3  5
  DENND4B WILD-TYPE 58 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      3    5
  DENND4B WILD-TYPE   58   94
        clus
vv       DENND4B MUTATED DENND4B WILD-TYPE
  FEMALE               3                58
  MALE                 5                94
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DENND4B MUTATED                         0                        8
  DENND4B WILD-TYPE                       1                      149
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  DENND4B MUTATED                                  0
  DENND4B WILD-TYPE                                2
D95V8, multiclass
                                  clus
vv                                 DENND4B MUTATED DENND4B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       8               149
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DENND4B MUTATED     6   1   0   1
  DENND4B WILD-TYPE 126   9   1  11
D95V9, multiclass
    clus
vv   DENND4B MUTATED DENND4B WILD-TYPE
  R0               6               126
  R1               1                 9
  R2               0                 1
  RX               1                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DENND4B MUTATED                                  0     0
  DENND4B WILD-TYPE                                1    37
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DENND4B MUTATED                           0     8
  DENND4B WILD-TYPE                         8   100
D95V10, multiclass
                                  clus
vv                                 DENND4B MUTATED DENND4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                37
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          8               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V11, binary
                   cls
clus                  0   1
  DENND4B MUTATED     0   7
  DENND4B WILD-TYPE   4 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      0    7
  DENND4B WILD-TYPE    4  136
                        clus
vv                       DENND4B MUTATED DENND4B WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               7               136
[1] 2 2
[1] FALSE

Clustering(96) Variable = ESX1 MUTATION ANALYSIS
D96V1, survival
                sevent
clus2             0  1
  ESX1 MUTATED    4  1
  ESX1 WILD-TYPE 86 65
  ESX1 MUTATED ESX1 WILD-TYPE 
             5            151 
  ESX1 MUTATED ESX1 WILD-TYPE 
             1             65 
$`ESX1 MUTATED`
TCGA-BC-A112 TCGA-DD-A4NV TCGA-DD-A73A TCGA-LG-A6GG TCGA-MI-A75I 
        5.03        66.35        10.98         0.49         8.71 

$`ESX1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       13.84         0.26        22.36         9.50        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C 
       93.67        12.26         0.30        80.75         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-NI-A4U2 
       13.38         9.57         5.10        14.24        12.85        58.88 
TCGA-O8-A75V 
        4.44 

  ESX1 MUTATED ESX1 WILD-TYPE 
          0.49           0.03 
  ESX1 MUTATED ESX1 WILD-TYPE 
         66.35         113.00 
  ESX1 MUTATED ESX1 WILD-TYPE 
          8.71          14.07 
[1] "0.5 - 66.3 (8.7)"   "0.0 - 113.0 (14.1)"
[1] "hr=" "1.6"
D96V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ESX1 MUTATED         1        1         0          1          0          0
  ESX1 WILD-TYPE      63       35         2         31          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  ESX1 MUTATED          0         0         0
  ESX1 WILD-TYPE        1         1         2
D96V3, multiclass
            clus
vv           ESX1 MUTATED ESX1 WILD-TYPE
  STAGE I               1             63
  STAGE II              1             35
  STAGE III             0              2
  STAGE IIIA            1             31
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  ESX1 MUTATED    1  2  2  0
  ESX1 WILD-TYPE 66 38 41  9
D96V4, multiclass
    clus
vv   ESX1 MUTATED ESX1 WILD-TYPE
  T1            1             66
  T2            2             38
  T3            2             41
  T4            0              9
[1] 4 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
  ESX1 MUTATED    2  0
  ESX1 WILD-TYPE 99  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESX1 MUTATED      2    0
  ESX1 WILD-TYPE   99    3
   clus
vv  ESX1 MUTATED ESX1 WILD-TYPE
  0            2             99
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  ESX1 MUTATED     3   0   2
  ESX1 WILD-TYPE 119   3  33
D96V6, multiclass
    clus
vv   ESX1 MUTATED ESX1 WILD-TYPE
  M0            3            119
  M1            0              3
  MX            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                cls
clus              0  1
  ESX1 MUTATED    1  4
  ESX1 WILD-TYPE 60 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESX1 MUTATED      1    4
  ESX1 WILD-TYPE   60   95
        clus
vv       ESX1 MUTATED ESX1 WILD-TYPE
  FEMALE            1             60
  MALE              4             95
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ESX1 MUTATED                         0                        5
  ESX1 WILD-TYPE                       1                      152
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  ESX1 MUTATED                                  0
  ESX1 WILD-TYPE                                2
D96V8, multiclass
                                  clus
vv                                 ESX1 MUTATED ESX1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    5            152
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ESX1 MUTATED     5   0   0   0
  ESX1 WILD-TYPE 127  10   1  12
D96V9, multiclass
    clus
vv   ESX1 MUTATED ESX1 WILD-TYPE
  R0            5            127
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESX1 MUTATED                                  0     0
  ESX1 WILD-TYPE                                1    37
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ESX1 MUTATED                           1     4
  ESX1 WILD-TYPE                         7   104
D96V10, multiclass
                                  clus
vv                                 ESX1 MUTATED ESX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             37
  BLACK OR AFRICAN AMERICAN                   1              7
  WHITE                                       4            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V11, binary
                cls
clus               0   1
  ESX1 MUTATED     0   5
  ESX1 WILD-TYPE   4 138
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESX1 MUTATED      0    5
  ESX1 WILD-TYPE    4  138
                        clus
vv                       ESX1 MUTATED ESX1 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            5            138
[1] 2 2
[1] FALSE

