[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/11541458/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/11548746/transformed.cor.cli.txt"

nPatients in clinical file=317, in cluster file=370, common to both=311
[1]  80 311
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               262 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               49               262 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              192               119 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              192               119 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38               273 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               38               273 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               37               274 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               37               274 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               33               278 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               33               278 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36               275 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36               275 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               290 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               21               290 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               304 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               304 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              116               195 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              116               195 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               91               220 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               91               220 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               97               214 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               97               214 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               53               258 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               53               258 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               94               217 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               94               217 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               91               220 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               91               220 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               243 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               243 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               149 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               149 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               294 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               17               294 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               17               294 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               17               294 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                258 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                53                258 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                32                279 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                32                279 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                295 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                295 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                294 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                294 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                35                276 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                35                276 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                274 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                37                274 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                19                292 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                19                292 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                294 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                294 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                282 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                282 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                287 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                287 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                300 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                300 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                283 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                283 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                81                230 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                81                230 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                283 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                28                283 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                289 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                289 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                49                262 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                49                262 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                62                249 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                62                249 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                220 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                220 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                95                216 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                95                216 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                288 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                288 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                41                270 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                41                270 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               50               261 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               50               261 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               72               239 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               72               239 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               292 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               292 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               283 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               283 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               278 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               33               278 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               43               268 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               43               268 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               279 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               32               279 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               92               219 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               92               219 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              127               184 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              127               184 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26               285 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26               285 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               274 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               274 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               287 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               287 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               231 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               231 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               297 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               297 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               292 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               19               292 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              162               149 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              162               149 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               275 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               36               275 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               212 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               99               212 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               91               220 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               91               220 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                271 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                271 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                66                245 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                66                245 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                258 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                53                258 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                251 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                60                251 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                52                259 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                52                259 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                30                281 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                30                281 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               107                204 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               107                204 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                97                214 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                97                214 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                59                252 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                59                252 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                212 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                99                212 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               129                182 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               129                182 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               153                158 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               153                158 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                34                277 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                34                277 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                62                249 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                62                249 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                66                245 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                66                245 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                42                269 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                42                269 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                30                281 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                30                281 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                291 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                291 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                302 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                302 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                94                217 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                94                217 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                253 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                58                253 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               252 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               252 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 311 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
         216          328          322           20           NA          849 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
          NA           NA           NA           NA           NA         1351 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
         421            8          680          289          444          387 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-BW-A5NP TCGA-BW-A5NQ 
         227          409          146           20           NA           NA 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
           2           NA           12           NA           NA           NA 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
          NA            3            2            3            4           NA 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A9FU TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
          NA         2425           NA           NA           NA         3437 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          662           NA           NA 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
        2415         2017          602         2301          204           NA 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
          NA         1495          183          887           NA           NA 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
          NA           NA         1008          989         2232          942 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
         917          816          928           NA         1711           NA 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
        2245         3308           NA           NA           NA         2398 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
         334           NA          230          334           44          843 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
        3071           NA           NA          347         2000         1800 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
          NA           NA         1931           NA           NA           NA 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
        1618         1828            9           58         1769          400 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
         436         1475         1240         1157          170           NA 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
         137          564          658         1029         1037          672 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
         959          930          890           NA          864           NA 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
         763          730          734          636           NA          527 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
          92          120          161         1742          216          252 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
         203          294          300          293          288          300 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
         259          141          382          344          386          450 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
         370          470          498          476          476         1067 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
        2405         2406         2198         1823         1882         1867 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
        1718         1788         1699         1644         1505         1451 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
         408          386          482          423          406            7 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
           6            6            6            6          400          408 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
           6            6            6          570          608          357 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
         334           NA          303          363           NA           NA 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
         987          729           NA          848           NA           NA 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
           4            1           10         1836           12           37 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1553         1636          860          935         1779           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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 
         447          364          621          520          236           NA 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
         366          182           NA           NA          342          260 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
          NA          295          279           NA           NA           92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
          NA           NA           NA           NA          631          519 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
         122           NA          360          407          741          387 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
         180          130          291          507          559          391 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
         630          330           NA          498          135           NA 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
          62          640          579          468          472          734 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
         455          526          438           NA          486           NA 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
         253          139           31           30          122           NA 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
         142          782          706          717           21          743 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
         395           NA         1066         2258          250 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=89,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=188,	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=9,	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=5,	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=28,	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 311 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 154  78  64  12 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  155    78    64    12 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 154  78  64  12 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  155    78    64    12 
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 = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    30  11
  1P GAIN WILD-TYPE 170  81
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               41               251 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11                81 
$`1P GAIN MUTATED`
TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BW-A5NO 
        0.66        37.32        27.52         2.99        44.42         0.66 
TCGA-CC-5262 TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A4NI 
        3.39        37.78         2.60        45.11         5.62        26.83 
TCGA-DD-A4NJ TCGA-DD-AACB TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AAD2 TCGA-DD-AAD5 
       30.51        59.18        60.10         1.91        21.63        34.09 
TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAVW 
       28.41        20.91        57.27        12.56        11.31        61.38 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A26S 
       13.41        12.69         0.20         0.20         0.20        19.99 
TCGA-G3-A25W TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 
       30.74        14.70        11.97        12.03         1.84        11.80 
TCGA-G3-AAV3 TCGA-KR-A7K7 TCGA-RC-A7SH TCGA-UB-A7MF TCGA-UB-AA0U 
        9.17        13.38        15.39         7.04         8.32 

$`1P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.78        10.59        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       46.78        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H 
        5.03        13.84         0.26        22.36         9.50        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       12.72         7.46        13.45         4.80         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.39         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-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-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        30.97        30.15        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       108.76        12.26         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
      100.96        13.48         0.53        11.41        65.75        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 
       38.04         5.59         5.62         4.50        18.54        33.83 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF 
       22.09        31.53        30.58        29.26        13.97         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       25.08        24.00        24.13         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        3.95         5.29         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.87        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       47.70        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.15        13.41         0.20         0.20        18.74 
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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        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-A25X TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42        17.10         7.76         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
       15.98         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.20              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            61.38            113.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            13.38             14.79 
[1] "0.2 - 61.4 (13.4)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED        17       13         0         11          3          2
  1P GAIN WILD-TYPE     129       59         2         41          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED          0         0         0
  1P GAIN WILD-TYPE        2         1         2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 17               129
  STAGE II                13                59
  STAGE III                0                 2
  STAGE IIIA              11                41
  STAGE IIIB               3                 4
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  1P GAIN MUTATED      17  15  13   4
  1P GAIN WILD-TYPE   138  63  51   8
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1              17               138
  T2                 15                63
  T3                 13                51
  T4                  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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    34   0
  1P GAIN WILD-TYPE 188   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     34    0
  1P GAIN WILD-TYPE  188    3
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              34               188
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    39   0  10
  1P GAIN WILD-TYPE 199   4  59
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              39               199
  M1               0                 4
  MX              10                59
[1] 3 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
  1P GAIN MUTATED    12  37
  1P GAIN WILD-TYPE  88 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     12   37
  1P GAIN WILD-TYPE   88  174
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              12                88
  MALE                37               174
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P GAIN MUTATED                         0                       48
  1P GAIN WILD-TYPE                       2                      255
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P GAIN MUTATED                                  1
  1P GAIN WILD-TYPE                                5
D1V8, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      48               255
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    41   4   0   2
  1P GAIN WILD-TYPE 233  10   1  14
D1V9, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              41               233
  R1               4                10
  R2               0                 1
  RX               2                14
[1] 4 2
[1] 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
  1P GAIN MUTATED                                  0    30
  1P GAIN WILD-TYPE                                1   111
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           3    16
  1P GAIN WILD-TYPE                        12   129
D1V10, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         30               111
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         16               129
[1] 4 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
  1P GAIN MUTATED     1  46
  1P GAIN WILD-TYPE   7 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   46
  1P GAIN WILD-TYPE    7  241
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              46               241
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   124  54
  1Q GAIN WILD-TYPE  76  38
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              178               114 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               54                38 
$`1Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U 
       10.78        10.59         0.66        37.32        10.13        27.52 
TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H 
        2.99        23.34         5.03        44.42        22.36        14.60 
TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA 
       12.72         4.80         0.66         0.39         3.39         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        79.73        37.78       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EF 
       21.76        51.29        90.71        79.40         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y 
       45.11        49.15        18.35        13.64        21.14         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       19.76        25.81        17.59        13.78         0.36        30.61 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN 
       30.97        30.15        26.83        30.51        39.78        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AA3A 
       73.81        12.26         0.30        10.98       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
        0.53        11.41        59.18        55.40        63.48        12.00 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        60.10         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       48.49        40.77         5.59         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       33.83        34.09        31.53        30.58        13.97        28.41 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       25.08        24.00        24.13        20.91         0.39         3.02 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        3.95        57.27         8.28         9.67         9.86         9.63 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        12.56        11.31        12.69        12.16        15.45 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 TCGA-ED-A459 
       61.38        58.78        55.86        54.05        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       12.69        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 
        0.62         9.96        23.97        19.10         8.12         0.13 
TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        0.03         1.22        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM 
       22.13        19.53        19.23        14.70        20.42        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       12.03         1.84         8.55        11.80         9.70         9.17 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.14         3.02         2.66        37.71         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       13.38        12.72         5.92         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       12.85        20.71         4.44        15.39        15.52        24.13 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WJ-A86L TCGA-WQ-A9G7 
       14.40         1.71        15.98         7.04         1.02         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.01         4.67        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CG 
       12.99        45.57        35.05         8.22 

$`1Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X 
        7.10        48.99        27.91        46.78        27.52        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A8YO 
        1.12        69.57        13.84         0.26         9.50         7.46 
TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
       13.45         0.07         2.86         4.24         3.32         0.10 
TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A1EB TCGA-DD-A1EC 
        0.10        83.57        53.33         0.46        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 TCGA-DD-A3A2 
       75.65         6.02        29.16        55.69         7.66        70.06 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       20.12       102.74       107.11        33.14        32.52        73.38 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76        80.75        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACG 
        7.56         1.45        27.72        65.75        12.53        15.42 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADB 
        6.41         0.30        38.04         5.62        22.09        29.26 
TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AAE2 
        3.78        17.33         5.29         7.10         6.67         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAEA TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVU 
        9.86         8.52        14.79        16.37        35.08        61.87 
TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E 
       56.48        49.48        15.85        13.91         0.20        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.20         0.20        11.93        22.85        14.40        32.45 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
       27.88         6.38         0.33        60.36         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A6UC 
       53.79        28.27        25.64         5.92        11.97         7.76 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-K7-A5RF 
        5.98        11.24         0.89         1.02         2.20        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MR-A8JO TCGA-NI-A4U2 
       17.06         4.01        24.36         4.27        10.85        58.88 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
       16.37        21.01         2.04        21.04        19.04        14.96 
TCGA-UB-A7MB TCGA-UB-AA0U TCGA-UB-AA0V TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZS-A9CF 
       17.29         8.32         4.57        13.55        25.71        74.24 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           113.00            108.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           14.365            14.875 
[1] "0.0 - 113.0 (14.4)" "0.1 - 108.8 (14.9)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED        86       51         1         25          5          3
  1Q GAIN WILD-TYPE      60       21         1         27          2          4
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED          2         1         2
  1Q GAIN WILD-TYPE        0         0         0
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 86                60
  STAGE II                51                21
  STAGE III                1                 1
  STAGE IIIA              25                27
  STAGE IIIB               5                 2
  STAGE IIIC               3                 4
  STAGE IV                 2                 0
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[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                T0+T1 T2 T3 T4
  1Q GAIN MUTATED      92 56 34  8
  1Q GAIN WILD-TYPE    63 22 30  4
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1              92                63
  T2                 56                22
  T3                 34                30
  T4                  8                 4
[1] 4 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
  1Q GAIN MUTATED   139   1
  1Q GAIN WILD-TYPE  83   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    139    1
  1Q GAIN WILD-TYPE   83    2
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             139                83
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED   149   4  39
  1Q GAIN WILD-TYPE  89   0  30
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0             149                89
  M1               4                 0
  MX              39                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"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    59 133
  1Q GAIN WILD-TYPE  41  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     59  133
  1Q GAIN WILD-TYPE   41   78
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              59                41
  MALE               133                78
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q GAIN MUTATED                         0                      189
  1Q GAIN WILD-TYPE                       2                      114
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q GAIN MUTATED                                  3
  1Q GAIN WILD-TYPE                                3
D2V8, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     189               114
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  1Q GAIN MUTATED   174   7   1   7
  1Q GAIN WILD-TYPE 100   7   0   9
D2V9, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             174               100
  R1               7                 7
  R2               1                 0
  RX               7                 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
  1Q GAIN MUTATED                                  1    96
  1Q GAIN WILD-TYPE                                0    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          10    80
  1Q GAIN WILD-TYPE                         5    65
D2V10, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         96                45
  BLACK OR AFRICAN AMERICAN                     10                 5
  WHITE                                         80                65
[1] 4 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
  1Q GAIN MUTATED     3 180
  1Q GAIN WILD-TYPE   5 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  180
  1Q GAIN WILD-TYPE    5  107
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             180               107
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    18  15
  2P GAIN WILD-TYPE 182  77
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               259 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               15                77 
$`2P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A5W4 TCGA-CC-A3M9 
       48.99        37.32        10.13        27.52         9.50         0.10 
TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       79.73        90.71        45.11        29.16        13.64        55.69 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AACB 
       30.61        33.14        10.98         1.45        13.48        59.18 
TCGA-DD-AACI TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO TCGA-DD-AAVW TCGA-ED-A7PY 
       53.19         5.62        22.09         3.02        61.38         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z 
       13.41         0.20        22.85        51.06        30.74        21.53 
TCGA-LG-A6GG TCGA-UB-A7MA TCGA-YA-A8S7 
       12.72        14.96        13.55 

$`2P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.78        10.59         0.66        27.91        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        5.03        44.42        13.84         0.26        22.36        14.60 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       12.72         7.46        13.45         4.80         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         0.39         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        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-A1EA 
        7.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
        6.02        18.35        21.14         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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        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 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30         7.56        27.72       100.96         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       65.75        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
        6.41        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       14.33        48.49        40.77        38.04         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        33.83        34.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       29.26        13.97        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       24.13        20.91         0.39        17.33         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       57.27         7.10         8.28         6.67         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        61.87        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20        13.15 
TCGA-ED-A8O5 TCGA-ED-A97K 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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        32.45        23.97 
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-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        11.84        13.38        24.36         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        24.13        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99         4.01         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            90.71            113.00 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            22.09             14.33 
[1] "0.1 - 90.7 (22.1)"  "0.0 - 113.0 (14.3)"
[1] "hr=" "1.3"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED        11        8         0         11          1          2
  2P GAIN WILD-TYPE     135       64         2         41          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED          1         0         1
  2P GAIN WILD-TYPE        1         1         1
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 11               135
  STAGE II                 8                64
  STAGE III                0                 2
  STAGE IIIA              11                41
  STAGE IIIB               1                 6
  STAGE IIIC               2                 5
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  2P GAIN MUTATED      12  11  13   2
  2P GAIN WILD-TYPE   143  67  51  10
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1              12               143
  T2                 11                67
  T3                 13                51
  T4                  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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    27   2
  2P GAIN WILD-TYPE 195   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27    2
  2P GAIN WILD-TYPE  195    1
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              27               195
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    29   2   7
  2P GAIN WILD-TYPE 209   2  62
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              29               209
  M1               2                 2
  MX               7                62
[1] 3 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
  2P GAIN MUTATED    21  17
  2P GAIN WILD-TYPE  79 194
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     21   17
  2P GAIN WILD-TYPE   79  194
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              21                79
  MALE                17               194
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P GAIN MUTATED                         0                       36
  2P GAIN WILD-TYPE                       2                      267
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P GAIN MUTATED                                  2
  2P GAIN WILD-TYPE                                4
D3V8, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      36               267
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  2P GAIN MUTATED    32   5   0   1
  2P GAIN WILD-TYPE 242   9   1  15
D3V9, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              32               242
  R1               5                 9
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  2P GAIN MUTATED                                  0    15
  2P GAIN WILD-TYPE                                1   126
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           1    22
  2P GAIN WILD-TYPE                        14   123
D3V10, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               126
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         22               123
[1] 4 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
  2P GAIN MUTATED     2  36
  2P GAIN WILD-TYPE   6 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   36
  2P GAIN WILD-TYPE    6  251
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              36               251
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    18  14
  2Q GAIN WILD-TYPE 182  78
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               32               260 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14                78 
$`2Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A1E9 TCGA-DD-A1EJ 
       48.99        37.32        10.13        79.73        90.71        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AA3A 
       13.64        55.69        30.61        10.98         1.45        13.48 
TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD6 TCGA-DD-AADO 
       59.18        53.19        40.77         5.62        22.09         3.02 
TCGA-DD-AADU TCGA-DD-AAVW TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS 
        8.28        61.38         0.20        13.41         0.20        22.85 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-AAV6 TCGA-LG-A6GG 
        1.22        51.06        30.74        21.53         2.14        12.72 
TCGA-UB-A7MA TCGA-YA-A8S7 
       14.96        13.55 

$`2Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.78        10.59         0.66        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         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-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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
        6.71        12.95        45.11        49.15         6.02        18.35 
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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        7.56        27.72       100.96         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       48.49        38.04         5.59         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       33.83        34.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       28.41         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        17.33         3.95         5.29        57.27         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        6.67         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX 
       79.07        79.10        72.26        59.93        61.87        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20         0.20        13.15         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        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-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       53.79        28.27        58.49        14.86        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
        8.55        11.80         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
        4.01         2.14        11.84        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       14.40         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.20              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            90.71            113.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           18.245            14.400 
[1] "0.2 - 90.7 (18.2)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED        12        9         0         10          1          1
  2Q GAIN WILD-TYPE     134       63         2         42          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED          1         0         1
  2Q GAIN WILD-TYPE        1         1         1
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 12               134
  STAGE II                 9                63
  STAGE III                0                 2
  STAGE IIIA              10                42
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  2Q GAIN MUTATED      13  11  12   1
  2Q GAIN WILD-TYPE   142  67  52  11
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1              13               142
  T2                 11                67
  T3                 12                52
  T4                  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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    29   1
  2Q GAIN WILD-TYPE 193   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     29    1
  2Q GAIN WILD-TYPE  193    2
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              29               193
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    29   2   6
  2Q GAIN WILD-TYPE 209   2  63
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              29               209
  M1               2                 2
  MX               6                63
[1] 3 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
  2Q GAIN MUTATED    21  16
  2Q GAIN WILD-TYPE  79 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21   16
  2Q GAIN WILD-TYPE   79  195
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              21                79
  MALE                16               195
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q GAIN MUTATED                         0                       35
  2Q GAIN WILD-TYPE                       2                      268
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q GAIN MUTATED                                  2
  2Q GAIN WILD-TYPE                                4
D4V8, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               268
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  2Q GAIN MUTATED    32   4   0   1
  2Q GAIN WILD-TYPE 242  10   1  15
D4V9, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              32               242
  R1               4                10
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  2Q GAIN MUTATED                                  0    16
  2Q GAIN WILD-TYPE                                1   125
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           1    20
  2Q GAIN WILD-TYPE                        14   125
D4V10, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               125
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         20               125
[1] 4 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
  2Q GAIN MUTATED     2  35
  2Q GAIN WILD-TYPE   6 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   35
  2Q GAIN WILD-TYPE    6  252
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              35               252
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    21   7
  3P GAIN WILD-TYPE 179  85
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28               264 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                85 
$`3P GAIN MUTATED`
TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A11C 
       13.84        14.60         0.66         0.10        37.78        21.76 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-A73E TCGA-DD-AACZ 
       12.95        29.16         5.62        78.84         1.45         5.62 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADR TCGA-DD-AADU 
       22.09        28.41        20.91        17.33        57.27         8.28 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3R2 
        4.64        12.69        16.37         0.20        22.85         6.38 
TCGA-G3-AAV2 TCGA-MI-A75G TCGA-NI-A8LF TCGA-UB-A7ME 
        9.70        18.38        16.37        15.98 