Clustering(97) Variable = SLFN12L MUTATION ANALYSIS
D97V1, survival
                   sevent
clus2                0  1
  SLFN12L MUTATED    2  4
  SLFN12L WILD-TYPE 88 62
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                6               150 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                4                62 
$`SLFN12L MUTATED`
TCGA-BC-A10S TCGA-BC-A3KF TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NS TCGA-G3-A25T 
       46.78         0.26         5.62        25.81        80.75        51.06 

$`SLFN12L WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-CC-5258 
       13.84        22.36         9.50        14.60        12.72         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 
       18.35        13.64        21.14        55.69        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       14.07        14.63        14.24        18.44        15.06        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81        93.67        12.26         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       66.35        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39         1.22        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  SLFN12L MUTATED SLFN12L WILD-TYPE 
             0.26              0.03 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
            80.75            113.00 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
           36.295            13.810 
[1] "0.3 - 80.8 (36.3)"  "0.0 - 113.0 (13.8)"
[1] "hr=" "1.1"
D97V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SLFN12L MUTATED         4        0         0          1          0          0
  SLFN12L WILD-TYPE      60       36         2         31          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  SLFN12L MUTATED          0         0         0
  SLFN12L WILD-TYPE        1         1         2
D97V3, multiclass
            clus
vv           SLFN12L MUTATED SLFN12L WILD-TYPE
  STAGE I                  4                60
  STAGE II                 0                36
  STAGE III                0                 2
  STAGE IIIA               1                31
  STAGE IIIB               0                 5
  STAGE IIIC               0                 6
  STAGE IV                 0                 1
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  SLFN12L MUTATED    4  0  2  0
  SLFN12L WILD-TYPE 63 40 41  9
D97V4, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  T1               4                63
  T2               0                40
  T3               2                41
  T4               0                 9
[1] 4 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
  SLFN12L MUTATED    2  0
  SLFN12L WILD-TYPE 99  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      2    0
  SLFN12L WILD-TYPE   99    3
   clus
vv  SLFN12L MUTATED SLFN12L WILD-TYPE
  0               2                99
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  SLFN12L MUTATED     5   0   1
  SLFN12L WILD-TYPE 117   3  34
D97V6, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  M0               5               117
  M1               0                 3
  MX               1                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"
D97V7, binary
                   cls
clus                 0  1
  SLFN12L MUTATED    3  3
  SLFN12L WILD-TYPE 58 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      3    3
  SLFN12L WILD-TYPE   58   96
        clus
vv       SLFN12L MUTATED SLFN12L WILD-TYPE
  FEMALE               3                58
  MALE                 3                96
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SLFN12L MUTATED                         0                        6
  SLFN12L WILD-TYPE                       1                      151
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  SLFN12L MUTATED                                  0
  SLFN12L WILD-TYPE                                2
D97V8, multiclass
                                  clus
vv                                 SLFN12L MUTATED SLFN12L WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 1
  HEPATOCELLULAR CARCINOMA                       6               151
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLFN12L MUTATED     6   0   0   0
  SLFN12L WILD-TYPE 126  10   1  12
D97V9, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  R0               6               126
  R1               0                10
  R2               0                 1
  RX               0                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLFN12L MUTATED                                  0     1
  SLFN12L WILD-TYPE                                1    36
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLFN12L MUTATED                           0     5
  SLFN12L WILD-TYPE                         8   103
D97V10, multiclass
                                  clus
vv                                 SLFN12L MUTATED SLFN12L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                36
  BLACK OR AFRICAN AMERICAN                      0                 8
  WHITE                                          5               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V11, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     0   5
  SLFN12L WILD-TYPE   4 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      0    5
  SLFN12L WILD-TYPE    4  138
                        clus
vv                       SLFN12L MUTATED SLFN12L WILD-TYPE
  HISPANIC OR LATINO                   0                 4
  NOT HISPANIC OR LATINO               5               138
[1] 2 2
[1] FALSE

Clustering(98) Variable = FKBP4 MUTATION ANALYSIS
D98V1, survival
                 sevent
clus2              0  1
  FKBP4 MUTATED    2  2
  FKBP4 WILD-TYPE 88 64
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             152 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              2              64 
$`FKBP4 MUTATED`
TCGA-DD-A3A0 TCGA-G3-A25S TCGA-G3-A3CJ TCGA-LG-A6GG 
       25.81         1.22        19.53         0.49 

$`FKBP4 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        14.07        14.63        14.24 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       18.44        15.06        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       93.67        12.26         0.30        80.75        66.35        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13        25.64         5.92        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97         9.93         7.99         4.37         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        1.84         1.02         2.66         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       13.38         9.57         5.10        14.24        12.85         8.71 
TCGA-NI-A4U2 TCGA-O8-A75V 
       58.88         4.44 

  FKBP4 MUTATED FKBP4 WILD-TYPE 
           0.49            0.03 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
          25.81          113.00 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
         10.375          13.875 
[1] "0.5 - 25.8 (10.4)"  "0.0 - 113.0 (13.9)"
[1] "hr=" "2.2"
D98V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FKBP4 MUTATED         2        2         0          0          0          0
  FKBP4 WILD-TYPE      62       34         2         32          5          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  FKBP4 MUTATED          0         0         0
  FKBP4 WILD-TYPE        1         1         2
D98V3, multiclass
            clus
vv           FKBP4 MUTATED FKBP4 WILD-TYPE
  STAGE I                2              62
  STAGE II               2              34
  STAGE III              0               2
  STAGE IIIA             0              32
  STAGE IIIB             0               5
  STAGE IIIC             0               6
  STAGE IV               0               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  FKBP4 MUTATED    2  2  0  0
  FKBP4 WILD-TYPE 65 38 43  9
D98V4, multiclass
    clus
vv   FKBP4 MUTATED FKBP4 WILD-TYPE
  T1             2              65
  T2             2              38
  T3             0              43
  T4             0               9
[1] 4 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
  FKBP4 MUTATED    2  0
  FKBP4 WILD-TYPE 99  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      2    0
  FKBP4 WILD-TYPE   99    3
   clus
vv  FKBP4 MUTATED FKBP4 WILD-TYPE
  0             2              99
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  FKBP4 MUTATED     4   0   0
  FKBP4 WILD-TYPE 118   3  35
D98V6, multiclass
    clus
vv   FKBP4 MUTATED FKBP4 WILD-TYPE
  M0             4             118
  M1             0               3
  MX             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                 cls
clus               0  1
  FKBP4 MUTATED    1  3
  FKBP4 WILD-TYPE 60 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      1    3
  FKBP4 WILD-TYPE   60   96
        clus
vv       FKBP4 MUTATED FKBP4 WILD-TYPE
  FEMALE             1              60
  MALE               3              96
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FKBP4 MUTATED                         0                        4
  FKBP4 WILD-TYPE                       1                      153
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  FKBP4 MUTATED                                  0
  FKBP4 WILD-TYPE                                2
D98V8, multiclass
                                  clus
vv                                 FKBP4 MUTATED FKBP4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     4             153
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FKBP4 MUTATED     3   1   0   0
  FKBP4 WILD-TYPE 129   9   1  12
D98V9, multiclass
    clus
vv   FKBP4 MUTATED FKBP4 WILD-TYPE
  R0             3             129
  R1             1               9
  R2             0               1
  RX             0              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP4 MUTATED                                  1     0
  FKBP4 WILD-TYPE                                0    37
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP4 MUTATED                           0     3
  FKBP4 WILD-TYPE                         8   105
D98V10, multiclass
                                  clus
vv                                 FKBP4 MUTATED FKBP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0              37
  BLACK OR AFRICAN AMERICAN                    0               8
  WHITE                                        3             105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V11, binary
                 cls
clus                0   1
  FKBP4 MUTATED     0   4
  FKBP4 WILD-TYPE   4 139
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      0    4
  FKBP4 WILD-TYPE    4  139
                        clus
vv                       FKBP4 MUTATED FKBP4 WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             4             139
[1] 2 2
[1] FALSE