$`3P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36         9.50        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.07         0.10         0.13        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       10.98        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI 
       31.53        30.58        29.26        13.97         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       24.00        24.13         0.39         3.02         3.95         5.29 
TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB 
        9.86         8.52        12.56        11.31        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-ED-A8O5 TCGA-ED-A97K 
        0.20         0.20        13.15        13.41         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        8.12         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-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
       13.55         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            78.84            113.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            15.29             14.40 
[1] "0.1 - 78.8 (15.3)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED        18        7         0          6          0          1
  3P GAIN WILD-TYPE     128       65         2         46          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED          1         0         0
  3P GAIN WILD-TYPE        1         1         2
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 18               128
  STAGE II                 7                65
  STAGE III                0                 2
  STAGE IIIA               6                46
  STAGE IIIB               0                 7
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  3P GAIN MUTATED      19   8   6   0
  3P GAIN WILD-TYPE   136  70  58  12
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1              19               136
  T2                  8                70
  T3                  6                58
  T4                  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"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21   1
  3P GAIN WILD-TYPE 201   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21    1
  3P GAIN WILD-TYPE  201    2
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              21               201
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    25   1   7
  3P GAIN WILD-TYPE 213   3  62
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              25               213
  M1               1                 3
  MX               7                62
[1] 3 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
  3P GAIN MUTATED     7  26
  3P GAIN WILD-TYPE  93 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      7   26
  3P GAIN WILD-TYPE   93  185
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               7                93
  MALE                26               185
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P GAIN MUTATED                         0                       33
  3P GAIN WILD-TYPE                       2                      270
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P GAIN MUTATED                                  0
  3P GAIN WILD-TYPE                                6
D5V8, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      33               270
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  3P GAIN MUTATED    29   0   0   4
  3P GAIN WILD-TYPE 245  14   1  12
D5V9, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              29               245
  R1               0                14
  R2               0                 1
  RX               4                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
  3P GAIN MUTATED                                  0    17
  3P GAIN WILD-TYPE                                1   124
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    14
  3P GAIN WILD-TYPE                        13   131
D5V10, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               124
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         14               131
[1] 4 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
  3P GAIN MUTATED     1  31
  3P GAIN WILD-TYPE   7 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   31
  3P GAIN WILD-TYPE    7  256
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              31               256
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    21  10
  3Q GAIN WILD-TYPE 179  82
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               31               261 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               10                82 
$`3Q GAIN MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-A3M9 
        0.66        10.13        13.84        14.60         0.66         0.10 
TCGA-DD-A114 TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NV 
       37.78        21.76        12.95        29.16         5.62        78.84 
TCGA-DD-A73E TCGA-DD-AACL TCGA-DD-AACZ TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN 
        1.45         1.91         5.62        28.41        20.91        17.33 
TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAVS 
       57.27         8.28         4.64        12.69        16.37        59.93 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-G3-A7M9 TCGA-LG-A9QD TCGA-MI-A75G TCGA-NI-A8LF 
       22.85         6.38         1.84         4.27        18.38        16.37 
TCGA-UB-A7MD 
        1.71 

$`3Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        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-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 
        9.50        12.72         7.46        13.45         4.80         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        2.86         0.39         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        79.73        83.57        53.33       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-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
        6.02        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        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       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F 
       80.75        10.98         9.30         7.56        10.98        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        60.10         0.30        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       29.26        13.97         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW 
        0.39         3.02         3.95         5.29         7.10         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        9.67         9.86         9.63         9.47         9.86         8.52 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       12.56        11.31        14.79        12.16        15.45        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU 
       15.65        35.08        79.07        79.10        72.26        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        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        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       32.45        23.97        19.10        27.88         8.12         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-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       24.36        12.72         5.92         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71        10.85        58.88         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       17.29        14.40        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.02         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.84            113.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.95             14.79 
[1] "0.1 - 78.8 (12.9)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED        19        8         0          5          1          1
  3Q GAIN WILD-TYPE     127       64         2         47          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED          1         0         0
  3Q GAIN WILD-TYPE        1         1         2
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 19               127
  STAGE II                 8                64
  STAGE III                0                 2
  STAGE IIIA               5                47
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  3Q GAIN MUTATED      20   9   7   0
  3Q GAIN WILD-TYPE   135  69  57  12
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              20               135
  T2                  9                69
  T3                  7                57
  T4                  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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    23   1
  3Q GAIN WILD-TYPE 199   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     23    1
  3Q GAIN WILD-TYPE  199    2
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              23               199
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    26   1   9
  3Q GAIN WILD-TYPE 212   3  60
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              26               212
  M1               1                 3
  MX               9                60
[1] 3 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
  3Q GAIN MUTATED     8  28
  3Q GAIN WILD-TYPE  92 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   28
  3Q GAIN WILD-TYPE   92  183
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8                92
  MALE                28               183
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q GAIN MUTATED                         0                       35
  3Q GAIN WILD-TYPE                       2                      268
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q GAIN MUTATED                                  1
  3Q GAIN WILD-TYPE                                5
D6V8, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               268
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    32   0   0   4
  3Q GAIN WILD-TYPE 242  14   1  12
D6V9, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              32               242
  R1               0                14
  R2               0                 1
  RX               4                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
  3Q GAIN MUTATED                                  0    17
  3Q GAIN WILD-TYPE                                1   124
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           3    16
  3Q GAIN WILD-TYPE                        12   129
D6V10, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17               124
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         16               129
[1] 4 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
  3Q GAIN MUTATED     2  33
  3Q GAIN WILD-TYPE   6 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   33
  3Q GAIN WILD-TYPE    6  254
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              33               254
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    17   2
  4P GAIN WILD-TYPE 183  90
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19               273 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                90 
$`4P GAIN MUTATED`
TCGA-BC-A10R TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       10.13         0.39         0.10         0.10       113.00         2.60 
TCGA-DD-A1EC TCGA-DD-A1EH TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACM TCGA-DD-AADB 
       19.79        49.15       100.96        53.19        58.16        29.26 
TCGA-DD-AADO TCGA-DD-AAVS TCGA-ED-A82E TCGA-ED-A8O5 TCGA-G3-A3CG TCGA-LG-A6GG 
        3.02        59.93        13.41         0.20        22.13        12.72 
TCGA-WQ-A9G7 
        0.99 

$`4P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 
       13.45         4.80         0.66         0.07         2.86         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         3.32         0.07         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.33         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       90.71        79.40        66.31        75.65         6.71        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-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        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 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30         7.56        10.98         1.45        27.72        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD 
       34.09        22.09        31.53        30.58        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       17.33         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        6.67         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        79.10        72.26        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        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-A8O6 TCGA-ED-A97K 
        0.20         0.20         0.20        13.15         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-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
        4.01         2.14        11.84        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           113.00            108.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            13.41             14.60 
[1] "0.1 - 113.0 (13.4)" "0.0 - 108.8 (14.6)"
[1] "hr=" "4.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED         7        6         1          5          0          0
  4P GAIN WILD-TYPE     139       66         1         47          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED          0         0         0
  4P GAIN WILD-TYPE        2         1         2
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  7               139
  STAGE II                 6                66
  STAGE III                1                 1
  STAGE IIIA               5                47
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  4P GAIN MUTATED       7   6   8   0
  4P GAIN WILD-TYPE   148  72  56  12
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               7               148
  T2                  6                72
  T3                  8                56
  T4                  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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    18   0
  4P GAIN WILD-TYPE 204   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     18    0
  4P GAIN WILD-TYPE  204    3
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              18               204
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    20   0   1
  4P GAIN WILD-TYPE 218   4  68
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              20               218
  M1               0                 4
  MX               1                68
[1] 3 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
  4P GAIN MUTATED     8  13
  4P GAIN WILD-TYPE  92 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8   13
  4P GAIN WILD-TYPE   92  198
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               8                92
  MALE                13               198
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P GAIN MUTATED                         0                       21
  4P GAIN WILD-TYPE                       2                      282
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P GAIN MUTATED                                  0
  4P GAIN WILD-TYPE                                6
D7V8, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      21               282
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  4P GAIN MUTATED    19   1   0   1
  4P GAIN WILD-TYPE 255  13   1  15
D7V9, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              19               255
  R1               1                13
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  4P GAIN MUTATED                                  0    12
  4P GAIN WILD-TYPE                                1   129
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           1     8
  4P GAIN WILD-TYPE                        14   137
D7V10, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12               129
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          8               137
[1] 4 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
  4P GAIN MUTATED     0  21
  4P GAIN WILD-TYPE   8 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   21
  4P GAIN WILD-TYPE    8  266
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              21               266
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     5   1
  4Q GAIN WILD-TYPE 195  91
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               286 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                91 
$`4Q GAIN MUTATED`
TCGA-CC-5261 TCGA-DD-A1EC TCGA-DD-AACI TCGA-ED-A82E TCGA-G3-A3CG TCGA-G3-AAUZ 
        0.39        19.79        53.19        13.41        22.13        11.24 

$`4Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         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-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-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        75.65         6.71        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-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        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 
      108.76        12.26         0.30        80.75        78.84        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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ 
       12.53        63.48        12.00        15.42         6.41        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       29.26        13.97        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         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-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98         1.84         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        4.57         1.02         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.39              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            53.19            113.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             16.6              14.5 
[1] "0.4 - 53.2 (16.6)"  "0.0 - 113.0 (14.5)"
[1] "hr=" "1.6"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED         3        3         0          1          0          0
  4Q GAIN WILD-TYPE     143       69         2         51          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q GAIN MUTATED          0         0         0
  4Q GAIN WILD-TYPE        2         1         2
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  3               143
  STAGE II                 3                69
  STAGE III                0                 2
  STAGE IIIA               1                51
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       3   3   1   0
  4Q GAIN WILD-TYPE   152  75  63  12
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               3               152
  T2                  3                75
  T3                  1                63
  T4                  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"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7   0
  4Q GAIN WILD-TYPE 215   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    0
  4Q GAIN WILD-TYPE  215    3
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               215
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED     7   0   0
  4Q GAIN WILD-TYPE 231   4  69
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               7               231
  M1               0                 4
  MX               0                69
[1] 3 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
  4Q GAIN MUTATED     2   5
  4Q GAIN WILD-TYPE  98 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    5
  4Q GAIN WILD-TYPE   98  206
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                98
  MALE                 5               206
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q GAIN MUTATED                         0                        7
  4Q GAIN WILD-TYPE                       2                      296
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q GAIN MUTATED                                  0
  4Q GAIN WILD-TYPE                                6
D8V8, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                       7               296
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  4Q GAIN MUTATED     5   1   0   1
  4Q GAIN WILD-TYPE 269  13   1  15
D8V9, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               269
  R1               1                13
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  4Q GAIN MUTATED                                  0     4
  4Q GAIN WILD-TYPE                                1   137
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           0     2
  4Q GAIN WILD-TYPE                        15   143
D8V10, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4               137
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          2               143
[1] 4 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
  4Q GAIN MUTATED     1   6
  4Q GAIN WILD-TYPE   7 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    6
  4Q GAIN WILD-TYPE    7  281
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               6               281
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    66  41
  5P GAIN WILD-TYPE 134  51
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              107               185 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               41                51 
$`5P GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       10.78        37.32        10.13         2.99         5.03        13.84 
TCGA-BC-A3KG TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC 
       22.36        13.45         4.24         3.32         0.10         0.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57        53.33       113.00        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       66.31         6.71        12.95        21.14        55.69         5.62 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND 
        7.66        17.59       102.74        13.78         0.36        73.38 
TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       39.78        73.81        78.84       100.96        13.48         0.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACZ 
       12.00        15.42        53.19        60.10        13.15         5.62 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADN 
       21.63        34.09        31.53        13.97         3.78        17.33 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEA 
        5.29        57.27         8.28         9.86         9.86        14.79 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 
       16.37        15.65        35.08        58.78        54.05        49.48 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        13.35         0.23         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        0.20        10.98         0.62         9.96        14.40        19.10 
TCGA-FV-A3I0 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W 
       27.88         0.03        60.36         0.39        51.06        30.74 
TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-AAV1 TCGA-G3-AAV2 
       58.49        22.13        14.70        17.10        11.80         9.70 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.20         2.66        11.84        24.36        12.72         5.92 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        20.71        58.88        16.37         4.44        21.01 
TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       19.04        24.13        15.98         7.04         8.32         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        4.01        23.21         0.69        24.43        35.05 

$`5P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.59         0.66        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       44.42         0.26         9.50        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A 
        0.10         0.07        79.73        37.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
        0.46        21.76        19.79        75.65        45.11        49.15 
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-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
       70.06        20.12       107.11        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        26.83        30.51        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACA 
        7.56        10.98         1.45        27.72        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACK 
       59.18        55.40        12.53        63.48         6.41         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA 
        5.59         4.50        18.54        33.83        22.09        30.58 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       29.26        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY 
        0.39         3.02         3.95         7.10         6.67         9.67 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.63         9.47         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       12.69        12.16        15.45        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ 
       72.26        59.93        61.87        61.38        56.48        55.86 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       47.70        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        22.85        32.45        23.97         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.13         0.33         1.22        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.53        19.23        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        8.55         9.17         0.89         2.14         3.02         1.02 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
       37.71        20.75        17.06         4.01         2.14        13.38 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-QA-A7B7 
        4.27         9.57        16.67        12.85        10.85         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.04        15.39        15.52        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.71         4.57         1.02        13.55         4.67        25.71 
TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       23.57        12.99        45.57        74.24         8.22 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           113.00            108.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             14.7              14.4 
[1] "0.0 - 113.0 (14.7)" "0.1 - 108.8 (14.4)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED        48       27         1         26          3          1
  5P GAIN WILD-TYPE      98       45         1         26          4          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED          1         0         0
  5P GAIN WILD-TYPE        1         1         2
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 48                98
  STAGE II                27                45
  STAGE III                1                 1
  STAGE IIIA              26                26
  STAGE IIIB               3                 4
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  5P GAIN MUTATED      50  31  32   3
  5P GAIN WILD-TYPE   105  47  32   9
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              50               105
  T2                 31                47
  T3                 32                32
  T4                  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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    80   0
  5P GAIN WILD-TYPE 142   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     80    0
  5P GAIN WILD-TYPE  142    3
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              80               142
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED    91   1  24
  5P GAIN WILD-TYPE 147   3  45
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              91               147
  M1               1                 3
  MX              24                45
[1] 3 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
  5P GAIN MUTATED    36  80
  5P GAIN WILD-TYPE  64 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     36   80
  5P GAIN WILD-TYPE   64  131
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              36                64
  MALE                80               131
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P GAIN MUTATED                         0                      113
  5P GAIN WILD-TYPE                       2                      190
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P GAIN MUTATED                                  3
  5P GAIN WILD-TYPE                                3
D9V8, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     113               190
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  5P GAIN MUTATED   102   6   0   5
  5P GAIN WILD-TYPE 172   8   1  11
D9V9, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             102               172
  R1               6                 8
  R2               0                 1
  RX               5                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
  5P GAIN MUTATED                                  0    54
  5P GAIN WILD-TYPE                                1    87
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                           5    51
  5P GAIN WILD-TYPE                        10    94
D9V10, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         54                87
  BLACK OR AFRICAN AMERICAN                      5                10
  WHITE                                         51                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"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 105
  5P GAIN WILD-TYPE   5 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  105
  5P GAIN WILD-TYPE    5  182
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             105               182
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    52  32
  5Q GAIN WILD-TYPE 148  60
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               84               208 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               32                60 
$`5Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-A3MB TCGA-CC-A3MC 
       10.78        37.32         2.99         5.03         0.10         0.13 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
       53.33       113.00        51.29        90.71        79.40         6.71 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A5 
       21.14        55.69         5.62         7.66        17.59       102.74 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NK TCGA-DD-A4NO TCGA-DD-A4NV 
       13.78         0.36        73.38        39.78        73.81        78.84 
TCGA-DD-A73A TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACF 
       10.98       100.96        13.48         0.53        55.40        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD2 
       15.42        53.19        60.10        13.15         5.62        21.63 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       13.97         3.78         0.39        17.33         5.29        57.27 
TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEK 
        8.28         9.86         9.86        14.79        15.65        35.08 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66Y 
       56.48        58.78        54.05        49.48        13.41         0.23 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
        0.20        13.15        10.98         0.62         9.96        14.40 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A5SM 
        0.03         0.39        51.06        30.74        22.13        17.10 
TCGA-G3-AAV1 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-LG-A9QC 
       11.80         2.20         2.66        11.84        12.72         5.92 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7SF TCGA-RG-A7D4 
       18.38        20.71        16.37         4.44        19.04        24.13 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.99         4.01        23.21         0.69        24.43        35.05 

$`5Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A119 
        0.10         0.07        79.73        37.78        83.57         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
        2.60         0.46        21.76        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-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 
       13.64        19.76        25.81        70.06        20.12       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       30.61        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       80.75         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACH 
       11.41        65.75        59.18        12.53        63.48         6.41 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30         1.91        58.16        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 
       38.04         5.59         4.50        18.54        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI 
       22.09        31.53        30.58        29.26        28.41        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADS 
       24.00        24.13        20.91         3.02         3.95         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        6.67         9.67         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        11.31        12.69        12.16        15.45        16.37 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       61.38        55.86        47.70        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 
       13.35         0.20         0.20         0.20        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3RK 
        0.20         0.20        18.74        19.99        11.74        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        32.45        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        6.38         0.13         0.33        60.36         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        58.49        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-HP-A5N0 
        9.17         0.89         2.14         3.02         1.02        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        4.27         9.57        16.67        12.85        10.85        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA 
       21.01         2.04        21.04        15.39        15.52        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 
        4.57         1.02        13.55         4.67        25.71        23.57 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        74.24         8.22 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           113.00            108.76 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           14.185            14.650 
[1] "0.0 - 113.0 (14.2)" "0.1 - 108.8 (14.6)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED        40       23         1         15          2          1
  5Q GAIN WILD-TYPE     106       49         1         37          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED          1         0         0
  5Q GAIN WILD-TYPE        1         1         2
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 40               106
  STAGE II                23                49
  STAGE III                1                 1
  STAGE IIIA              15                37
  STAGE IIIB               2                 5
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  5Q GAIN MUTATED      42  27  20   2
  5Q GAIN WILD-TYPE   113  51  44  10
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1              42               113
  T2                 27                51
  T3                 20                44
  T4                  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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    63   0
  5Q GAIN WILD-TYPE 159   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     63    0
  5Q GAIN WILD-TYPE  159    3
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              63               159
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED    71   1  19
  5Q GAIN WILD-TYPE 167   3  50
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              71               167
  M1               1                 3
  MX              19                50
[1] 3 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
  5Q GAIN MUTATED    24  67
  5Q GAIN WILD-TYPE  76 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     24   67
  5Q GAIN WILD-TYPE   76  144
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              24                76
  MALE                67               144
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q GAIN MUTATED                         0                       89
  5Q GAIN WILD-TYPE                       2                      214
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q GAIN MUTATED                                  2
  5Q GAIN WILD-TYPE                                4
D10V8, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      89               214
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  5Q GAIN MUTATED    83   4   0   3
  5Q GAIN WILD-TYPE 191  10   1  13
D10V9, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              83               191
  R1               4                10
  R2               0                 1
  RX               3                13
[1] 4 2
[1] 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
  5Q GAIN MUTATED                                  0    44
  5Q GAIN WILD-TYPE                                1    97
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           4    39
  5Q GAIN WILD-TYPE                        11   106
D10V10, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         44                97
  BLACK OR AFRICAN AMERICAN                      4                11
  WHITE                                         39               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"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2  85
  5Q GAIN WILD-TYPE   6 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2   85
  5Q GAIN WILD-TYPE    6  202
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              85               202
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    60  26
  6P GAIN WILD-TYPE 140  66
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               86               206 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               26                66 
$`6P GAIN MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
        7.10        10.78        27.52        13.84        22.36        14.60 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 
       13.45         0.66         4.24         0.13        37.78         7.33 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A8 TCGA-DD-A3A9 
       45.11        49.15        55.69         5.62         0.36        30.61 
TCGA-DD-A4NN TCGA-DD-A4NS TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
       29.56        80.75         9.30        10.98         1.45         0.53 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI 
       65.75        59.18        12.53        63.48        12.00        53.19 
TCGA-DD-AACJ TCGA-DD-AACP TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADN 
       60.10        13.15        33.83        30.58        20.91        17.33 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEH 
        3.02         5.29         9.86         9.86        12.69        15.65 
TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAW2 
       35.08        72.26        59.93        61.38        58.78        49.48 
TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       47.70        13.35         0.20        13.41         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S 
       10.98         0.62        22.85        27.88         6.38         1.22 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL 
       53.79        58.49        22.13        19.23        14.70        20.42 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K2 TCGA-LG-A6GG 
        7.76        11.80         9.17         0.89        11.84        12.72 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-RC-A7SK 
       18.38        12.85        20.71        16.37        21.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-A9G7 
       24.13        14.96        14.40         7.04         8.32         0.99 
TCGA-YA-A8S7 TCGA-ZS-A9CD 
       13.55        45.57 