Clustering(99) Variable = AQP7 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  AQP7 MUTATED    7  1
  AQP7 WILD-TYPE 83 65
  AQP7 MUTATED AQP7 WILD-TYPE 
             8            148 
  AQP7 MUTATED AQP7 WILD-TYPE 
             1             65 
$`AQP7 MUTATED`
TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NV 
        2.60        79.40        49.15        15.06        39.78        66.35 
TCGA-EP-A12J TCGA-G3-A25U 
       18.74        53.79 

$`AQP7 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       12.72         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        45.11         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL 
       21.70        14.07        14.63        14.24        18.44        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81        93.67        12.26         0.30        80.75 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        22.85        14.40        32.45        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        51.06        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       21.53        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97         9.93         7.99         4.37         7.76 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K0 
        5.98         1.84         1.02         2.66         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       11.84        13.38         0.49         9.57         5.10        14.24 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.85         8.71        58.88         4.44 

  AQP7 MUTATED AQP7 WILD-TYPE 
          2.60           0.03 
  AQP7 MUTATED AQP7 WILD-TYPE 
          79.4          113.0 
  AQP7 MUTATED AQP7 WILD-TYPE 
        44.465         13.525 
[1] "2.6 - 79.4 (44.5)"  "0.0 - 113.0 (13.5)"
[1] "hr=" "5.9"
D99V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AQP7 MUTATED         3        2         1          2          0          0
  AQP7 WILD-TYPE      61       34         1         30          5          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  AQP7 MUTATED          0         0         0
  AQP7 WILD-TYPE        1         1         2
D99V3, multiclass
            clus
vv           AQP7 MUTATED AQP7 WILD-TYPE
  STAGE I               3             61
  STAGE II              2             34
  STAGE III             1              1
  STAGE IIIA            2             30
  STAGE IIIB            0              5
  STAGE IIIC            0              6
  STAGE IV              0              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  AQP7 MUTATED    3  2  3  0
  AQP7 WILD-TYPE 64 38 40  9
D99V4, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  T1            3             64
  T2            2             38
  T3            3             40
  T4            0              9
[1] 4 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
  AQP7 MUTATED    7  0
  AQP7 WILD-TYPE 94  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      7    0
  AQP7 WILD-TYPE   94    3
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            7             94
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  AQP7 MUTATED     7   0   1
  AQP7 WILD-TYPE 115   3  34
D99V6, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  M0            7            115
  M1            0              3
  MX            1             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"
D99V7, binary
                cls
clus              0  1
  AQP7 MUTATED    3  5
  AQP7 WILD-TYPE 58 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      3    5
  AQP7 WILD-TYPE   58   94
        clus
vv       AQP7 MUTATED AQP7 WILD-TYPE
  FEMALE            3             58
  MALE              5             94
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AQP7 MUTATED                         0                        8
  AQP7 WILD-TYPE                       1                      149
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  AQP7 MUTATED                                  0
  AQP7 WILD-TYPE                                2
D99V8, multiclass
                                  clus
vv                                 AQP7 MUTATED AQP7 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    8            149
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AQP7 MUTATED     8   0   0   0
  AQP7 WILD-TYPE 124  10   1  12
D99V9, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  R0            8            124
  R1            0             10
  R2            0              1
  RX            0             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AQP7 MUTATED                                  0     2
  AQP7 WILD-TYPE                                1    35
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AQP7 MUTATED                           2     4
  AQP7 WILD-TYPE                         6   104
D99V10, multiclass
                                  clus
vv                                 AQP7 MUTATED AQP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2             35
  BLACK OR AFRICAN AMERICAN                   2              6
  WHITE                                       4            104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V11, binary
                cls
clus               0   1
  AQP7 MUTATED     0   8
  AQP7 WILD-TYPE   4 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      0    8
  AQP7 WILD-TYPE    4  135
                        clus
vv                       AQP7 MUTATED AQP7 WILD-TYPE
  HISPANIC OR LATINO                0              4
  NOT HISPANIC OR LATINO            8            135
[1] 2 2
[1] FALSE