$`6P GAIN WILD-TYPE`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       10.59         0.66        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I 
       69.57         5.03        44.42         0.26         9.50        12.72 
TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        7.46         4.80         0.07         2.86         0.39         3.39 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.10         0.07         0.10        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33       113.00         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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95         6.02        29.16        18.35        13.64        21.14 
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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76        12.26         0.30        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC 
        7.56        27.72       100.96        13.48        11.41        55.40 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       15.42         6.41         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       18.54        21.63        34.09        22.09        31.53        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        28.41         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39         3.95        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.67         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       11.31        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       79.07        79.10        61.87        56.48        55.86        54.05 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20        13.15         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       11.74         9.96        11.93        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 
       25.64         5.92        19.53        11.97        17.10        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV6 
        5.98         1.84        11.24         8.55         9.70         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06         4.01         2.14        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
        4.27         9.57        16.67        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MD 
       21.01         2.04        19.04        15.39        17.29         1.71 
TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
       15.98         4.57         1.02         4.01         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        23.57         0.69        24.43        12.99        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            80.75            113.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.500            14.595 
[1] "0.1 - 80.8 (14.5)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED        42       25         1         20          2          1
  6P GAIN WILD-TYPE     104       47         1         32          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED          1         0         1
  6P GAIN WILD-TYPE        1         1         1
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 42               104
  STAGE II                25                47
  STAGE III                1                 1
  STAGE IIIA              20                32
  STAGE IIIB               2                 5
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  6P GAIN MUTATED      42  27  24   3
  6P GAIN WILD-TYPE   113  51  40   9
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1              42               113
  T2                 27                51
  T3                 24                40
  T4                  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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    71   0
  6P GAIN WILD-TYPE 151   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     71    0
  6P GAIN WILD-TYPE  151    3
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              71               151
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    77   2  18
  6P GAIN WILD-TYPE 161   2  51
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              77               161
  M1               2                 2
  MX              18                51
[1] 3 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
  6P GAIN MUTATED    26  71
  6P GAIN WILD-TYPE  74 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     26   71
  6P GAIN WILD-TYPE   74  140
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              26                74
  MALE                71               140
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P GAIN MUTATED                         0                       94
  6P GAIN WILD-TYPE                       2                      209
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P GAIN MUTATED                                  3
  6P GAIN WILD-TYPE                                3
D11V8, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      94               209
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  6P GAIN MUTATED    87   5   1   4
  6P GAIN WILD-TYPE 187   9   0  12
D11V9, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              87               187
  R1               5                 9
  R2               1                 0
  RX               4                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
  6P GAIN MUTATED                                  0    52
  6P GAIN WILD-TYPE                                1    89
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           6    39
  6P GAIN WILD-TYPE                         9   106
D11V10, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         52                89
  BLACK OR AFRICAN AMERICAN                      6                 9
  WHITE                                         39               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"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3  92
  6P GAIN WILD-TYPE   5 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   92
  6P GAIN WILD-TYPE    5  195
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              92               195
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    29  16
  6Q GAIN WILD-TYPE 171  76
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               45               247 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                76 
$`6Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A3EP TCGA-CC-5263 TCGA-CC-A3MC 
       10.78        22.36        14.60        13.45         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A39Y TCGA-DD-A3A9 
       37.78         7.33        45.11        49.15         5.62        30.61 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AADN 
        9.30        10.98        59.18        12.53        60.10        17.33 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAEH TCGA-DD-AAEK 
        3.02         5.29         9.86         9.86        15.65        35.08 
TCGA-DD-AAW2 TCGA-ED-A66X TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25S TCGA-G3-A25U 
       49.48        13.35        10.98         0.62         1.22        53.79 
TCGA-G3-A3CG TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-LG-A6GG 
       22.13        19.23        14.70        11.80        11.84        12.72 
TCGA-MI-A75G TCGA-MI-A75H TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC 
       18.38        12.85        21.04        15.52        24.13        14.40 
TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZS-A9CD 
        7.04        13.55        45.57 

$`6Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
        0.26         9.50        12.72         7.46         4.80         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        79.73        83.57        53.33       113.00 
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-A1EE TCGA-DD-A1EF TCGA-DD-A1EI 
       66.31        19.79        75.65         6.71        12.95         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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       78.84        10.98         7.56         1.45        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACE 
       13.48         0.53        11.41        65.75        55.40        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        53.19         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       34.09        22.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       28.41         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        0.39         3.95        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.67         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 
       61.38        56.48        58.78        55.86        54.05        47.70 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       13.41        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        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-A25V TCGA-G3-A25W TCGA-G3-A25X 
       60.36         0.39        51.06        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SJ 
       14.86        21.53        25.64         5.92        19.53        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
       11.24         8.55         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06         4.01         2.14        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        4.27         9.57        16.67        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37         4.44        21.01         2.04        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       14.96        17.29         1.71        15.98         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             60.1             113.0 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.55             14.86 
[1] "0.1 - 60.1 (13.6)"  "0.0 - 113.0 (14.9)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED        21       13         1         13          1          1
  6Q GAIN WILD-TYPE     125       59         1         39          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q GAIN MUTATED          1         0         1
  6Q GAIN WILD-TYPE        1         1         1
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 21               125
  STAGE II                13                59
  STAGE III                1                 1
  STAGE IIIA              13                39
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  6Q GAIN MUTATED      21  13  15   3
  6Q GAIN WILD-TYPE   134  65  49   9
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1              21               134
  T2                 13                65
  T3                 15                49
  T4                  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"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    41   0
  6Q GAIN WILD-TYPE 181   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     41    0
  6Q GAIN WILD-TYPE  181    3
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              41               181
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    41   2  10
  6Q GAIN WILD-TYPE 197   2  59
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              41               197
  M1               2                 2
  MX              10                59
[1] 3 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
  6Q GAIN MUTATED    12  41
  6Q GAIN WILD-TYPE  88 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     12   41
  6Q GAIN WILD-TYPE   88  170
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              12                88
  MALE                41               170
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q GAIN MUTATED                         0                       52
  6Q GAIN WILD-TYPE                       2                      251
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q GAIN MUTATED                                  1
  6Q GAIN WILD-TYPE                                5
D12V8, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      52               251
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    47   2   1   3
  6Q GAIN WILD-TYPE 227  12   0  13
D12V9, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              47               227
  R1               2                12
  R2               1                 0
  RX               3                13
[1] 4 2
[1] 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
  6Q GAIN MUTATED                                  0    29
  6Q GAIN WILD-TYPE                                1   112
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           4    20
  6Q GAIN WILD-TYPE                        11   125
D12V10, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         29               112
  BLACK OR AFRICAN AMERICAN                      4                11
  WHITE                                         20               125
[1] 4 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
  6Q GAIN MUTATED     2  50
  6Q GAIN WILD-TYPE   6 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   50
  6Q GAIN WILD-TYPE    6  237
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              50               237
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    58  27
  7P GAIN WILD-TYPE 142  65
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               85               207 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               27                65 
$`7P GAIN MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U 
        7.10        10.78        10.59        37.32        10.13        27.52 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 
       13.45         0.66         2.86         0.10        79.73       113.00 
TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EJ 
        2.60        51.29        90.71        19.79         6.71        29.16 
TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A7 TCGA-DD-A4NA 
       21.14         5.62        19.76        70.06        13.78        33.14 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73D 
       73.38        26.83        39.78        12.26        78.84        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACI 
        1.45       100.96        12.53        63.48        12.00        53.19 
TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AADD TCGA-DD-AADL 
       13.15         5.62         4.50        33.83        28.41        20.91 
TCGA-DD-AADS TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA 
        7.10         9.86         9.86         4.64        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAVP TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66Y 
       12.16        79.07        58.78        49.48        47.70         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20         0.20         0.20         0.20         0.62         9.96 
TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T 
       22.85         6.38         0.33        60.36         1.22        51.06 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL TCGA-G3-A5SM 
       28.27        58.49        22.13        19.53        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75G 
        7.76        11.80         2.14        11.84        12.72        18.38 
TCGA-NI-A8LF TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
       16.37        15.98         8.32         0.99         4.01        13.55 
TCGA-ZP-A9D1 
        0.69 

$`7P GAIN WILD-TYPE`
TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
        0.66        48.99        27.91        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-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        7.46         4.80         0.07         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        3.32         0.10         0.07         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB 
       53.33         7.33         0.46        21.76        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65        12.95        45.11        49.15         6.02        18.35 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 
       13.64        55.69        25.81         7.66        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF 
      102.74       107.11         0.36        30.61        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F 
        0.30        80.75        10.98         9.30         7.56        27.72 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42         6.41        60.10         0.30         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD1 
       14.33        48.49        40.77        38.04         5.59        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       13.97         3.78        25.08        24.00        24.13         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
       17.33         3.02         3.95         5.29        57.27         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
        6.67         9.67         9.63         9.47         8.52        12.56 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       11.31        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       55.86        54.05        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
       13.35         0.20        13.15        13.41         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        11.74        10.98        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       32.45        23.97        19.10        27.88         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.03         0.39        53.79        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 
       25.64         5.92        19.23        14.70        11.97        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27         9.57        16.67        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       10.85        58.88         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV 
       14.40         1.71         7.04         4.57         1.02         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.10              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           113.00            108.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            13.15             14.96 
[1] "0.1 - 113.0 (13.2)" "0.0 - 108.8 (15.0)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED        42       21         0         18          3          4
  7P GAIN WILD-TYPE     104       51         2         34          4          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED          1         0         0
  7P GAIN WILD-TYPE        1         1         2
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 42               104
  STAGE II                21                51
  STAGE III                0                 2
  STAGE IIIA              18                34
  STAGE IIIB               3                 4
  STAGE IIIC               4                 3
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  7P GAIN MUTATED      44  25  22   3
  7P GAIN WILD-TYPE   111  53  42   9
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              44               111
  T2                 25                53
  T3                 22                42
  T4                  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"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    63   2
  7P GAIN WILD-TYPE 159   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     63    2
  7P GAIN WILD-TYPE  159    1
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              63               159
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED    76   1  17
  7P GAIN WILD-TYPE 162   3  52
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              76               162
  M1               1                 3
  MX              17                52
[1] 3 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
  7P GAIN MUTATED    33  61
  7P GAIN WILD-TYPE  67 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     33   61
  7P GAIN WILD-TYPE   67  150
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              33                67
  MALE                61               150
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P GAIN MUTATED                         0                       93
  7P GAIN WILD-TYPE                       2                      210
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P GAIN MUTATED                                  1
  7P GAIN WILD-TYPE                                5
D13V8, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      93               210
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    82   6   0   5
  7P GAIN WILD-TYPE 192   8   1  11
D13V9, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              82               192
  R1               6                 8
  R2               0                 1
  RX               5                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
  7P GAIN MUTATED                                  1    39
  7P GAIN WILD-TYPE                                0   102
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                           4    48
  7P GAIN WILD-TYPE                        11    97
D13V10, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         39               102
  BLACK OR AFRICAN AMERICAN                      4                11
  WHITE                                         48                97
[1] 4 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
  7P GAIN MUTATED     4  87
  7P GAIN WILD-TYPE   4 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   87
  7P GAIN WILD-TYPE    4  200
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              87               200
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    53  29
  7Q GAIN WILD-TYPE 147  63
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               82               210 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               29                63 
$`7Q GAIN MUTATED`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U 
        7.10        10.78        10.59        37.32        10.13        27.52 
TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A3M9 TCGA-CC-A3MB 
        9.50        13.45         0.66         2.86         0.10         0.10 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE 
      113.00         2.60        51.29        90.71        19.79         6.71 
TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A4NA 
       29.16        21.14         5.62        19.76        70.06        33.14 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73C 
       73.38        26.83        39.78        12.26        78.84         7.56 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
        1.45       100.96        65.75        12.53        63.48        12.00 
TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADS 
       53.19        13.15        28.41        20.91         0.39         7.10 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAVX 
        9.86         4.64        12.69        14.79        12.16        56.48 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PY TCGA-EP-A26S 
       49.48        47.70        13.41         0.23         0.20        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.74         0.62         9.96        22.85         8.12         6.38 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
       51.06        28.27        58.49        22.13        19.53        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A6GG 
       17.10         7.76        11.80         2.14        11.84        12.72 
TCGA-MI-A75G TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-RC-A7S9 TCGA-UB-A7MD TCGA-UB-AA0U 
       18.38        58.88        16.37        21.04         1.71         8.32 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
        0.99         4.01        13.55         0.69 

$`7Q GAIN WILD-TYPE`
TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
        0.66        48.99        27.91        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-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       13.84         0.26        22.36        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.07         0.39         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        7.33         0.46        21.76        79.40        66.31        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-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69        25.81         7.66        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NF 
      107.11        13.78         0.36        30.61        32.52        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73F 
        0.30        80.75        10.98         9.30        10.98        27.72 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG 
       13.48         0.53        11.41        59.18        55.40        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
        6.41        60.10         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        13.97         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       24.13        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
        8.52        12.56        11.31        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI 
       61.87        61.38        58.78        55.86        54.05        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41         0.20         0.20         0.20        18.74 
TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       10.98        11.93        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       27.88         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        1.22        53.79        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M7 
        5.92        19.23        14.70        11.97        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06         4.01         2.14        13.38        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        4.44        21.01         2.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       24.13        14.96        17.29        14.40        15.98         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.57         1.02         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.10              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           113.00            108.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.28             14.91 
[1] "0.1 - 113.0 (13.3)" "0.0 - 108.8 (14.9)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED        39       22         0         18          2          4
  7Q GAIN WILD-TYPE     107       50         2         34          5          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED          1         0         0
  7Q GAIN WILD-TYPE        1         1         2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 39               107
  STAGE II                22                50
  STAGE III                0                 2
  STAGE IIIA              18                34
  STAGE IIIB               2                 5
  STAGE IIIC               4                 3
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      41  26  21   3
  7Q GAIN WILD-TYPE   114  52  43   9
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              41               114
  T2                 26                52
  T3                 21                43
  T4                  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"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    62   2
  7Q GAIN WILD-TYPE 160   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     62    2
  7Q GAIN WILD-TYPE  160    1
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              62               160
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED    70   1  20
  7Q GAIN WILD-TYPE 168   3  49
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              70               168
  M1               1                 3
  MX              20                49
[1] 3 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
  7Q GAIN MUTATED    29  62
  7Q GAIN WILD-TYPE  71 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     29   62
  7Q GAIN WILD-TYPE   71  149
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              29                71
  MALE                62               149
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q GAIN MUTATED                         0                       90
  7Q GAIN WILD-TYPE                       2                      213
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q GAIN MUTATED                                  1
  7Q GAIN WILD-TYPE                                5
D14V8, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      90               213
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    79   5   0   5
  7Q GAIN WILD-TYPE 195   9   1  11
D14V9, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              79               195
  R1               5                 9
  R2               0                 1
  RX               5                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
  7Q GAIN MUTATED                                  1    35
  7Q GAIN WILD-TYPE                                0   106
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                           5    49
  7Q GAIN WILD-TYPE                        10    96
D14V10, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         35               106
  BLACK OR AFRICAN AMERICAN                      5                10
  WHITE                                         49                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"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     4  85
  7Q GAIN WILD-TYPE   4 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   85
  7Q GAIN WILD-TYPE    4  202
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              85               202
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    45  17
  8P GAIN WILD-TYPE 155  75
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               62               230 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               17                75 
$`8P GAIN MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A1HT 
       10.78        10.59        48.99        46.78         0.07         3.32 
TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF 
        0.10         7.33         2.60        90.71        19.79        12.95 
TCGA-DD-A1EI TCGA-DD-A3A1 TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NS 
        6.02         7.66        29.56        73.81        12.26        80.75 
TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACZ TCGA-DD-AAD1 
        0.53        12.53        53.19        60.10         5.62        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR 
       21.63        34.09        22.09        28.41        20.91        57.27 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX 
        8.28         9.63         9.86        35.08        61.38        56.48 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XP TCGA-ED-A82E 
       49.48        13.41        13.35         0.23        13.15        13.41 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A5SJ 
       10.98         9.96         0.39        58.49        21.53        11.97 
TCGA-G3-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-KR-A7K2 
       20.42         5.98        11.24        11.80         9.17        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75H TCGA-MR-A8JO TCGA-UB-A7MC TCGA-WQ-A9G7 
       13.38         4.27        12.85        10.85        14.40         0.99 
TCGA-WQ-AB4B TCGA-ZS-A9CD 
        4.01        45.57 

$`8P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        7.10         0.66        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        5.03        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         0.39         3.39         4.24         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-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        45.11        49.15        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       21.14        55.69         5.62        19.76        25.81        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-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       26.83        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72       100.96        13.48        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACK 
       55.40        63.48        12.00        15.42         6.41         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA 
       38.04         5.59         4.50        33.83        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       29.26        13.97         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        17.33         3.02         3.95         5.29         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        6.67         9.67         9.86         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 
       59.93        61.87        58.78        55.86        54.05        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         1.22        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-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.53        19.23        14.70        17.10         7.76        12.03 
TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
        1.84         8.55         9.70         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C 
        4.01         2.14        24.36        12.72         5.92         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       16.67        18.38        20.71        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         2.04        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       24.13        14.96        17.29         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        8.32         4.57         1.02        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
       23.21        23.57         0.69        24.43        12.99        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.71            113.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           12.900            15.435 
[1] "0.1 - 90.7 (12.9)"  "0.0 - 113.0 (15.4)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED        32       16         0         14          1          1
  8P GAIN WILD-TYPE     114       56         2         38          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED          1         0         0
  8P GAIN WILD-TYPE        1         1         2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 32               114
  STAGE II                16                56
  STAGE III                0                 2
  STAGE IIIA              14                38
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  8P GAIN MUTATED      32  16  17   2
  8P GAIN WILD-TYPE   123  62  47  10
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              32               123
  T2                 16                62
  T3                 17                47
  T4                  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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    56   0
  8P GAIN WILD-TYPE 166   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     56    0
  8P GAIN WILD-TYPE  166    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              56               166
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    58   1   9
  8P GAIN WILD-TYPE 180   3  60
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              58               180
  M1               1                 3
  MX               9                60
[1] 3 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
  8P GAIN MUTATED    14  54
  8P GAIN WILD-TYPE  86 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     14   54
  8P GAIN WILD-TYPE   86  157
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              14                86
  MALE                54               157
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P GAIN MUTATED                         1                       66
  8P GAIN WILD-TYPE                       1                      237
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P GAIN MUTATED                                  1
  8P GAIN WILD-TYPE                                5
D15V8, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      66               237
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    59   2   1   4
  8P GAIN WILD-TYPE 215  12   0  12
D15V9, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              59               215
  R1               2                12
  R2               1                 0
  RX               4                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
  8P GAIN MUTATED                                  0    37
  8P GAIN WILD-TYPE                                1   104
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           1    28
  8P GAIN WILD-TYPE                        14   117
D15V10, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         37               104
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         28               117
[1] 4 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
  8P GAIN MUTATED     3  61
  8P GAIN WILD-TYPE   5 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   61
  8P GAIN WILD-TYPE    5  226
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              61               226
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   105  44
  8Q GAIN WILD-TYPE  95  48
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              149               143 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               44                48 
$`8Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       10.78        10.59        48.99        46.78        27.52         2.99 
TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.26        14.60         4.80         0.07         3.32         0.10 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        79.73        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF 
        2.60        21.76        90.71        19.79         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       45.11         6.02        13.64        21.14         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI 
        7.66        17.59         0.36        73.38        30.97        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        29.56        73.81        12.26         0.30        80.75 
TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       10.98       100.96         0.53        11.41        65.75        59.18 
TCGA-DD-AACD TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM 
       12.53        15.42         6.41        53.19        60.10        58.16 
TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 
       13.15         5.62        18.54        21.63        34.09        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADK 
       30.58        29.26        13.97        28.41        25.08        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        17.33         3.02         5.29        57.27 
TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAE9 
        8.28         9.86         9.63         9.86        11.31        12.69 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW 
       15.45        16.37        15.65        35.08        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E 
       13.41        13.35         0.23         0.20        13.15        13.41 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        22.85        14.40        23.97         8.12         6.38 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z 
       60.36         0.39        51.06        30.74        58.49        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A7M6 
       22.13        19.53        14.70        11.97        20.42        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-HP-A5MZ TCGA-K7-A6G5 
        5.98        11.24        11.80         9.17         2.66         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       11.84        13.38         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 
       20.71        10.85         4.44        19.04        15.39        24.13 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       14.40         1.71        15.98         8.32         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       13.55         4.67        12.99        45.57         8.22 

$`8Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
        7.10         0.66        27.91        37.32        10.13        27.52 
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-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       13.84        22.36         9.50        12.72         7.46        13.45 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MA 
        0.66         2.86         0.39         3.39         4.24         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       37.78        83.57         0.46        51.29        79.40        66.31 
TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A3A0 
       75.65        49.15        29.16        18.35        55.69        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       33.14        32.52        30.15        39.78        56.25       108.76 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       78.84        10.98         9.30         7.56         1.45        27.72 
TCGA-DD-AA3A TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACK TCGA-DD-AACL 
       13.48        55.40        63.48        12.00         0.30         1.91 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       14.33        48.49        40.77        38.04         5.59         4.50 
TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADP TCGA-DD-AADS 
       33.83        31.53         3.78        24.00         3.95         7.10 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        6.67         9.67         9.47         8.52         4.64        12.56 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       14.79        12.16        15.65        79.07        79.10        72.26 
TCGA-DD-AAVU TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       61.87        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A26S TCGA-FV-A23B TCGA-FV-A2QR 
        0.20         0.20         0.20        19.99        32.45        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25U 
       27.88         0.13         0.03         0.33         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SM 
       28.27        14.86        25.64         5.92        19.23        17.10 
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
        7.76         1.84         8.55         9.70         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        3.02         1.02         2.20        37.71        20.75        17.06 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-NI-A4U2 
        2.14        24.36        12.72         5.92        18.38        58.88 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SK TCGA-UB-A7MA 
       16.37        21.01         2.04        21.04        15.52        14.96 
TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       17.29         7.04         4.57         1.02        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        35.05        74.24 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           113.00            108.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.64             15.52 
[1] "0.1 - 113.0 (13.6)" "0.0 - 108.8 (15.5)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED        74       43         0         30          2          2
  8Q GAIN WILD-TYPE      72       29         2         22          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED          2         1         0
  8Q GAIN WILD-TYPE        0         0         2
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 74                72
  STAGE II                43                29
  STAGE III                0                 2
  STAGE IIIA              30                22
  STAGE IIIB               2                 5
  STAGE IIIC               2                 5
  STAGE IV                 2                 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                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      77 46 34  4
  8Q GAIN WILD-TYPE    78 32 30  8
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              77                78
  T2                 46                32
  T3                 34                30
  T4                  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"
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   120   1
  8Q GAIN WILD-TYPE 102   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    120    1
  8Q GAIN WILD-TYPE  102    2
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             120               102
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED   126   2  34
  8Q GAIN WILD-TYPE 112   2  35
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0             126               112
  M1               2                 2
  MX              34                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"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    38 124
  8Q GAIN WILD-TYPE  62  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     38  124
  8Q GAIN WILD-TYPE   62   87
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              38                62
  MALE               124                87
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q GAIN MUTATED                         1                      160
  8Q GAIN WILD-TYPE                       1                      143
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q GAIN MUTATED                                  1
  8Q GAIN WILD-TYPE                                5
D16V8, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                     160               143
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   143   8   1   7
  8Q GAIN WILD-TYPE 131   6   0   9
D16V9, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             143               131
  R1               8                 6
  R2               1                 0
  RX               7                 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
  8Q GAIN MUTATED                                  1    82
  8Q GAIN WILD-TYPE                                0    59
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           8    66
  8Q GAIN WILD-TYPE                         7    79
D16V10, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         82                59
  BLACK OR AFRICAN AMERICAN                      8                 7
  WHITE                                         66                79
[1] 4 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
  8Q GAIN MUTATED     7 148
  8Q GAIN WILD-TYPE   1 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7  148
  8Q GAIN WILD-TYPE    1  139
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO             148               139
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED     9   3
  9P GAIN WILD-TYPE 191  89
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12               280 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                89 
$`9P GAIN MUTATED`
TCGA-5C-AAPD TCGA-BW-A5NO TCGA-DD-A3A7 TCGA-DD-A4NV TCGA-DD-AACB TCGA-DD-AADJ 
        0.66         0.66        13.78        78.84        59.18        24.00 
TCGA-ED-A66Y TCGA-ED-A7XO TCGA-EP-A2KB TCGA-G3-A25U TCGA-KR-A7K2 TCGA-ZP-A9D1 
        0.23         0.20        10.98        53.79        11.84         0.69 

$`9P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         4.80         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-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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        65.75        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       34.09        22.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       28.41         3.78        25.08        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        32.45        23.97 
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-A25V 
        0.33        60.36         0.39         1.22        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.20              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            78.84            113.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           11.410            14.745 
[1] "0.2 - 78.8 (11.4)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P GAIN MUTATED         5        2         0          7          1          0
  9P GAIN WILD-TYPE     141       70         2         45          6          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P GAIN MUTATED          1         0         0
  9P GAIN WILD-TYPE        1         1         2
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  5               141
  STAGE II                 2                70
  STAGE III                0                 2
  STAGE IIIA               7                45
  STAGE IIIB               1                 6
  STAGE IIIC               0                 7
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  9P GAIN MUTATED       6   3   8   0
  9P GAIN WILD-TYPE   149  75  56  12
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               6               149
  T2                  3                75
  T3                  8                56
  T4                  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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    14   0
  9P GAIN WILD-TYPE 208   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    0
  9P GAIN WILD-TYPE  208    3
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              14               208
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    13   1   3
  9P GAIN WILD-TYPE 225   3  66
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              13               225
  M1               1                 3
  MX               3                66
[1] 3 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
  9P GAIN MUTATED     8   9
  9P GAIN WILD-TYPE  92 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      8    9
  9P GAIN WILD-TYPE   92  202
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               8                92
  MALE                 9               202
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P GAIN MUTATED                         0                       15
  9P GAIN WILD-TYPE                       2                      288
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P GAIN MUTATED                                  2
  9P GAIN WILD-TYPE                                4
D17V8, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      15               288
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  9P GAIN MUTATED    14   0   0   3
  9P GAIN WILD-TYPE 260  14   1  13
D17V9, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              14               260
  R1               0                14
  R2               0                 1
  RX               3                13
[1] 4 2
[1] 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
  9P GAIN MUTATED                                  0    10
  9P GAIN WILD-TYPE                                1   131
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           1     5
  9P GAIN WILD-TYPE                        14   140
D17V10, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10               131
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          5               140
[1] 4 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
  9P GAIN MUTATED     1  14
  9P GAIN WILD-TYPE   7 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   14
  9P GAIN WILD-TYPE    7  273
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              14               273
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     7   3
  9Q GAIN WILD-TYPE 193  89
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10               282 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                89 
$`9Q GAIN MUTATED`
TCGA-BW-A5NO TCGA-DD-A3A6 TCGA-DD-A4NV TCGA-DD-AADJ TCGA-ED-A66Y TCGA-EP-A2KB 
        0.66       107.11        78.84        24.00         0.23        10.98 
TCGA-G3-A25U TCGA-KR-A7K2 TCGA-WQ-A9G7 TCGA-ZP-A9D1 
       53.79        11.84         0.99         0.69 

$`9Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.07         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-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-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        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-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       102.74        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        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 
      108.76        12.26         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        7.56        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        0.30         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK 
       29.26        13.97        28.41         3.78        25.08        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        17.33         3.02         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       57.27         7.10         8.28         6.67         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.91        13.35         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41         0.20         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       19.99        11.74         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        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-A25X TCGA-G3-A25Y 
        1.22        51.06        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.23              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           107.11            113.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            11.41             14.65 
[1] "0.2 - 107.1 (11.4)" "0.0 - 113.0 (14.6)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q GAIN MUTATED         4        3         0          7          0          0
  9Q GAIN WILD-TYPE     142       69         2         45          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q GAIN MUTATED          1         0         0
  9Q GAIN WILD-TYPE        1         1         2
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  4               142
  STAGE II                 3                69
  STAGE III                0                 2
  STAGE IIIA               7                45
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  9Q GAIN MUTATED       5   4   8   0
  9Q GAIN WILD-TYPE   150  74  56  12
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1               5               150
  T2                  4                74
  T3                  8                56
  T4                  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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    13   0
  9Q GAIN WILD-TYPE 209   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13    0
  9Q GAIN WILD-TYPE  209    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              13               209
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    13   1   3
  9Q GAIN WILD-TYPE 225   3  66
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              13               225
  M1               1                 3
  MX               3                66
[1] 3 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
  9Q GAIN MUTATED    10   7
  9Q GAIN WILD-TYPE  90 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    7
  9Q GAIN WILD-TYPE   90  204
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              10                90
  MALE                 7               204
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q GAIN MUTATED                         0                       16
  9Q GAIN WILD-TYPE                       2                      287
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q GAIN MUTATED                                  1
  9Q GAIN WILD-TYPE                                5
D18V8, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      16               287
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    14   0   0   3
  9Q GAIN WILD-TYPE 260  14   1  13
D18V9, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              14               260
  R1               0                14
  R2               0                 1
  RX               3                13
[1] 4 2
[1] 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
  9Q GAIN MUTATED                                  0     9
  9Q GAIN WILD-TYPE                                1   132
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1     7
  9Q GAIN WILD-TYPE                        14   138
D18V10, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9               132
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          7               138
[1] 4 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
  9Q GAIN MUTATED     1  15
  9Q GAIN WILD-TYPE   7 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   15
  9Q GAIN WILD-TYPE    7  272
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              15               272
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    33  12
  10P GAIN WILD-TYPE 167  80
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                45                247 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 80 
$`10P GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
       10.78        37.32        10.13         0.10        79.73        37.78 
TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73D TCGA-DD-A73G 
        2.60        13.64        30.61        78.84        10.98       100.96 
TCGA-DD-AACB TCGA-DD-AACM TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AADF 
       59.18        58.16         5.62        34.09        28.41         3.78 
TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED 
       17.33         6.67         9.86        11.31        12.69        15.45 
TCGA-DD-AAEK TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-ED-A8O6 
       35.08        13.41        13.35         0.23        13.41         0.20 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       10.98        22.85         0.39        11.97        20.42        17.10 
TCGA-G3-AAV6 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA 
        2.14        10.85        16.37        15.39        15.52        14.96 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-YA-A8S7 
       15.98         8.32        13.55 

$`10P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.59         0.66        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        3.32         0.10         0.07         0.13        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-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        18.35        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        80.75        10.98         9.30         7.56 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        60.10         0.30         1.91        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        33.83        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       13.97        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.56        14.79        12.16        16.37        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.15         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        14.86        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A6UC 
       25.64         5.92        19.53        19.23        14.70         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 
        4.44        21.01         2.04        21.04        19.04        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29        14.40         1.71         7.04         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99         4.01         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.10               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            100.96             113.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.55              14.70 
[1] "0.1 - 101.0 (13.6)" "0.0 - 113.0 (14.7)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P GAIN MUTATED        21       15         0         13          0
  10P GAIN WILD-TYPE     125       57         2         39          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED            0        1         0         1
  10P GAIN WILD-TYPE          7        1         1         1
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  21                125
  STAGE II                 15                 57
  STAGE III                 0                  2
  STAGE IIIA               13                 39
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  10P GAIN MUTATED      21  17  14   1
  10P GAIN WILD-TYPE   134  61  50  11
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1               21                134
  T2                  17                 61
  T3                  14                 50
  T4                   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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    39   0
  10P GAIN WILD-TYPE 183   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     39    0
  10P GAIN WILD-TYPE  183    3
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               39                183
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    40   2  11
  10P GAIN WILD-TYPE 198   2  58
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               40                198
  M1                2                  2
  MX               11                 58
[1] 3 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
  10P GAIN MUTATED    19  34
  10P GAIN WILD-TYPE  81 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     19   34
  10P GAIN WILD-TYPE   81  177
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               19                 81
  MALE                 34                177
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P GAIN MUTATED                         1                       51
  10P GAIN WILD-TYPE                       1                      252
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P GAIN MUTATED                                  1
  10P GAIN WILD-TYPE                                5
D19V8, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       51                252
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    47   3   0   3
  10P GAIN WILD-TYPE 227  11   1  13
D19V9, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               47                227
  R1                3                 11
  R2                0                  1
  RX                3                 13
[1] 4 2
[1] 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
  10P GAIN MUTATED                                  0    29
  10P GAIN WILD-TYPE                                1   112
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           3    21
  10P GAIN WILD-TYPE                        12   124
D19V10, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          29                112
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          21                124
[1] 4 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
  10P GAIN MUTATED     3  49
  10P GAIN WILD-TYPE   5 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   49
  10P GAIN WILD-TYPE    5  238
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               49                238
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    19   7
  10Q GAIN WILD-TYPE 181  85
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                266 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                 85 
$`10Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-DD-A113 TCGA-DD-A39Z TCGA-DD-A3A9 TCGA-DD-A4NV TCGA-DD-A73G 
       10.78        79.73        19.76        30.61        78.84       100.96 
TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADN TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEK 
       59.18        28.41        17.33        12.69        15.45        35.08 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZQ 
       13.35         0.23        13.41        10.98        22.85         0.39 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-RC-A7SH TCGA-UB-A7MA 
       20.42        17.10         2.14        16.37        15.39        14.96 
TCGA-UB-AA0U TCGA-YA-A8S7 
        8.32        13.55 

$`10Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45         4.80         0.66         0.07         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-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
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       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI 
       31.53        30.58        29.26        13.97         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       24.00        24.13        20.91         0.39         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG 
       12.56        11.31        14.79        12.16        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       47.70        13.41        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20         0.20        13.15         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        32.45        23.97        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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
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-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       19.23        14.70        11.97         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        0.89         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V 
       17.29        14.40         1.71        15.98         7.04         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.23               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            100.96             113.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             15.91              14.15 
[1] "0.2 - 101.0 (15.9)" "0.0 - 113.0 (14.2)"
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q GAIN MUTATED        10       11         0          9          0
  10Q GAIN WILD-TYPE     136       61         2         43          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q GAIN MUTATED            0        1         0         1
  10Q GAIN WILD-TYPE          7        1         1         1
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  10                136
  STAGE II                 11                 61
  STAGE III                 0                  2
  STAGE IIIA                9                 43
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED      10  12   9   1
  10Q GAIN WILD-TYPE   145  66  55  11
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1               10                145
  T2                  12                 66
  T3                   9                 55
  T4                   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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    23   0
  10Q GAIN WILD-TYPE 199   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     23    0
  10Q GAIN WILD-TYPE  199    3
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               23                199
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    24   2   6
  10Q GAIN WILD-TYPE 214   2  63
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               24                214
  M1                2                  2
  MX                6                 63
[1] 3 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
  10Q GAIN MUTATED    14  18
  10Q GAIN WILD-TYPE  86 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   18
  10Q GAIN WILD-TYPE   86  193
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                 86
  MALE                 18                193
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q GAIN MUTATED                         0                       31
  10Q GAIN WILD-TYPE                       2                      272
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q GAIN MUTATED                                  1
  10Q GAIN WILD-TYPE                                5
D20V8, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       31                272
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    29   2   0   1
  10Q GAIN WILD-TYPE 245  12   1  15
D20V9, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               29                245
  R1                2                 12
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  10Q GAIN MUTATED                                  0    15
  10Q GAIN WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0    16
  10Q GAIN WILD-TYPE                        15   129
D20V10, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                126
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          16                129
[1] 4 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
  10Q GAIN MUTATED     3  28
  10Q GAIN WILD-TYPE   5 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   28
  10Q GAIN WILD-TYPE    5  259
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               28                259
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    10   3
  11P GAIN WILD-TYPE 190  89
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                279 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 89 
$`11P GAIN MUTATED`
TCGA-BC-A69H TCGA-BD-A3EP TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NV TCGA-DD-AAD1 
       14.60        13.45         7.33         5.62        78.84        18.54 
TCGA-ED-A66Y TCGA-ED-A82E TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-LG-A6GG TCGA-UB-A7ME 
        0.23        13.41         0.39        22.13        12.72        15.98 
TCGA-WQ-A9G7 
        0.99 

$`11P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A69I TCGA-BC-A8YO 
       13.84         0.26        22.36         9.50        12.72         7.46 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         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-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        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-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-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
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       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         5.62         4.50        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
        0.20         0.20         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K 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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33        60.36         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       28.27        30.74        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U 
       14.96        17.29        14.40         1.71         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.23               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             78.84             113.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.41              14.79 
[1] "0.2 - 78.8 (13.4)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED         7        2         0          5          0
  11P GAIN WILD-TYPE     139       70         2         47          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED            0        1         0         0
  11P GAIN WILD-TYPE          7        1         1         2
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   7                139
  STAGE II                  2                 70
  STAGE III                 0                  2
  STAGE IIIA                5                 47
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       7   2   7   0
  11P GAIN WILD-TYPE   148  76  57  12
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                7                148
  T2                   2                 76
  T3                   7                 57
  T4                   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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     9   0
  11P GAIN WILD-TYPE 213   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    0
  11P GAIN WILD-TYPE  213    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                9                213
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED    13   1   2
  11P GAIN WILD-TYPE 225   3  67
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               13                225
  M1                1                  3
  MX                2                 67
[1] 3 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
  11P GAIN MUTATED     6  10
  11P GAIN WILD-TYPE  94 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6   10
  11P GAIN WILD-TYPE   94  201
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                6                 94
  MALE                 10                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P GAIN MUTATED                         0                       16
  11P GAIN WILD-TYPE                       2                      287
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P GAIN MUTATED                                  0
  11P GAIN WILD-TYPE                                6
D21V8, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       16                287
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  11P GAIN MUTATED    12   2   1   1
  11P GAIN WILD-TYPE 262  12   0  15
D21V9, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               12                262
  R1                2                 12
  R2                1                  0
  RX                1                 15
[1] 4 2
[1] 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
  11P GAIN MUTATED                                  0     8
  11P GAIN WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           1     7
  11P GAIN WILD-TYPE                        14   138
D21V10, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                133
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           7                138
[1] 4 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
  11P GAIN MUTATED     0  16
  11P GAIN WILD-TYPE   8 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   16
  11P GAIN WILD-TYPE    8  271
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               16                271
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    10   4
  11Q GAIN WILD-TYPE 190  88
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                278 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 88 
$`11Q GAIN MUTATED`
TCGA-BC-A69I TCGA-BD-A3EP TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NV 
       12.72        13.45         7.33         5.62        25.81        78.84 
TCGA-DD-AAD1 TCGA-DD-AADW TCGA-DD-AAE0 TCGA-ED-A66Y TCGA-ED-A82E TCGA-G3-A3CG 
       18.54         6.67         9.86         0.23        13.41        22.13 
TCGA-LG-A6GG TCGA-WQ-A9G7 
       12.72         0.99 