Clustering(100) Variable = MAP4K5 MUTATION ANALYSIS
D100V1, survival
                  sevent
clus2               0  1
  MAP4K5 MUTATED    6  1
  MAP4K5 WILD-TYPE 84 65
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               7              149 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
               1               65 
$`MAP4K5 MUTATED`
TCGA-BC-A69H TCGA-BC-A69I TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
       14.60        12.72        19.79        75.65        45.11        49.15 
TCGA-G3-A25U 
       53.79 

$`MAP4K5 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-CC-5258 
       44.42        13.84         0.26        22.36         9.50         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.16         2.86         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EF 
       21.76        51.29        90.71        79.40        66.31        12.95 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86        21.53        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97         9.93         7.99         4.37 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-K7-A6G5 
        7.76         5.98         1.84         1.02         2.66         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
        2.14        11.84        13.38         0.49         9.57         5.10 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       14.24        12.85         8.71        58.88         4.44 

  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           12.72             0.03 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           75.65           113.00 
  MAP4K5 MUTATED MAP4K5 WILD-TYPE 
           45.11            13.64 
[1] "12.7 - 75.7 (45.1)" "0.0 - 113.0 (13.6)"
[1] "hr=" "4.9"
D100V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MAP4K5 MUTATED         5        1         1          1          0          0
  MAP4K5 WILD-TYPE      59       35         1         31          5          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  MAP4K5 MUTATED          0         0         0
  MAP4K5 WILD-TYPE        1         1         2
D100V3, multiclass
            clus
vv           MAP4K5 MUTATED MAP4K5 WILD-TYPE
  STAGE I                 5               59
  STAGE II                1               35
  STAGE III               1                1
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              0                6
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  MAP4K5 MUTATED    5  1  2  0
  MAP4K5 WILD-TYPE 62 39 41  9
D100V4, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  T1              5               62
  T2              1               39
  T3              2               41
  T4              0                9
[1] 4 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
  MAP4K5 MUTATED    7  0
  MAP4K5 WILD-TYPE 94  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      7    0
  MAP4K5 WILD-TYPE   94    3
   clus
vv  MAP4K5 MUTATED MAP4K5 WILD-TYPE
  0              7               94
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  MAP4K5 MUTATED     8   0   0
  MAP4K5 WILD-TYPE 114   3  35
D100V6, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  M0              8              114
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V7, binary
                  cls
clus                0  1
  MAP4K5 MUTATED    2  6
  MAP4K5 WILD-TYPE 59 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      2    6
  MAP4K5 WILD-TYPE   59   93
        clus
vv       MAP4K5 MUTATED MAP4K5 WILD-TYPE
  FEMALE              2               59
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MAP4K5 MUTATED                         0                        8
  MAP4K5 WILD-TYPE                       1                      149
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  MAP4K5 MUTATED                                  0
  MAP4K5 WILD-TYPE                                2
D100V8, multiclass
                                  clus
vv                                 MAP4K5 MUTATED MAP4K5 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      8              149
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP4K5 MUTATED     7   0   0   1
  MAP4K5 WILD-TYPE 125  10   1  11
D100V9, multiclass
    clus
vv   MAP4K5 MUTATED MAP4K5 WILD-TYPE
  R0              7              125
  R1              0               10
  R2              0                1
  RX              1               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP4K5 MUTATED                                  0     2
  MAP4K5 WILD-TYPE                                1    35
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP4K5 MUTATED                           0     6
  MAP4K5 WILD-TYPE                         8   102
D100V10, multiclass
                                  clus
vv                                 MAP4K5 MUTATED MAP4K5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2               35
  BLACK OR AFRICAN AMERICAN                     0                8
  WHITE                                         6              102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V11, binary
                  cls
clus                 0   1
  MAP4K5 MUTATED     0   7
  MAP4K5 WILD-TYPE   4 136
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K5 MUTATED      0    7
  MAP4K5 WILD-TYPE    4  136
                        clus
vv                       MAP4K5 MUTATED MAP4K5 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              7              136
[1] 2 2
[1] FALSE