$`11Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A8YO 
       13.84         0.26        22.36         9.50        14.60         7.46 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         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-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        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       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       59.18        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62         4.50        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        13.15         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        11.84        13.38        24.36         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       14.40         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.23               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             78.84             113.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.720             14.825 
[1] "0.2 - 78.8 (12.7)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED         8        1         0          6          0
  11Q GAIN WILD-TYPE     138       71         2         46          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED            0        1         0         0
  11Q GAIN WILD-TYPE          7        1         1         2
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   8                138
  STAGE II                  1                 71
  STAGE III                 0                  2
  STAGE IIIA                6                 46
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       8   1   8   0
  11Q GAIN WILD-TYPE   147  77  56  12
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                147
  T2                   1                 77
  T3                   8                 56
  T4                   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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   0
  11Q GAIN WILD-TYPE 210   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    0
  11Q GAIN WILD-TYPE  210    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               12                210
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED    15   1   1
  11Q GAIN WILD-TYPE 223   3  68
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               15                223
  M1                1                  3
  MX                1                 68
[1] 3 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
  11Q GAIN MUTATED     7  10
  11Q GAIN WILD-TYPE  93 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   10
  11Q GAIN WILD-TYPE   93  201
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                7                 93
  MALE                 10                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q GAIN MUTATED                         0                       17
  11Q GAIN WILD-TYPE                       2                      286
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q GAIN MUTATED                                  0
  11Q GAIN WILD-TYPE                                6
D22V8, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       17                286
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  11Q GAIN MUTATED    13   2   1   1
  11Q GAIN WILD-TYPE 261  12   0  15
D22V9, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               13                261
  R1                2                 12
  R2                1                  0
  RX                1                 15
[1] 4 2
[1] 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
  11Q GAIN MUTATED                                  0     9
  11Q GAIN WILD-TYPE                                1   132
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           1     7
  11Q GAIN WILD-TYPE                        14   138
D22V10, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                132
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           7                138
[1] 4 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
  11Q GAIN MUTATED     0  16
  11Q GAIN WILD-TYPE   8 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   16
  11Q GAIN WILD-TYPE    8  271
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               16                271
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    19  10
  12P GAIN WILD-TYPE 181  82
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                29                263 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                 82 
$`12P GAIN MUTATED`
TCGA-5C-A9VG TCGA-BW-A5NO TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A3A7 TCGA-DD-A4NR 
       10.78         0.66         2.60        12.95        13.78         0.30 
TCGA-DD-A73G TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACZ TCGA-DD-AADF TCGA-DD-AADR 
      100.96        53.19         0.30         5.62         3.78        57.27 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 
        0.23         0.20         0.20        13.41         9.96        27.88 
TCGA-G3-A25T TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-MI-A75C 
       51.06         1.84        11.80         2.14        11.84         9.57 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-UB-A7MA TCGA-UB-A7ME TCGA-WQ-A9G7 
       16.37        21.01        14.96        15.98         0.99 

$`12P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         4.80         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-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-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       60.10         1.91        58.16        13.15        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       40.77        38.04         5.59         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        17.33         3.02         3.95         5.29         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       22.85        14.40        32.45        23.97        19.10         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-A25X TCGA-G3-A25Y 
        1.22        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       10.85        58.88         4.44         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        24.13        17.29        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 
        7.04         8.32         4.57         1.02         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.20               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            100.96             113.00 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             10.78              15.42 
[1] "0.2 - 101.0 (10.8)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED        13        7         0         10          3
  12P GAIN WILD-TYPE     133       65         2         42          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED            1        0         0         0
  12P GAIN WILD-TYPE          6        2         1         2
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  13                133
  STAGE II                  7                 65
  STAGE III                 0                  2
  STAGE IIIA               10                 42
  STAGE IIIB                3                  4
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      13   7  13   2
  12P GAIN WILD-TYPE   142  71  51  10
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               13                142
  T2                   7                 71
  T3                  13                 51
  T4                   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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26   0
  12P GAIN WILD-TYPE 196   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26    0
  12P GAIN WILD-TYPE  196    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               26                196
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    30   0   5
  12P GAIN WILD-TYPE 208   4  64
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               30                208
  M1                0                  4
  MX                5                 64
[1] 3 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
  12P GAIN MUTATED    15  20
  12P GAIN WILD-TYPE  85 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15   20
  12P GAIN WILD-TYPE   85  191
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               15                 85
  MALE                 20                191
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P GAIN MUTATED                         0                       32
  12P GAIN WILD-TYPE                       2                      271
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P GAIN MUTATED                                  3
  12P GAIN WILD-TYPE                                3
D23V8, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       32                271
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  12P GAIN MUTATED    30   1   0   2
  12P GAIN WILD-TYPE 244  13   1  14
D23V9, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               30                244
  R1                1                 13
  R2                0                  1
  RX                2                 14
[1] 4 2
[1] 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
  12P GAIN MUTATED                                  0    17
  12P GAIN WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           2    15
  12P GAIN WILD-TYPE                        13   130
D23V10, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                124
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          15                130
[1] 4 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
  12P GAIN MUTATED     0  33
  12P GAIN WILD-TYPE   8 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   33
  12P GAIN WILD-TYPE    8  254
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               33                254
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    21  10
  12Q GAIN WILD-TYPE 179  82
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                31                261 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                10                 82 
$`12Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A3KF TCGA-BW-A5NO TCGA-DD-A11A TCGA-DD-A1EF TCGA-DD-A1EJ 
       10.78         0.26         0.66         2.60        12.95        29.16 
TCGA-DD-A3A7 TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AACI 
       13.78        73.38        30.15         0.30       100.96        53.19 
TCGA-DD-AACK TCGA-DD-AACZ TCGA-DD-AADR TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ 
        0.30         5.62        57.27         0.23         0.20         0.20 
TCGA-ED-A82E TCGA-EP-A3JL TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A7M9 TCGA-G3-AAV1 
       13.41         9.96        27.88        51.06         1.84        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-MI-A75C TCGA-NI-A8LF TCGA-PD-A5DF TCGA-UB-A7ME 
        2.14        11.84         9.57        16.37        21.01        15.98 
TCGA-WQ-A9G7 
        0.99 

$`12Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.07         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-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        45.11        49.15         6.02        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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NI 
        0.36        30.61        33.14        32.52        30.97        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       10.98         1.45        27.72        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       15.42         6.41        60.10         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 
       14.33        48.49        40.77        38.04         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       24.00        24.13        20.91         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        3.95         5.29         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       15.85        13.91        13.35         0.20         0.20        13.15 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 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-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         0.62        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E 
       13.38        24.36        12.72         5.92         4.27        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71        10.85        58.88         4.44 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U 
       14.96        17.29        14.40         1.71         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.20               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            100.96             113.00 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             11.80              14.96 
[1] "0.2 - 101.0 (11.8)" "0.0 - 113.0 (15.0)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED        14        6         0         10          4
  12Q GAIN WILD-TYPE     132       66         2         42          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED            2        0         0         0
  12Q GAIN WILD-TYPE          5        2         1         2
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  14                132
  STAGE II                  6                 66
  STAGE III                 0                  2
  STAGE IIIA               10                 42
  STAGE IIIB                4                  3
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED      15   6  14   2
  12Q GAIN WILD-TYPE   140  72  50  10
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1               15                140
  T2                   6                 72
  T3                  14                 50
  T4                   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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    26   1
  12Q GAIN WILD-TYPE 196   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     26    1
  12Q GAIN WILD-TYPE  196    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               26                196
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    32   0   5
  12Q GAIN WILD-TYPE 206   4  64
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               32                206
  M1                0                  4
  MX                5                 64
[1] 3 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
  12Q GAIN MUTATED    17  20
  12Q GAIN WILD-TYPE  83 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     17   20
  12Q GAIN WILD-TYPE   83  191
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               17                 83
  MALE                 20                191
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q GAIN MUTATED                         0                       35
  12Q GAIN WILD-TYPE                       2                      268
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q GAIN MUTATED                                  2
  12Q GAIN WILD-TYPE                                4
D24V8, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       35                268
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  12Q GAIN MUTATED    33   0   0   2
  12Q GAIN WILD-TYPE 241  14   1  14
D24V9, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               33                241
  R1                0                 14
  R2                0                  1
  RX                2                 14
[1] 4 2
[1] 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
  12Q GAIN MUTATED                                  0    16
  12Q GAIN WILD-TYPE                                1   125
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           2    18
  12Q GAIN WILD-TYPE                        13   127
D24V10, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                125
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          18                127
[1] 4 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
  12Q GAIN MUTATED     0  34
  12Q GAIN WILD-TYPE   8 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   34
  12Q GAIN WILD-TYPE    8  253
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               34                253
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     9   8
  13Q GAIN WILD-TYPE 191  84
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                17                275 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 84 
$`13Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-BD-A3EP TCGA-CC-5263 TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A7 
        0.26        13.45         4.24        45.11        29.16        13.78 
TCGA-DD-AACB TCGA-DD-AAE3 TCGA-DD-AAVW TCGA-ED-A66Y TCGA-EP-A3JL TCGA-FV-A23B 
       59.18         9.86        61.38         0.23         9.96        32.45 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MC 
       11.80         2.14        21.04        24.13        14.40 

$`13Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
       13.84        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         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-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-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65         6.71        12.95        49.15         6.02 
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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
      107.11         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.63         9.47         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       15.45        16.37        15.65        15.65        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY 
       79.10        72.26        59.93        61.87        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91        13.35         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        13.15        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        11.74        10.98         0.62        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        14.40        23.97        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-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.17         0.89         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37         4.44        21.01         2.04        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        14.96        17.29         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.23               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             61.38             113.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.78              14.70 
[1] "0.2 - 61.4 (13.8)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.7"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED         8        2         0          5          1
  13Q GAIN WILD-TYPE     138       70         2         47          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED            2        1         0         0
  13Q GAIN WILD-TYPE          5        1         1         2
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   8                138
  STAGE II                  2                 70
  STAGE III                 0                  2
  STAGE IIIA                5                 47
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED       9   3   6   1
  13Q GAIN WILD-TYPE   146  75  58  11
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1                9                146
  T2                   3                 75
  T3                   6                 58
  T4                   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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    16   1
  13Q GAIN WILD-TYPE 206   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     16    1
  13Q GAIN WILD-TYPE  206    2
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               16                206
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    16   1   2
  13Q GAIN WILD-TYPE 222   3  67
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               16                222
  M1                1                  3
  MX                2                 67
[1] 3 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
  13Q GAIN MUTATED     9  10
  13Q GAIN WILD-TYPE  91 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9   10
  13Q GAIN WILD-TYPE   91  201
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                9                 91
  MALE                 10                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q GAIN MUTATED                         0                       19
  13Q GAIN WILD-TYPE                       2                      284
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                                6
D25V8, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       19                284
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  13Q GAIN MUTATED    16   0   0   2
  13Q GAIN WILD-TYPE 258  14   1  14
D25V9, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               16                258
  R1                0                 14
  R2                0                  1
  RX                2                 14
[1] 4 2
[1] 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
  13Q GAIN MUTATED                                  0     8
  13Q GAIN WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           2     8
  13Q GAIN WILD-TYPE                        13   137
D25V10, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                133
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                           8                137
[1] 4 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
  13Q GAIN MUTATED     1  16
  13Q GAIN WILD-TYPE   7 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   16
  13Q GAIN WILD-TYPE    7  271
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               16                271
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    11   6
  14Q GAIN WILD-TYPE 189  86
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                17                275 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 86 
$`14Q GAIN MUTATED`
TCGA-BD-A3EP TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A4ND TCGA-DD-AACB 
       13.45         0.10        37.78         7.33        73.38        59.18 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ES-A2HS TCGA-FV-A3I0 
        9.86         4.64         0.23         0.20        22.85        27.88 
TCGA-G3-A3CG TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-UB-A7ME TCGA-YA-A8S7 
       22.13         2.14        11.84        15.98        13.55 

$`14Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46         4.80         0.66         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.39         4.24         3.32         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        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       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       65.75        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        8.52        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       15.45        16.37        15.65        15.65        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        13.15        13.41         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        32.45        23.97        19.10         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-A25X 
        1.22        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.17         0.89         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 
       37.71        20.75        17.06         4.01         2.14        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       18.38        12.85        20.71        10.85        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.10               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             73.38             113.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             13.45              14.70 
[1] "0.1 - 73.4 (13.4)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED         9        2         0          5          0
  14Q GAIN WILD-TYPE     137       70         2         47          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q GAIN MUTATED            0        1         0         0
  14Q GAIN WILD-TYPE          7        1         1         2
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   9                137
  STAGE II                  2                 70
  STAGE III                 0                  2
  STAGE IIIA                5                 47
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED       9   2   6   0
  14Q GAIN WILD-TYPE   146  76  58  12
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1                9                146
  T2                   2                 76
  T3                   6                 58
  T4                   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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    13   0
  14Q GAIN WILD-TYPE 209   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     13    0
  14Q GAIN WILD-TYPE  209    3
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               13                209
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED    13   1   3
  14Q GAIN WILD-TYPE 225   3  66
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               13                225
  M1                1                  3
  MX                3                 66
[1] 3 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
  14Q GAIN MUTATED     7  10
  14Q GAIN WILD-TYPE  93 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7   10
  14Q GAIN WILD-TYPE   93  201
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                7                 93
  MALE                 10                201
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q GAIN MUTATED                         0                       15
  14Q GAIN WILD-TYPE                       2                      288
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q GAIN MUTATED                                  2
  14Q GAIN WILD-TYPE                                4
D26V8, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       15                288
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  14Q GAIN MUTATED    15   1   1   0
  14Q GAIN WILD-TYPE 259  13   0  16
D26V9, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               15                259
  R1                1                 13
  R2                1                  0
  RX                0                 16
[1] 4 2
[1] 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
  14Q GAIN MUTATED                                  0     8
  14Q GAIN WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           2     7
  14Q GAIN WILD-TYPE                        13   138
D26V10, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                133
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                           7                138
[1] 4 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
  14Q GAIN MUTATED     1  15
  14Q GAIN WILD-TYPE   7 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   15
  14Q GAIN WILD-TYPE    7  272
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               15                272
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    23   4
  15Q GAIN WILD-TYPE 177  88
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                265 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 88 
$`15Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-CC-A3M9 TCGA-DD-A4NI 
       10.78        37.32        23.34        22.36         0.10        26.83 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AADU 
       78.84       100.96        59.18        13.15         5.62         8.28 
TCGA-DD-AAE3 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A8O6 
        9.86        11.31        14.79        35.08        13.35         0.20 
TCGA-ES-A2HS TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A6UC TCGA-MI-A75G 
       22.85         0.39        51.06        58.49         7.76        18.38 
TCGA-MR-A8JO TCGA-RC-A7SK TCGA-WQ-AB4B 
       10.85        15.52         4.01 

$`15Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       69.57         5.03        44.42        13.84         0.26         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
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-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-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        30.51        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       108.76        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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        11.41        65.75        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       63.48        12.00        15.42         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30         1.91        58.16        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       38.04         5.59         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       34.09        22.09        31.53        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       28.41         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        8.52         4.64        12.56        12.69        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        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-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33        60.36         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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       17.10        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27         9.57        16.67        12.85        20.71 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            100.96             113.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             14.79              14.40 
[1] "0.1 - 101.0 (14.8)" "0.0 - 113.0 (14.4)"
[1] "hr=" "2.3"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED        11        8         0          6          2
  15Q GAIN WILD-TYPE     135       64         2         46          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED            0        0         0         0
  15Q GAIN WILD-TYPE          7        2         1         2
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  11                135
  STAGE II                  8                 64
  STAGE III                 0                  2
  STAGE IIIA                6                 46
  STAGE IIIB                2                  5
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED      11   9   7   2
  15Q GAIN WILD-TYPE   144  69  57  10
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1               11                144
  T2                   9                 69
  T3                   7                 57
  T4                   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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    23   0
  15Q GAIN WILD-TYPE 199   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     23    0
  15Q GAIN WILD-TYPE  199    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               23                199
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    25   0   4
  15Q GAIN WILD-TYPE 213   4  65
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               25                213
  M1                0                  4
  MX                4                 65
[1] 3 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
  15Q GAIN MUTATED     7  22
  15Q GAIN WILD-TYPE  93 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7   22
  15Q GAIN WILD-TYPE   93  189
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 93
  MALE                 22                189
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q GAIN MUTATED                         1                       28
  15Q GAIN WILD-TYPE                       1                      275
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q GAIN MUTATED                                  0
  15Q GAIN WILD-TYPE                                6
D27V8, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       28                275
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  15Q GAIN MUTATED    27   1   0   1
  15Q GAIN WILD-TYPE 247  13   1  15
D27V9, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               27                247
  R1                1                 13
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  15Q GAIN MUTATED                                  0    15
  15Q GAIN WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           0    14
  15Q GAIN WILD-TYPE                        15   131
D27V10, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                126
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                          14                131
[1] 4 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
  15Q GAIN MUTATED     0  28
  15Q GAIN WILD-TYPE   8 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   28
  15Q GAIN WILD-TYPE    8  259
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               28                259
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    17   6
  16P GAIN WILD-TYPE 183  86
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                269 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 86 
$`16P GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A1EL TCGA-DD-A3A5 
       10.13         5.03        79.73         2.60        13.64       102.74 
TCGA-DD-AACI TCGA-DD-AADN TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAW0 TCGA-ED-A459 
       53.19        17.33         9.86         8.52        54.05        13.41 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SM TCGA-G3-AAV1 
        0.20        13.41         1.22        51.06        17.10        11.80 
TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-UB-A7MB TCGA-UB-AA0U 
       11.84        10.85        16.37        17.29         8.32 

$`16P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         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-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-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       29.16        18.35        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-A3A6 
       25.81         7.66        70.06        17.59        20.12       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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       59.18        55.40        12.53        63.48        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
        6.41        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       25.08        24.00        24.13        20.91         0.39         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.67         9.86         9.63         9.47         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        47.70        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-A8O5 
        0.23         0.20         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K 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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        9.70         9.17         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        2.14        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        24.13        14.96        14.40         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        7.04         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.20               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            102.74             113.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             13.41              14.79 
[1] "0.2 - 102.7 (13.4)" "0.0 - 113.0 (14.8)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED         9        8         1          3          0
  16P GAIN WILD-TYPE     137       64         1         49          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED            1        0         0         0
  16P GAIN WILD-TYPE          6        2         1         2
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   9                137
  STAGE II                  8                 64
  STAGE III                 1                  1
  STAGE IIIA                3                 49
  STAGE IIIB                0                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  16P GAIN MUTATED       9   8   6   1
  16P GAIN WILD-TYPE   146  70  58  11
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                9                146
  T2                   8                 70
  T3                   6                 58
  T4                   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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    16   0
  16P GAIN WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     16    0
  16P GAIN WILD-TYPE  206    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               16                206
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    17   0   7
  16P GAIN WILD-TYPE 221   4  62
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               17                221
  M1                0                  4
  MX                7                 62
[1] 3 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
  16P GAIN MUTATED     6  18
  16P GAIN WILD-TYPE  94 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6   18
  16P GAIN WILD-TYPE   94  193
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                6                 94
  MALE                 18                193
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P GAIN MUTATED                         1                       22
  16P GAIN WILD-TYPE                       1                      281
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P GAIN MUTATED                                  1
  16P GAIN WILD-TYPE                                5
D28V8, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       22                281
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    21   2   0   1
  16P GAIN WILD-TYPE 253  12   1  15
D28V9, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               21                253
  R1                2                 12
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  16P GAIN MUTATED                                  0    10
  16P GAIN WILD-TYPE                                1   131
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           2    12
  16P GAIN WILD-TYPE                        13   133
D28V10, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                131
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          12                133
[1] 4 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
  16P GAIN MUTATED     1  21
  16P GAIN WILD-TYPE   7 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   21
  16P GAIN WILD-TYPE    7  266
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               21                266
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     7   3
  16Q GAIN WILD-TYPE 193  89
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                282 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 89 
$`16Q GAIN MUTATED`
TCGA-DD-A1EL TCGA-DD-AADN TCGA-DD-AAE3 TCGA-ED-A82E TCGA-G3-A25T TCGA-G3-A5SM 
       13.64        17.33         9.86        13.41        51.06        17.10 
TCGA-G3-AAV1 TCGA-KR-A7K2 TCGA-MR-A8JO TCGA-YA-A8S7 
       11.80        11.84        10.85        13.55 