Clustering(101) Variable = BCL11A MUTATION ANALYSIS
D101V1, survival
                  sevent
clus2               0  1
  BCL11A MUTATED    2  4
  BCL11A WILD-TYPE 88 62
  BCL11A MUTATED BCL11A WILD-TYPE 
               6              150 
  BCL11A MUTATED BCL11A WILD-TYPE 
               4               62 
$`BCL11A MUTATED`
TCGA-CC-5262 TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A3A0 
        3.39         0.10        45.11         6.02        13.64        25.81 

$`BCL11A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       27.91        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
       44.42        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       12.72         0.07         0.16         2.86         0.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.10         0.07         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       75.65        12.95        49.15        29.16        18.35        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        14.07        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       14.24        18.44        15.06        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81        93.67        12.26         0.30        80.75        66.35 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR 
        9.96        11.93        22.85        14.40        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97         9.93         7.99 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        4.37         7.76         5.98         1.84         1.02         2.66 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75C 
        4.01         2.14        11.84        13.38         0.49         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
        5.10        14.24        12.85         8.71        58.88         4.44 

  BCL11A MUTATED BCL11A WILD-TYPE 
            0.10             0.03 
  BCL11A MUTATED BCL11A WILD-TYPE 
           45.11           113.00 
  BCL11A MUTATED BCL11A WILD-TYPE 
            9.83            13.99 
[1] "0.1 - 45.1 (9.8)"   "0.0 - 113.0 (14.0)"
[1] "hr=" "2.3"
D101V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BCL11A MUTATED         3        1         0          1          0          1
  BCL11A WILD-TYPE      61       35         2         31          5          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  BCL11A MUTATED          0         0         0
  BCL11A WILD-TYPE        1         1         2
D101V3, multiclass
            clus
vv           BCL11A MUTATED BCL11A WILD-TYPE
  STAGE I                 3               61
  STAGE II                1               35
  STAGE III               0                2
  STAGE IIIA              1               31
  STAGE IIIB              0                5
  STAGE IIIC              1                5
  STAGE IV                0                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of 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    3  1  1  1
  BCL11A WILD-TYPE 64 39 42  8
D101V4, multiclass
    clus
vv   BCL11A MUTATED BCL11A WILD-TYPE
  T1              3               64
  T2              1               39
  T3              1               42
  T4              1                8
[1] 4 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
  BCL11A MUTATED    5  0
  BCL11A WILD-TYPE 96  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      5    0
  BCL11A WILD-TYPE   96    3
   clus
vv  BCL11A MUTATED BCL11A WILD-TYPE
  0              5               96
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  BCL11A MUTATED     6   0   0
  BCL11A WILD-TYPE 116   3  35
D101V6, multiclass
    clus
vv   BCL11A MUTATED BCL11A WILD-TYPE
  M0              6              116
  M1              0                3
  MX              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V7, binary
                  cls
clus                0  1
  BCL11A MUTATED    0  6
  BCL11A WILD-TYPE 61 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      0    6
  BCL11A WILD-TYPE   61   93
        clus
vv       BCL11A MUTATED BCL11A WILD-TYPE
  FEMALE              0               61
  MALE                6               93
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BCL11A MUTATED                         0                        6
  BCL11A WILD-TYPE                       1                      151
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  BCL11A MUTATED                                  0
  BCL11A WILD-TYPE                                2
D101V8, multiclass
                                  clus
vv                                 BCL11A MUTATED BCL11A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      6              151
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCL11A MUTATED     5   0   0   0
  BCL11A WILD-TYPE 127  10   1  12
D101V9, multiclass
    clus
vv   BCL11A MUTATED BCL11A WILD-TYPE
  R0              5              127
  R1              0               10
  R2              0                1
  RX              0               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL11A MUTATED                                  0     3
  BCL11A WILD-TYPE                                1    34
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCL11A MUTATED                           1     2
  BCL11A WILD-TYPE                         7   106
D101V10, multiclass
                                  clus
vv                                 BCL11A MUTATED BCL11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3               34
  BLACK OR AFRICAN AMERICAN                     1                7
  WHITE                                         2              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V11, binary
                  cls
clus                 0   1
  BCL11A MUTATED     0   6
  BCL11A WILD-TYPE   4 137
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCL11A MUTATED      0    6
  BCL11A WILD-TYPE    4  137
                        clus
vv                       BCL11A MUTATED BCL11A WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              6              137
[1] 2 2
[1] FALSE