$`16Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         0.07         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-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-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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        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       108.76        12.26         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO 
       25.08        24.00        24.13        20.91         0.39         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         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-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        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-A25U TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        18.38        12.85        20.71        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04         8.32         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        4.01         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              9.86               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             51.06             113.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            13.480             14.745 
[1] "9.9 - 51.1 (13.5)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED         4        2         0          4          0
  16Q GAIN WILD-TYPE     142       70         2         48          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED            1        0         0         0
  16Q GAIN WILD-TYPE          6        2         1         2
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   4                142
  STAGE II                  2                 70
  STAGE III                 0                  2
  STAGE IIIA                4                 48
  STAGE IIIB                0                  7
  STAGE IIIC                1                  6
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED       4   2   4   1
  16Q GAIN WILD-TYPE   151  76  60  11
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1                4                151
  T2                   2                 76
  T3                   4                 60
  T4                   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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     9   0
  16Q GAIN WILD-TYPE 213   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      9    0
  16Q GAIN WILD-TYPE  213    3
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                9                213
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED     8   0   3
  16Q GAIN WILD-TYPE 230   4  66
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                8                230
  M1                0                  4
  MX                3                 66
[1] 3 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
  16Q GAIN MUTATED     2   9
  16Q GAIN WILD-TYPE  98 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    9
  16Q GAIN WILD-TYPE   98  202
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                2                 98
  MALE                  9                202
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q GAIN MUTATED                         1                        9
  16Q GAIN WILD-TYPE                       1                      294
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                                5
D29V8, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                        9                294
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    10   0   0   1
  16Q GAIN WILD-TYPE 264  14   1  15
D29V9, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               10                264
  R1                0                 14
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  16Q GAIN MUTATED                                  0     5
  16Q GAIN WILD-TYPE                                1   136
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           1     5
  16Q GAIN WILD-TYPE                        14   140
D29V10, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                136
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           5                140
[1] 4 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
  16Q GAIN MUTATED     1   8
  16Q GAIN WILD-TYPE   7 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    8
  16Q GAIN WILD-TYPE    7  279
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                8                279
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    18   8
  17P GAIN WILD-TYPE 182  84
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                26                266 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                 84 
$`17P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A3A7 TCGA-DD-A4NO 
       37.32         0.66         0.10        37.78        13.78        73.81 
TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACI TCGA-DD-AACS 
      108.76        10.98        11.41        59.18        53.19        48.49 
TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AADD TCGA-DD-AAE3 TCGA-ED-A66X TCGA-ED-A66Y 
        4.50        34.09        28.41         9.86        13.35         0.23 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-AAV6 TCGA-NI-A8LF 
       10.98        22.85        60.36        30.74         2.14        16.37 
TCGA-UB-A7MA TCGA-UB-AA0U 
       14.96         8.32 

$`17P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
       13.45         4.80         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        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-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       56.25        29.56        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         9.30         7.56         1.45        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       13.48         0.53        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       58.16        13.15        14.33        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
        5.62        18.54        21.63        33.83        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        13.97         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.86         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91         0.20         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         0.62         9.96        11.93        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       28.27        58.49        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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
        8.55        11.80         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71        10.85        58.88         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       14.40         1.71        15.98         7.04         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.10               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            108.76             113.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            15.665             14.400 
[1] "0.1 - 108.8 (15.7)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED        12        6         0          7          2
  17P GAIN WILD-TYPE     134       66         2         45          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED            0        0         0         0
  17P GAIN WILD-TYPE          7        2         1         2
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  12                134
  STAGE II                  6                 66
  STAGE III                 0                  2
  STAGE IIIA                7                 45
  STAGE IIIB                2                  5
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  17P GAIN MUTATED      12   7   9   0
  17P GAIN WILD-TYPE   143  71  55  12
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1               12                143
  T2                   7                 71
  T3                   9                 55
  T4                   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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    19   0
  17P GAIN WILD-TYPE 203   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     19    0
  17P GAIN WILD-TYPE  203    3
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               19                203
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED    21   0   7
  17P GAIN WILD-TYPE 217   4  62
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               21                217
  M1                0                  4
  MX                7                 62
[1] 3 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
  17P GAIN MUTATED     9  19
  17P GAIN WILD-TYPE  91 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   19
  17P GAIN WILD-TYPE   91  192
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                 91
  MALE                 19                192
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P GAIN MUTATED                         0                       27
  17P GAIN WILD-TYPE                       2                      276
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P GAIN MUTATED                                  1
  17P GAIN WILD-TYPE                                5
D30V8, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       27                276
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    23   4   0   1
  17P GAIN WILD-TYPE 251  10   1  15
D30V9, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               23                251
  R1                4                 10
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  17P GAIN MUTATED                                  0    13
  17P GAIN WILD-TYPE                                1   128
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           2    12
  17P GAIN WILD-TYPE                        13   133
D30V10, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                128
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          12                133
[1] 4 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
  17P GAIN MUTATED     1  26
  17P GAIN WILD-TYPE   7 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   26
  17P GAIN WILD-TYPE    7  261
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               26                261
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    51  22
  17Q GAIN WILD-TYPE 149  70
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                73                219 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                 70 
$`17Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       48.99        37.32         2.99        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       13.84        14.60         0.66         2.86         0.39         4.24 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EI 
        0.13        37.78         7.33         2.60        79.40         6.02 
TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NO TCGA-DD-A4NP 
        5.62        17.59        13.78        30.61        73.81       108.76 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACE 
       10.98         1.45        11.41        65.75        59.18        63.48 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD5 
       53.19        60.10        48.49         5.59         4.50        34.09 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AAE3 
       13.97        28.41         3.02        57.27         8.28         9.86 
TCGA-DD-AAEA TCGA-DD-AAEE TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A8O6 
       14.79        16.37        13.35         0.23         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A495 TCGA-FV-A4ZP TCGA-G3-A25U 
       10.98         0.62        22.85         0.03        60.36        53.79 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-AAUZ 
       30.74        21.53        19.23        11.97        12.03        11.24 
TCGA-G3-AAV6 TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-UB-A7MA 
        2.14        18.38        20.71        16.37         4.44        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CZ TCGA-ZP-A9D2 
       17.29        14.40         8.32         1.02        23.21        24.43 
TCGA-ZP-A9D4 
       12.99 

$`17Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.78        10.59         0.66        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A216 
       46.78        27.52        27.52        25.32        69.57        44.42 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36         9.50        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.80         0.07         3.39         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B 
        0.10        79.73        83.57        53.33       113.00         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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK 
        6.71        12.95        45.11        49.15        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-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA 
       70.06        20.12       102.74       107.11         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       32.52        73.38        30.97        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       39.78        56.25        29.56        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       78.84        10.98         9.30         7.56        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       13.48         0.53        55.40        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
        6.41         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       40.77        38.04         5.62        18.54        21.63        33.83 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI 
       22.09        31.53        30.58        29.26         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       24.00        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        5.29         7.10         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.47         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       12.16        15.45        15.65        15.65        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       12.69        15.85        13.91         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       11.74         9.96        11.93        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       19.10        27.88         8.12         6.38         0.13         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.39         1.22        51.06        28.27        58.49        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL 
       22.13        25.64         5.92        19.53        14.70        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV1 
       17.10         7.76         5.98         1.84         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF 
        9.57        16.67        12.85        10.85        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98         7.04         4.57         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CD 
       13.55         4.67        25.71        23.57         0.69        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            108.76             113.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.84              15.39 
[1] "0.0 - 108.8 (13.8)" "0.1 - 113.0 (15.4)"
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED        35       17         0         15          3
  17Q GAIN WILD-TYPE     111       55         2         37          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED            1        1         0         1
  17Q GAIN WILD-TYPE          6        1         1         1
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  35                111
  STAGE II                 17                 55
  STAGE III                 0                  2
  STAGE IIIA               15                 37
  STAGE IIIB                3                  4
  STAGE IIIC                1                  6
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED      37  20  19   5
  17Q GAIN WILD-TYPE   118  58  45   7
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1               37                118
  T2                  20                 58
  T3                  19                 45
  T4                   5                  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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    53   0
  17Q GAIN WILD-TYPE 169   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     53    0
  17Q GAIN WILD-TYPE  169    3
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               53                169
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED    57   2  22
  17Q GAIN WILD-TYPE 181   2  47
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               57                181
  M1                2                  2
  MX               22                 47
[1] 3 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
  17Q GAIN MUTATED    20  61
  17Q GAIN WILD-TYPE  80 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     20   61
  17Q GAIN WILD-TYPE   80  150
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               20                 80
  MALE                 61                150
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q GAIN MUTATED                         0                       80
  17Q GAIN WILD-TYPE                       2                      223
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q GAIN MUTATED                                  1
  17Q GAIN WILD-TYPE                                5
D31V8, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       80                223
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    67   7   1   6
  17Q GAIN WILD-TYPE 207   7   0  10
D31V9, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               67                207
  R1                7                  7
  R2                1                  0
  RX                6                 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
  17Q GAIN MUTATED                                  0    43
  17Q GAIN WILD-TYPE                                1    98
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           5    30
  17Q GAIN WILD-TYPE                        10   115
D31V10, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          43                 98
  BLACK OR AFRICAN AMERICAN                       5                 10
  WHITE                                          30                115
[1] 4 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
  17Q GAIN MUTATED     3  76
  17Q GAIN WILD-TYPE   5 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   76
  17Q GAIN WILD-TYPE    5  211
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               76                211
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    17   7
  18P GAIN WILD-TYPE 183  85
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                268 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 85 
$`18P GAIN MUTATED`
TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN 
        0.66         4.24         0.13        79.73         7.33        29.56 
TCGA-DD-AACF TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADR 
       12.00        13.97        28.41         3.78        24.00        57.27 
TCGA-DD-AAE9 TCGA-DD-AAVP TCGA-ED-A66X TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T 
       12.69        79.07        13.35         9.96        60.36        51.06 
TCGA-G3-A25X TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D1 
       58.49        15.39        24.13         0.99        23.21         0.69 

$`18P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
        3.39         3.32         0.10         0.07         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH 
       59.18        55.40        12.53        63.48        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL 
       31.53        30.58        29.26        25.08        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        17.33         3.02         3.95         5.29         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        9.86         8.52         4.64        12.56        11.31        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K 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-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        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-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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.52        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04         8.32         4.57         1.02         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55         4.67        25.71        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             79.73             113.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.68              14.50 
[1] "0.1 - 79.7 (14.7)"  "0.0 - 113.0 (14.5)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED        10        6         0          8          0
  18P GAIN WILD-TYPE     136       66         2         44          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED            0        1         0         0
  18P GAIN WILD-TYPE          7        1         1         2
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  10                136
  STAGE II                  6                 66
  STAGE III                 0                  2
  STAGE IIIA                8                 44
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  18P GAIN MUTATED      12   6  10   0
  18P GAIN WILD-TYPE   143  72  54  12
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1               12                143
  T2                   6                 72
  T3                  10                 54
  T4                   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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    22   0
  18P GAIN WILD-TYPE 200   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22    0
  18P GAIN WILD-TYPE  200    3
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               22                200
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    23   1   4
  18P GAIN WILD-TYPE 215   3  65
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               23                215
  M1                1                  3
  MX                4                 65
[1] 3 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
  18P GAIN MUTATED     7  21
  18P GAIN WILD-TYPE  93 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7   21
  18P GAIN WILD-TYPE   93  190
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                7                 93
  MALE                 21                190
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P GAIN MUTATED                         0                       28
  18P GAIN WILD-TYPE                       2                      275
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P GAIN MUTATED                                  0
  18P GAIN WILD-TYPE                                6
D32V8, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       28                275
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  18P GAIN MUTATED    23   1   1   2
  18P GAIN WILD-TYPE 251  13   0  14
D32V9, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               23                251
  R1                1                 13
  R2                1                  0
  RX                2                 14
[1] 4 2
[1] 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
  18P GAIN MUTATED                                  0    19
  18P GAIN WILD-TYPE                                1   122
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           2     7
  18P GAIN WILD-TYPE                        13   138
D32V10, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          19                122
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                           7                138
[1] 4 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
  18P GAIN MUTATED     0  28
  18P GAIN WILD-TYPE   8 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   28
  18P GAIN WILD-TYPE    8  259
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               28                259
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    12   6
  18Q GAIN WILD-TYPE 188  86
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                274 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                 86 
$`18Q GAIN MUTATED`
TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A4NN 
        0.66         4.24         0.13        79.73         7.33        29.56 
TCGA-DD-AACF TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADJ TCGA-DD-AADR TCGA-DD-AAE3 
       12.00        13.97        28.41        24.00        57.27         9.86 
TCGA-EP-A3JL TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-RC-A7SH TCGA-ZP-A9D1 
        9.96        60.36        51.06        58.49        15.39         0.69 

$`18Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
        7.46        13.45         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
        3.39         3.32         0.10         0.07         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH 
       59.18        55.40        12.53        63.48        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK 
       31.53        30.58        29.26         3.78        25.08        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        17.33         3.02         3.95         5.29 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        7.10         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.47         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        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        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         0.62        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33         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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72         5.92         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.13               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             79.73             113.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.68              14.50 
[1] "0.1 - 79.7 (14.7)"  "0.0 - 113.0 (14.5)"
[1] "hr=" "1"  
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED         8        5         0          7          0
  18Q GAIN WILD-TYPE     138       67         2         45          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED            0        1         0         0
  18Q GAIN WILD-TYPE          7        1         1         2
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   8                138
  STAGE II                  5                 67
  STAGE III                 0                  2
  STAGE IIIA                7                 45
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED       9   5   8   0
  18Q GAIN WILD-TYPE   146  73  56  12
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                9                146
  T2                   5                 73
  T3                   8                 56
  T4                   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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    18   0
  18Q GAIN WILD-TYPE 204   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     18    0
  18Q GAIN WILD-TYPE  204    3
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               18                204
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED    18   1   3
  18Q GAIN WILD-TYPE 220   3  66
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               18                220
  M1                1                  3
  MX                3                 66
[1] 3 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
  18Q GAIN MUTATED     5  17
  18Q GAIN WILD-TYPE  95 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   17
  18Q GAIN WILD-TYPE   95  194
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                5                 95
  MALE                 17                194
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q GAIN MUTATED                         0                       22
  18Q GAIN WILD-TYPE                       2                      281
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q GAIN MUTATED                                  0
  18Q GAIN WILD-TYPE                                6
D33V8, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       22                281
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  18Q GAIN MUTATED    17   1   1   2
  18Q GAIN WILD-TYPE 257  13   0  14
D33V9, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               17                257
  R1                1                 13
  R2                1                  0
  RX                2                 14
[1] 4 2
[1] 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
  18Q GAIN MUTATED                                  0    15
  18Q GAIN WILD-TYPE                                1   126
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           1     6
  18Q GAIN WILD-TYPE                        14   139
D33V10, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                126
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                           6                139
[1] 4 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
  18Q GAIN MUTATED     0  22
  18Q GAIN WILD-TYPE   8 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   22
  18Q GAIN WILD-TYPE    8  265
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               22                265
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    29  18
  19P GAIN WILD-TYPE 171  74
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                47                245 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                 74 
$`19P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-DD-A113 TCGA-DD-A118 
       37.32        13.45         0.66         0.39        79.73       113.00 
TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X 
        7.33        90.71        19.79        12.95        21.14        55.69 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ 
       13.78        30.61        73.38        29.56        73.81        12.26 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AAE0 
       78.84       100.96        38.04        29.26         3.78         9.86 
TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
        9.86        35.08         0.23         0.20         0.20        13.41 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
       10.98         0.62        22.85        32.45        23.97        27.88 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 
       51.06        58.49        17.10         5.98         8.55        11.84 
TCGA-MI-A75G TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-YA-A8S7 TCGA-ZP-A9D1 
       18.38        21.04        15.39        13.55         0.69 

$`19P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        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-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.10         0.13        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       53.33         2.60         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        75.65         6.71        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        18.35        13.64         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-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        33.14        32.52        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       30.51        39.78        56.25       108.76         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-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         8.28         6.67         9.67         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP 
       12.16        15.45        16.37        15.65        15.65        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        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-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 
       11.74         9.96        11.93        14.40        19.10         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-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       11.97        20.42         7.76        12.03         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        4.01         2.14        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF 
       58.88        16.37         4.44        21.01         2.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04         8.32         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
        4.01         4.67        25.71        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.20               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            113.00             108.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             18.38              14.33 
[1] "0.2 - 113.0 (18.4)" "0.0 - 108.8 (14.3)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED        20       13         0          9          1
  19P GAIN WILD-TYPE     126       59         2         43          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED            0        2         1         1
  19P GAIN WILD-TYPE          7        0         0         1
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  20                126
  STAGE II                 13                 59
  STAGE III                 0                  2
  STAGE IIIA                9                 43
  STAGE IIIB                1                  6
  STAGE IIIC                0                  7
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  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                 T0+T1  T2  T3  T4
  19P GAIN MUTATED      22  15  11   1
  19P GAIN WILD-TYPE   133  63  53  11
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1               22                133
  T2                  15                 63
  T3                  11                 53
  T4                   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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    36   1
  19P GAIN WILD-TYPE 186   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     36    1
  19P GAIN WILD-TYPE  186    2
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               36                186
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED    37   3   9
  19P GAIN WILD-TYPE 201   1  60
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               37                201
  M1                3                  1
  MX                9                 60
[1] 3 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
  19P GAIN MUTATED    22  27
  19P GAIN WILD-TYPE  78 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22   27
  19P GAIN WILD-TYPE   78  184
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               22                 78
  MALE                 27                184
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P GAIN MUTATED                         0                       47
  19P GAIN WILD-TYPE                       2                      256
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P GAIN MUTATED                                  2
  19P GAIN WILD-TYPE                                4
D34V8, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       47                256
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  19P GAIN MUTATED    44   1   1   3
  19P GAIN WILD-TYPE 230  13   0  13
D34V9, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               44                230
  R1                1                 13
  R2                1                  0
  RX                3                 13
[1] 4 2
[1] 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
  19P GAIN MUTATED                                  0    17
  19P GAIN WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           3    28
  19P GAIN WILD-TYPE                        12   117
D34V10, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                124
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          28                117
[1] 4 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
  19P GAIN MUTATED     3  44
  19P GAIN WILD-TYPE   5 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   44
  19P GAIN WILD-TYPE    5  243
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               44                243
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    38  22
  19Q GAIN WILD-TYPE 162  70
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                60                232 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                22                 70 
$`19Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 
       37.32        10.13        13.45         0.66         0.39         0.10 
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EF 
       79.73       113.00         7.33        90.71        19.79        12.95 
TCGA-DD-A1EG TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN 
       45.11        21.14        55.69        30.61        73.38        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AACG TCGA-DD-AACP 
       73.81        12.26        78.84       100.96        15.42        13.15 
TCGA-DD-AACW TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADM 
       38.04        29.26        13.97        28.41         3.78         0.39 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEK TCGA-ED-A66Y TCGA-ED-A7PZ 
        9.86        12.56        14.79        35.08         0.23         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-FV-A23B 
        0.20        13.41        10.98         0.62        22.85        32.45 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SM 
       23.97        27.88         0.39        51.06        58.49        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-KR-A7K2 TCGA-MI-A75G TCGA-NI-A8LF 
       12.03         5.98         8.55        11.84        18.38        16.37 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7ME TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       21.04        15.39        15.98         4.01        13.55         0.69 

$`19Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        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-BC-A8YO TCGA-BD-A3ER 
       22.36         9.50        14.60        12.72         7.46         4.80 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA 
        0.07         2.86         3.39         4.24         3.32         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A 
        0.10         0.13        37.78        83.57        53.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        21.76        51.29        79.40        66.31        75.65 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        49.15         6.02        29.16        18.35        13.64 
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-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       56.25       108.76         0.30        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 
        7.56        10.98         1.45        27.72        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        65.75        59.18        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ 
       58.16        14.33        48.49        40.77         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       31.53        30.58        25.08        24.00        24.13        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         6.67         9.67         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
        8.52         4.64        11.31        12.69        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         9.96 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       11.93        14.40        19.10         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36         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-A5SL TCGA-G3-A6UC 
       19.53        19.23        14.70        11.97        20.42         7.76 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24        11.80         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71        10.85        58.88         4.44        21.01         2.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.52        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71         7.04         8.32         4.57         1.02         0.99 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.10               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            113.00             108.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            15.405             14.365 
[1] "0.1 - 113.0 (15.4)" "0.0 - 108.8 (14.4)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED        29       16         0         10          0
  19Q GAIN WILD-TYPE     117       56         2         42          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED            0        2         1         1
  19Q GAIN WILD-TYPE          7        0         0         1
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  29                117
  STAGE II                 16                 56
  STAGE III                 0                  2
  STAGE IIIA               10                 42
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  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                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED      31  18  12   1
  19Q GAIN WILD-TYPE   124  60  52  11
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1               31                124
  T2                  18                 60
  T3                  12                 52
  T4                   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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    43   1
  19Q GAIN WILD-TYPE 179   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     43    1
  19Q GAIN WILD-TYPE  179    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               43                179
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    46   3  13
  19Q GAIN WILD-TYPE 192   1  56
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               46                192
  M1                3                  1
  MX               13                 56
[1] 3 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
  19Q GAIN MUTATED    24  38
  19Q GAIN WILD-TYPE  76 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   38
  19Q GAIN WILD-TYPE   76  173
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               24                 76
  MALE                 38                173
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q GAIN MUTATED                         0                       60
  19Q GAIN WILD-TYPE                       2                      243
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q GAIN MUTATED                                  2
  19Q GAIN WILD-TYPE                                4
D35V8, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       60                243
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  19Q GAIN MUTATED    57   1   1   3
  19Q GAIN WILD-TYPE 217  13   0  13
D35V9, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               57                217
  R1                1                 13
  R2                1                  0
  RX                3                 13
[1] 4 2
[1] 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
  19Q GAIN MUTATED                                  0    25
  19Q GAIN WILD-TYPE                                1   116
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           3    34
  19Q GAIN WILD-TYPE                        12   111
D35V10, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          25                116
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          34                111
[1] 4 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
  19Q GAIN MUTATED     3  58
  19Q GAIN WILD-TYPE   5 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   58
  19Q GAIN WILD-TYPE    5  229
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               58                229
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    50  33
  20P GAIN WILD-TYPE 150  59
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                83                209 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                33                 59 
$`20P GAIN MUTATED`
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF 
       10.59        48.99        37.32        10.13        13.84         0.26 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB 
       14.60        13.45         0.66         0.39         0.10         0.10 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EG 
      113.00         7.33         2.60         0.46        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4ND 
       49.15        29.16        21.14        13.78        30.61        73.38 
TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB 
       29.56         0.30        78.84       100.96         0.53        59.18 
TCGA-DD-AACC TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD6 
       55.40         6.41        53.19        13.15         5.62        22.09 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU 
       28.41         3.78        17.33         3.02         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEH TCGA-DD-AAEK 
        6.67         9.86         9.86        12.69        15.65        35.08 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         0.23         0.20        13.41         0.20        10.98 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S 
        9.96        22.85        32.45         6.38         0.39         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 
       58.49        14.86        17.10         7.76        12.03         1.84 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.80         0.89         2.14         2.66        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       12.72        18.38        16.37        24.13        14.96        17.29 
TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
        8.32         0.99         4.01        13.55        45.57 

$`20P GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.78         0.66        27.91        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO 
        5.03        44.42        22.36         9.50        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        79.73        37.78        83.57        53.33 
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-A1EE TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X 
       75.65         6.71         6.02        18.35        13.64        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-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11         0.36        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B 
       73.81       108.76        12.26        80.75        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
        7.56        10.98         1.45        27.72        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ 
       65.75        12.53        63.48        12.00        15.42        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30         1.91        58.16        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       38.04         5.59         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI 
       34.09        31.53        30.58        29.26        13.97        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ 
       24.00        24.13        20.91         0.39         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
       57.27         9.67         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        11.31        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       15.65        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       47.70        13.41        12.69        15.85        13.91         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20         0.20        13.15         0.20         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ 
       19.99        11.74         0.62        11.93        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         8.12         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
       60.36        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-A5SL TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       11.97        20.42         5.98        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF 
        9.17         3.02         1.02         2.20        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       17.06         4.01         2.14        24.36         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V 
       15.52        14.40         1.71        15.98         7.04         4.57 
TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        1.02         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        35.05        74.24         8.22 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.10               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            113.00             108.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.72              16.37 
[1] "0.1 - 113.0 (12.7)" "0.0 - 108.8 (16.4)"
[1] "hr=" "1.8"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED        37       21         1         20          4
  20P GAIN WILD-TYPE     109       51         1         32          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED            2        2         0         1
  20P GAIN WILD-TYPE          5        0         1         1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  37                109
  STAGE II                 21                 51
  STAGE III                 1                  1
  STAGE IIIA               20                 32
  STAGE IIIB                4                  3
  STAGE IIIC                2                  5
  STAGE IV                  2                  0
  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                 T0+T1  T2  T3  T4
  20P GAIN MUTATED      38  23  27   3
  20P GAIN WILD-TYPE   117  55  37   9
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               38                117
  T2                  23                 55
  T3                  27                 37
  T4                   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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    66   1
  20P GAIN WILD-TYPE 156   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     66    1
  20P GAIN WILD-TYPE  156    2
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               66                156
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P GAIN MUTATED    73   3  15
  20P GAIN WILD-TYPE 165   1  54
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               73                165
  M1                3                  1
  MX               15                 54
[1] 3 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
  20P GAIN MUTATED    34  57
  20P GAIN WILD-TYPE  66 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     34   57
  20P GAIN WILD-TYPE   66  154
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               34                 66
  MALE                 57                154
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P GAIN MUTATED                         0                       89
  20P GAIN WILD-TYPE                       2                      214
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P GAIN MUTATED                                  2
  20P GAIN WILD-TYPE                                4
D36V8, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       89                214
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  20P GAIN MUTATED    79   5   1   5
  20P GAIN WILD-TYPE 195   9   0  11
D36V9, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               79                195
  R1                5                  9
  R2                1                  0
  RX                5                 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
  20P GAIN MUTATED                                  0    39
  20P GAIN WILD-TYPE                                1   102
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                           4    46
  20P GAIN WILD-TYPE                        11    99
D36V10, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          39                102
  BLACK OR AFRICAN AMERICAN                       4                 11
  WHITE                                          46                 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"
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     3  82
  20P GAIN WILD-TYPE   5 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   82
  20P GAIN WILD-TYPE    5  205
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               82                205
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    56  31
  20Q GAIN WILD-TYPE 144  61
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                87                205 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                31                 61 
$`20Q GAIN MUTATED`
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A217 TCGA-BC-A3KF 
       10.59        48.99        37.32        10.13        13.84         0.26 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MB 
       14.60        13.45         0.66         0.39         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        0.13       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39V TCGA-DD-A3A7 
       12.95        45.11        49.15        29.16        21.14        13.78 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NN TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73G 
       30.61        73.38        29.56         0.30        78.84       100.96 
TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACS 
        0.53        59.18        55.40        53.19        13.15        48.49 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN 
        5.62         4.50        22.09        28.41         3.78        17.33 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE3 
        3.02         7.10         8.28         6.67         9.86         9.86 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEH TCGA-DD-AAEK TCGA-ED-A66X TCGA-ED-A66Y 
       12.69        14.79        15.65        35.08        13.35         0.23 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS 
        0.20        13.41         0.20        10.98         9.96        22.85 
TCGA-FV-A23B TCGA-FV-A3R2 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A5SM 
       32.45         6.38         0.39         1.22        58.49        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-HP-A5MZ 
        7.76        12.03         1.84        11.80         2.14         2.66 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-NI-A8LF TCGA-PD-A5DF 
       11.84        13.38        12.72        18.38        16.37        21.01 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 
       24.13        14.96        17.29        15.98         8.32         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZS-A9CD 
        4.01        13.55        45.57 

$`20Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.78         0.66        27.91        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO 
        5.03        44.42        22.36         9.50        12.72         7.46 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        4.80         0.07         2.86         3.39         4.24         3.32 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11D 
        0.07        79.73        37.78        83.57        53.33        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        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-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH 
      107.11         0.36        33.14        32.52        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       12.26        80.75        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACD 
        1.45        27.72        13.48        11.41        65.75        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
        1.91        58.16        14.33        40.77        38.04         5.59 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA 
       18.54        21.63        33.83        34.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       29.26        13.97        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE1 
        0.39         3.95         5.29        57.27         9.67         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEB 
        9.47         8.52         4.64        12.56        11.31        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.45        16.37        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91         0.20         0.20         0.20        13.15         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 
       14.40        23.97        19.10        27.88         8.12         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36        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-A5SL TCGA-G3-A7M7 
       19.53        19.23        14.70        11.97        20.42         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 
       11.24         8.55         9.70         9.17         0.89         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
        2.14        24.36         5.92         4.27         9.57        16.67 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 
       12.85        20.71        10.85        58.88         4.44         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MD 
       21.04        19.04        15.39        15.52        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        7.04         4.57         1.02         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.10               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            113.00             108.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.15              15.85 
[1] "0.1 - 113.0 (13.2)" "0.0 - 108.8 (15.8)"
[1] "hr=" "1.5"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED        40       20         1         22          5
  20Q GAIN WILD-TYPE     106       52         1         30          2
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED            2        1         0         1
  20Q GAIN WILD-TYPE          5        1         1         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  40                106
  STAGE II                 20                 52
  STAGE III                 1                  1
  STAGE IIIA               22                 30
  STAGE IIIB                5                  2
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  20Q GAIN MUTATED      41  21  29   4
  20Q GAIN WILD-TYPE   114  57  35   8
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               41                114
  T2                  21                 57
  T3                  29                 35
  T4                   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"
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    69   1
  20Q GAIN WILD-TYPE 153   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     69    1
  20Q GAIN WILD-TYPE  153    2
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               69                153
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20Q GAIN MUTATED    77   2  16
  20Q GAIN WILD-TYPE 161   2  53
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               77                161
  M1                2                  2
  MX               16                 53
[1] 3 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
  20Q GAIN MUTATED    33  62
  20Q GAIN WILD-TYPE  67 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     33   62
  20Q GAIN WILD-TYPE   67  149
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               33                 67
  MALE                 62                149
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q GAIN MUTATED                         0                       93
  20Q GAIN WILD-TYPE                       2                      210
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q GAIN MUTATED                                  2
  20Q GAIN WILD-TYPE                                4
D37V8, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       93                210
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  20Q GAIN MUTATED    82   5   1   5
  20Q GAIN WILD-TYPE 192   9   0  11
D37V9, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               82                192
  R1                5                  9
  R2                1                  0
  RX                5                 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
  20Q GAIN MUTATED                                  0    43
  20Q GAIN WILD-TYPE                                1    98
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                           4    46
  20Q GAIN WILD-TYPE                        11    99
D37V10, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          43                 98
  BLACK OR AFRICAN AMERICAN                       4                 11
  WHITE                                          46                 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"
D37V11, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2  87
  20Q GAIN WILD-TYPE   6 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   87
  20Q GAIN WILD-TYPE    6  200
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               87                200
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    14   5
  21Q GAIN WILD-TYPE 186  87
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                273 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 87 
$`21Q GAIN MUTATED`
TCGA-5C-A9VG TCGA-BC-A217 TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5263 TCGA-DD-A113 
       10.78        13.84         0.66         0.39         4.24        79.73 
TCGA-DD-A3A5 TCGA-DD-A4NV TCGA-DD-AAEK TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS 
      102.74        78.84        35.08        13.41        10.98        22.85 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-AAUZ TCGA-MI-A75G TCGA-RC-A7SH 
       27.88        51.06        22.13        11.24        18.38        15.39 
TCGA-UB-AA0U 
        8.32 

$`21Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        4.80         0.07         2.86         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        37.78        83.57        53.33 
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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       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        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        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       108.76        12.26         0.30        80.75        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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       24.00        24.13        20.91         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        9.67         9.86         9.63         9.47         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        16.37        15.65        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.15         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        23.97        19.10         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-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
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-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        8.55        11.80         9.70         9.17         0.89         2.14 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V 
       17.29        14.40         1.71        15.98         7.04         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.02         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.39               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            102.74             113.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             15.39              14.40 
[1] "0.4 - 102.7 (15.4)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED         5       10         1          7          0
  21Q GAIN WILD-TYPE     141       62         1         45          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED            0        0         0         0
  21Q GAIN WILD-TYPE          7        2         1         2
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   5                141
  STAGE II                 10                 62
  STAGE III                 1                  1
  STAGE IIIA                7                 45
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       5  10   8   0
  21Q GAIN WILD-TYPE   150  68  56  12
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                5                150
  T2                  10                 68
  T3                   8                 56
  T4                   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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16   0
  21Q GAIN WILD-TYPE 206   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16    0
  21Q GAIN WILD-TYPE  206    3
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               16                206
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    18   0   5
  21Q GAIN WILD-TYPE 220   4  64
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               18                220
  M1                0                  4
  MX                5                 64
[1] 3 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
  21Q GAIN MUTATED     7  16
  21Q GAIN WILD-TYPE  93 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7   16
  21Q GAIN WILD-TYPE   93  195
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 93
  MALE                 16                195
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q GAIN MUTATED                         0                       22
  21Q GAIN WILD-TYPE                       2                      281
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q GAIN MUTATED                                  1
  21Q GAIN WILD-TYPE                                5
D38V8, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       22                281
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    17   2   0   4
  21Q GAIN WILD-TYPE 257  12   1  12
D38V9, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               17                257
  R1                2                 12
  R2                0                  1
  RX                4                 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
  21Q GAIN MUTATED                                  0     8
  21Q GAIN WILD-TYPE                                1   133
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           1    13
  21Q GAIN WILD-TYPE                        14   132
D38V10, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                133
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          13                132
[1] 4 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
  21Q GAIN MUTATED     2  20
  21Q GAIN WILD-TYPE   6 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   20
  21Q GAIN WILD-TYPE    6  267
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               20                267
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    26   9
  22Q GAIN WILD-TYPE 174  83
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                35                257 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 83 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A69H TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 
       10.13         5.03        14.60         0.66         0.07         0.39 
TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-DD-A4ND TCGA-DD-A73G 
        0.10       113.00        51.29        29.16        73.38       100.96 
TCGA-DD-AACB TCGA-DD-AACJ TCGA-DD-AAE0 TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVY 
       59.18        60.10         9.86        15.45        35.08        58.78 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A2QR 
       13.35         0.20        13.41         0.20        22.85        19.10 
TCGA-FV-A3I0 TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-UB-A7MA 
       27.88        58.49        22.13        12.03        11.80        14.96 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZS-A9CG 
       15.98         8.32         0.99        13.55         8.22 

$`22Q GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
       22.36         9.50        12.72         7.46        13.45         4.80 
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-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.13        79.73        37.78        83.57        53.33         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.76        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65         6.71        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
        6.02        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        30.15        26.83        30.51        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       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       24.00        24.13        20.91         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
       12.56        11.31        12.69        14.79        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.87        61.38        56.48        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y 
       47.70        13.41        12.69        15.85        13.91         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20         0.20         0.20        13.15         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       11.93        14.40        32.45        23.97         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-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-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       20.42        17.10         7.76         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29        14.40         1.71         7.04         4.57         1.02 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        4.01         4.67        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       24.43        12.99        45.57        35.05        74.24 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            113.00             108.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              14.6               14.4 
[1] "0.1 - 113.0 (14.6)" "0.0 - 108.8 (14.4)"
[1] "hr=" "1.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED        10       14         0         11          1
  22Q GAIN WILD-TYPE     136       58         2         41          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED            2        0         0         0
  22Q GAIN WILD-TYPE          5        2         1         2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  10                136
  STAGE II                 14                 58
  STAGE III                 0                  2
  STAGE IIIA               11                 41
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED      11  14  14   2
  22Q GAIN WILD-TYPE   144  64  50  10
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1               11                144
  T2                  14                 64
  T3                  14                 50
  T4                   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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    28   1
  22Q GAIN WILD-TYPE 194   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     28    1
  22Q GAIN WILD-TYPE  194    2
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               28                194
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    32   0   9
  22Q GAIN WILD-TYPE 206   4  60
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               32                206
  M1                0                  4
  MX                9                 60
[1] 3 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
  22Q GAIN MUTATED    15  26
  22Q GAIN WILD-TYPE  85 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     15   26
  22Q GAIN WILD-TYPE   85  185
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               15                 85
  MALE                 26                185
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q GAIN MUTATED                         0                       39
  22Q GAIN WILD-TYPE                       2                      264
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q GAIN MUTATED                                  2
  22Q GAIN WILD-TYPE                                4
D39V8, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       39                264
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  22Q GAIN MUTATED    34   3   0   4
  22Q GAIN WILD-TYPE 240  11   1  12
D39V9, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               34                240
  R1                3                 11
  R2                0                  1
  RX                4                 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
  22Q GAIN MUTATED                                  0    22
  22Q GAIN WILD-TYPE                                1   119
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           1    18
  22Q GAIN WILD-TYPE                        14   127
D39V10, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                119
  BLACK OR AFRICAN AMERICAN                       1                 14
  WHITE                                          18                127
[1] 4 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
  22Q GAIN MUTATED     2  39
  22Q GAIN WILD-TYPE   6 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   39
  22Q GAIN WILD-TYPE    6  248
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               39                248
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    32  12
  XQ GAIN WILD-TYPE 168  80
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               44               248 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12                80 
$`XQ GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A3KF TCGA-BW-A5NO TCGA-CC-5260 TCGA-DD-A11A 
       27.52         1.12         0.26         0.66         2.86         2.60 
TCGA-DD-A39V TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NV 
       21.14        17.59        13.78        30.97        39.78        78.84 
TCGA-DD-A73D TCGA-DD-A73G TCGA-DD-AACD TCGA-DD-AACJ TCGA-DD-AACS TCGA-DD-AAD2 
       10.98       100.96        12.53        60.10        48.49        21.63 
TCGA-DD-AADO TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAVQ TCGA-DD-AAVY 
        3.02         8.28         9.86        12.69        79.10        58.78 
TCGA-DD-AAW2 TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A4ZQ 
       49.48        18.74        11.74         9.96        22.85         0.39 
TCGA-G3-A25U TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-AAV3 
       53.79        22.13        19.53        14.70        20.42         9.17 
TCGA-K7-A6G5 TCGA-LG-A6GG TCGA-MI-A75G TCGA-O8-A75V TCGA-UB-A7ME TCGA-WQ-A9G7 
        4.01        12.72        18.38         4.44        15.98         0.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57         8.22 

$`XQ GAIN WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       70.06        20.12       102.74       107.11         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        32.52        73.38        30.15        26.83        30.51 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F 
       80.75        10.98         9.30         7.56         1.45        27.72 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK 
       63.48        12.00        15.42         6.41        53.19         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        13.15        14.33        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         5.62         4.50        18.54        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW 
       17.33         3.95         5.29        57.27         7.10         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.47         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        11.31        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 
       61.87        61.38        56.48        55.86        54.05        47.70 
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        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20         0.20         0.20        19.99        10.98         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        32.45        23.97        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-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        51.06        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SM 
       21.53        25.64         5.92        19.23        11.97        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       11.80         9.70         0.89         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 
        2.20         2.66        37.71        20.75        17.06         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        13.38        24.36         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        12.85        20.71        10.85        58.88        16.37 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       21.01         2.04        21.04        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       24.13        14.96        17.29        14.40         1.71         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        8.32         4.57         1.02         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.26              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           100.96            113.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            15.34             14.40 
[1] "0.3 - 101.0 (15.3)" "0.0 - 113.0 (14.4)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ GAIN MUTATED        23       13         0          9          2          1
  XQ GAIN WILD-TYPE     123       59         2         43          5          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ GAIN MUTATED          0         0         0
  XQ GAIN WILD-TYPE        2         1         2
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 23               123
  STAGE II                13                59
  STAGE III                0                 2
  STAGE IIIA               9                43
  STAGE IIIB               2                 5
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  XQ GAIN MUTATED      23  14  11   2
  XQ GAIN WILD-TYPE   132  64  53  10
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1              23               132
  T2                 14                64
  T3                 11                53
  T4                  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"
D40V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    33   0
  XQ GAIN WILD-TYPE 189   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     33    0
  XQ GAIN WILD-TYPE  189    3
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              33               189
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    37   0  13
  XQ GAIN WILD-TYPE 201   4  56
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              37               201
  M1               0                 4
  MX              13                56
[1] 3 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
  XQ GAIN MUTATED    12  38
  XQ GAIN WILD-TYPE  88 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   38
  XQ GAIN WILD-TYPE   88  173
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12                88
  MALE                38               173
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ GAIN MUTATED                         0                       50
  XQ GAIN WILD-TYPE                       2                      253
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ GAIN MUTATED                                  0
  XQ GAIN WILD-TYPE                                6
D40V8, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      50               253
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  XQ GAIN MUTATED    42   3   0   4
  XQ GAIN WILD-TYPE 232  11   1  12
D40V9, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              42               232
  R1               3                11
  R2               0                 1
  RX               4                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
  XQ GAIN MUTATED                                  1    22
  XQ GAIN WILD-TYPE                                0   119
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           3    22
  XQ GAIN WILD-TYPE                        12   123
D40V10, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         22               119
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         22               123
[1] 4 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
  XQ GAIN MUTATED     1  47
  XQ GAIN WILD-TYPE   7 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   47
  XQ GAIN WILD-TYPE    7  240
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              47               240
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    46  21
  1P LOSS WILD-TYPE 154  71
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               67               225 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21                71 
$`1P LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10S TCGA-BC-A217 TCGA-BC-A69H TCGA-CC-5258 
       10.78        10.59        46.78        13.84        14.60         0.07 
TCGA-CC-5261 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 
        0.39         0.10         0.13        79.73       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A1 
        0.46        90.71        49.15        29.16        55.69         7.66 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACH 
       30.61        30.15        29.56         9.30         0.53         6.41 
TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AADA TCGA-DD-AADJ 
       13.15        40.77        38.04        18.54        30.58        24.00 
TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAEK 
        3.02         6.67         9.86         9.63         9.86        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVZ TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       79.10        59.93        55.86        13.35         0.23         0.20 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS 
       13.41         0.20         0.20        10.98         0.62        22.85 
TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X 
       27.88         0.33        60.36         1.22        53.79        58.49 
TCGA-G3-A25Y TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-LG-A9QC 
       14.86        20.42        17.10         2.14        11.84         5.92 
TCGA-MI-A75G TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       18.38        15.52        24.13        14.40         0.99         4.01 
TCGA-ZP-A9D1 
        0.69 

$`1P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
        7.10         0.66        48.99        27.91        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57         5.03        44.42         0.26        22.36         9.50 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 
       12.72         7.46        13.45         4.80         0.66         2.86 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A114 
        3.39         4.24         3.32         0.10         0.07        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
       83.57        53.33         2.60        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        33.14        32.52        73.38        30.97 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       10.98         1.45        27.72       100.96        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 
       14.33        48.49         5.59         5.62         4.50        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       33.83        34.09        22.09        31.53        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       28.41         3.78        25.08        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       17.33         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.67         9.47         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       15.65        79.07        72.26        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       58.78        54.05        49.48        47.70        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       15.85        13.91         0.20         0.20         0.20        13.15 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK 
        0.20        18.74        19.99        11.74         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        23.97        19.10         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.13         0.03         0.39        51.06        28.27        30.74 
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-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       14.70        11.97         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        13.38        24.36        12.72 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.39        14.96        17.29         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV 
        7.04         8.32         4.57         1.02        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.00            108.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.41             14.96 
[1] "0.1 - 113.0 (13.4)" "0.0 - 108.8 (15.0)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED        31       19         1         13          1          1
  1P LOSS WILD-TYPE     115       53         1         39          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED          2         0         1
  1P LOSS WILD-TYPE        0         1         1
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 31               115
  STAGE II                19                53
  STAGE III                1                 1
  STAGE IIIA              13                39
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 2                 0
  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                T0+T1  T2  T3  T4
  1P LOSS MUTATED      33  20  18   1
  1P LOSS WILD-TYPE   122  58  46  11
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1              33               122
  T2                 20                58
  T3                 18                46
  T4                  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"
D41V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    53   1
  1P LOSS WILD-TYPE 169   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     53    1
  1P LOSS WILD-TYPE  169    2
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              53               169
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED    62   3   7
  1P LOSS WILD-TYPE 176   1  62
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              62               176
  M1               3                 1
  MX               7                62
[1] 3 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
  1P LOSS MUTATED    27  45
  1P LOSS WILD-TYPE  73 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     27   45
  1P LOSS WILD-TYPE   73  166
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              27                73
  MALE                45               166
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1P LOSS MUTATED                         0                       69
  1P LOSS WILD-TYPE                       2                      234
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1P LOSS MUTATED                                  3
  1P LOSS WILD-TYPE                                3
D41V8, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      69               234
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  1P LOSS MUTATED    64   3   1   4
  1P LOSS WILD-TYPE 210  11   0  12
D41V9, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              64               210
  R1               3                11
  R2               1                 0
  RX               4                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
  1P LOSS MUTATED                                  0    36
  1P LOSS WILD-TYPE                                1   105
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           2    33
  1P LOSS WILD-TYPE                        13   112
D41V10, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         36               105
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         33               112
[1] 4 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
  1P LOSS MUTATED     2  67
  1P LOSS WILD-TYPE   6 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   67
  1P LOSS WILD-TYPE    6  220
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              67               220
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    11   7
  1Q LOSS WILD-TYPE 189  85
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               274 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7                85 
$`1Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-A3MB TCGA-DD-A11B TCGA-DD-A1EJ 
       46.78        13.84         0.07         0.10         0.46        29.16 
TCGA-DD-A3A1 TCGA-DD-AACH TCGA-DD-AACW TCGA-DD-AADW TCGA-DD-AAEK TCGA-ED-A82E 
        7.66         6.41        38.04         6.67        35.08        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A4ZP TCGA-G3-A25U TCGA-UB-AA0U 
        0.20         0.20        22.85        60.36        53.79         8.32 

$`1Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         2.86         0.39         3.39         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-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-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
        6.71        12.95        45.11        49.15         6.02        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-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        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        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       108.76        12.26         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI 
       55.40        12.53        63.48        12.00        15.42        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       29.26        13.97        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        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-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15         0.20        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        11.93        14.40        32.45        23.97 
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-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.33         0.39         1.22        51.06        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        4.57         1.02         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            60.36            113.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           10.865            14.745 
[1] "0.1 - 60.4 (10.9)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.6"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED         5        6         0          6          0          1
  1Q LOSS WILD-TYPE     141       66         2         46          7          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  1Q LOSS MUTATED          0         0         0
  1Q LOSS WILD-TYPE        2         1         2
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  5               141
  STAGE II                 6                66
  STAGE III                0                 2
  STAGE IIIA               6                46
  STAGE IIIB               0                 7
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       6   6   7   0
  1Q LOSS WILD-TYPE   149  72  57  12
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               6               149
  T2                  6                72
  T3                  7                57
  T4                  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"
D42V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    13   1
  1Q LOSS WILD-TYPE 209   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     13    1
  1Q LOSS WILD-TYPE  209    2
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              13               209
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED    16   0   3
  1Q LOSS WILD-TYPE 222   4  66
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              16               222
  M1               0                 4
  MX               3                66
[1] 3 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
  1Q LOSS MUTATED     5  14
  1Q LOSS WILD-TYPE  95 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      5   14
  1Q LOSS WILD-TYPE   95  197
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               5                95
  MALE                14               197
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  1Q LOSS MUTATED                         0                       18
  1Q LOSS WILD-TYPE                       2                      285
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  1Q LOSS MUTATED                                  1
  1Q LOSS WILD-TYPE                                5
D42V8, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      18               285
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    15   2   0   2
  1Q LOSS WILD-TYPE 259  12   1  14
D42V9, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              15               259
  R1               2                12
  R2               0                 1
  RX               2                14
[1] 4 2
[1] 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
  1Q LOSS MUTATED                                  0    11
  1Q LOSS WILD-TYPE                                1   130
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           0     7
  1Q LOSS WILD-TYPE                        15   138
D42V10, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11               130
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                          7               138
[1] 4 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
  1Q LOSS MUTATED     1  16
  1Q LOSS WILD-TYPE   7 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   16
  1Q LOSS WILD-TYPE    7  271
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              16               271
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    19   6
  2P LOSS WILD-TYPE 181  86
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               25               267 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6                86 
$`2P LOSS MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BC-A69H TCGA-BD-A3EP TCGA-DD-A11C 
       10.78        23.34         0.26        14.60        13.45        21.76 
TCGA-DD-A39Y TCGA-DD-AACE TCGA-DD-AACU TCGA-DD-AADI TCGA-DD-AADL TCGA-DD-AADN 
        5.62        63.48        40.77        25.08        20.91        17.33 
TCGA-DD-AADW TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-FV-A3I1 
        6.67        13.41         0.23         0.20         0.20         8.12 
TCGA-G3-A25S TCGA-G3-A5SM TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH 
        1.22        17.10         3.02         2.20        11.84        15.39 
TCGA-WQ-AB4B 
        4.01 

$`2P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
        9.50        12.72         7.46         4.80         0.66         0.07 
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-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-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-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        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       108.76        12.26         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK 
       29.26        13.97        28.41         3.78        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW 
       79.07        79.10        72.26        59.93        61.87        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO 
       12.69        15.85        13.91        13.35         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       14.70        11.97        20.42         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
        1.84        11.24         8.55        11.80         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        0.89         2.14         1.02         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         0.99        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.20              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            63.48            113.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            11.84             14.86 
[1] "0.2 - 63.5 (11.8)"  "0.0 - 113.0 (14.9)"
[1] "hr=" "1.2"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED        14       10         0          3          0          0
  2P LOSS WILD-TYPE     132       62         2         49          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2P LOSS MUTATED          0         0         0
  2P LOSS WILD-TYPE        2         1         2
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 14               132
  STAGE II                10                62
  STAGE III                0                 2
  STAGE IIIA               3                49
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  2P LOSS MUTATED      14  10   3   1
  2P LOSS WILD-TYPE   141  68  61  11
D43V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1              14               141
  T2                 10                68
  T3                  3                61
  T4                  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"
D43V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18   0
  2P LOSS WILD-TYPE 204   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18    0
  2P LOSS WILD-TYPE  204    3
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              18               204
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED    23   0   5
  2P LOSS WILD-TYPE 215   4  64
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              23               215
  M1               0                 4
  MX               5                64
[1] 3 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
  2P LOSS MUTATED     6  22
  2P LOSS WILD-TYPE  94 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6   22
  2P LOSS WILD-TYPE   94  189
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               6                94
  MALE                22               189
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2P LOSS MUTATED                         0                       27
  2P LOSS WILD-TYPE                       2                      276
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2P LOSS MUTATED                                  1
  2P LOSS WILD-TYPE                                5
D43V8, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      27               276
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    25   1   0   2
  2P LOSS WILD-TYPE 249  13   1  14
D43V9, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              25               249
  R1               1                13
  R2               0                 1
  RX               2                14
[1] 4 2
[1] 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
  2P LOSS MUTATED                                  0    15
  2P LOSS WILD-TYPE                                1   126
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1    12
  2P LOSS WILD-TYPE                        14   133
D43V10, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               126
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         12               133
[1] 4 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
  2P LOSS MUTATED     0  26
  2P LOSS WILD-TYPE   8 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   26
  2P LOSS WILD-TYPE    8  261
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              26               261
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    21   8
  2Q LOSS WILD-TYPE 179  84
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               263 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8                84 
$`2Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Y TCGA-BC-A3KF TCGA-BD-A3EP TCGA-DD-A115 TCGA-DD-A11C 
       10.78        23.34         0.26        13.45        83.57        21.76 
TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-A73B TCGA-DD-AACE TCGA-DD-AADI TCGA-DD-AADL 
        5.62        30.51         9.30        63.48        25.08        20.91 
TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE6 TCGA-ED-A459 TCGA-ED-A66Y 
       17.33         6.67         9.47         4.64        13.41         0.23 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-FV-A3I1 TCGA-G3-A5SM TCGA-G3-AAV7 
        0.20         0.20         0.20         8.12        17.10         3.02 
TCGA-GJ-A9DB TCGA-KR-A7K2 TCGA-RC-A7SH TCGA-UB-A7MF TCGA-WQ-AB4B 
        2.20        11.84        15.39         7.04         4.01 

$`2Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO 
        9.50        14.60        12.72         7.46         4.80         0.66 
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-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.33       113.00         7.33         2.60         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-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-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        26.83        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 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        7.56        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        65.75        59.18        55.40        12.53 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       13.97        28.41         3.78        24.00        24.13         0.39 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
        9.67         9.86         9.63         9.86         8.52        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.65        15.65        35.08        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       54.05        49.48        47.70        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       13.35         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K 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-A2QQ 
        9.96        11.93        22.85        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH 
       30.74        58.49        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-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 
       11.80         9.70         9.17         0.89         2.14         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 
       15.98         8.32         4.57         1.02         0.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.20              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            83.57            113.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             9.47             14.96 
[1] "0.2 - 83.6 (9.5)"   "0.0 - 113.0 (15.0)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED        15       10         0          7          0          0
  2Q LOSS WILD-TYPE     131       62         2         45          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  2Q LOSS MUTATED          0         0         0
  2Q LOSS WILD-TYPE        2         1         2
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 15               131
  STAGE II                10                62
  STAGE III                0                 2
  STAGE IIIA               7                45
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  2Q LOSS MUTATED      15  10   7   1
  2Q LOSS WILD-TYPE   140  68  57  11
D44V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1              15               140
  T2                 10                68
  T3                  7                57
  T4                  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"
D44V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    23   0
  2Q LOSS WILD-TYPE 199   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23    0
  2Q LOSS WILD-TYPE  199    3
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              23               199
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    27   0   6
  2Q LOSS WILD-TYPE 211   4  63
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              27               211
  M1               0                 4
  MX               6                63
[1] 3 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
  2Q LOSS MUTATED     9  24
  2Q LOSS WILD-TYPE  91 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9   24
  2Q LOSS WILD-TYPE   91  187
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               9                91
  MALE                24               187
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  2Q LOSS MUTATED                         0                       32
  2Q LOSS WILD-TYPE                       2                      271
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  2Q LOSS MUTATED                                  1
  2Q LOSS WILD-TYPE                                5
D44V8, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      32               271
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    30   0   0   3
  2Q LOSS WILD-TYPE 244  14   1  13
D44V9, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              30               244
  R1               0                14
  R2               0                 1
  RX               3                13
[1] 4 2
[1] 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
  2Q LOSS MUTATED                                  0    18
  2Q LOSS WILD-TYPE                                1   123
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           1    14
  2Q LOSS WILD-TYPE                        14   131
D44V10, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18               123
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         14               131
[1] 4 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
  2Q LOSS MUTATED     1  29
  2Q LOSS WILD-TYPE   7 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   29
  2Q LOSS WILD-TYPE    7  258
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              29               258
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    28  10
  3P LOSS WILD-TYPE 172  82
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               38               254 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                82 
$`3P LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-5263 TCGA-CC-A3MA 
       10.78         0.66        10.13         5.03         4.24         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A3A9 TCGA-DD-A4NA 
        0.10        79.73       113.00        90.71        30.61        33.14 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU 
       26.83        73.81         3.02         9.67        79.10        61.87 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A3I0 
        0.23         0.20         0.20        13.41         0.20        27.88 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 
       51.06        58.49        11.80         2.14        11.84        13.38 
TCGA-LG-A9QC TCGA-MR-A8JO TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-WQ-AB4B 
        5.92        10.85        14.40         1.71         7.04         4.01 
TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.69        35.05 

$`3P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
        7.10        10.59        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        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-A4NB TCGA-DD-A4ND 
      102.74       107.11        13.78         0.36        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       24.00        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
        0.20         0.20        13.15         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       22.85        14.40        32.45        23.97        19.10         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-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       22.13        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       17.06         4.01         2.14        24.36        12.72         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME 
       15.39        15.52        24.13        14.96        17.29        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV 
        8.32         4.57         1.02         0.99        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.00            108.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           10.815            15.405 
[1] "0.1 - 113.0 (10.8)" "0.0 - 108.8 (15.4)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED        10       13         0         13          1          2
  3P LOSS WILD-TYPE     136       59         2         39          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED          0         0         1
  3P LOSS WILD-TYPE        2         1         1
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 10               136
  STAGE II                13                59
  STAGE III                0                 2
  STAGE IIIA              13                39
  STAGE IIIB               1                 6
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  3P LOSS MUTATED      11  14  15   3
  3P LOSS WILD-TYPE   144  64  49   9
D45V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              11               144
  T2                 14                64
  T3                 15                49
  T4                  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"
D45V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    30   1
  3P LOSS WILD-TYPE 192   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     30    1
  3P LOSS WILD-TYPE  192    2
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              30               192
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED    33   1   9
  3P LOSS WILD-TYPE 205   3  60
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              33               205
  M1               1                 3
  MX               9                60
[1] 3 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
  3P LOSS MUTATED    16  27
  3P LOSS WILD-TYPE  84 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16   27
  3P LOSS WILD-TYPE   84  184
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              16                84
  MALE                27               184
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3P LOSS MUTATED                         1                       38
  3P LOSS WILD-TYPE                       1                      265
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3P LOSS MUTATED                                  4
  3P LOSS WILD-TYPE                                2
D45V8, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      38               265
  HEPATOCHOLANGIOCARCINOMA (MIXED)               4                 2
[1] 3 2
[1] 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
  3P LOSS MUTATED    41   0   0   2
  3P LOSS WILD-TYPE 233  14   1  14
D45V9, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              41               233
  R1               0                14
  R2               0                 1
  RX               2                14
[1] 4 2
[1] 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
  3P LOSS MUTATED                                  0    20
  3P LOSS WILD-TYPE                                1   121
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                           1    22
  3P LOSS WILD-TYPE                        14   123
D45V10, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         20               121
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         22               123
[1] 4 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
  3P LOSS MUTATED     0  40
  3P LOSS WILD-TYPE   8 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   40
  3P LOSS WILD-TYPE    8  247
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              40               247
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    22   5
  3Q LOSS WILD-TYPE 178  87
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               27               265 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                87 
$`3Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1E9 TCGA-DD-A4NA 
       10.78         5.03        79.73       113.00        90.71        33.14 
TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AADO TCGA-DD-AADY TCGA-DD-AAVQ TCGA-DD-AAVU 
       26.83        73.81         3.02         9.67        79.10        61.87 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-G3-AAV1 
        0.23         0.20        13.41         0.20         0.20        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MR-A8JO TCGA-UB-A7MC 
        2.14        11.84        13.38         5.92        10.85        14.40 
TCGA-WQ-AB4B TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        4.01         0.69        35.05 

$`3Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         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-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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        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-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        33.83        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       24.00        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A12J 
        0.20         0.20         0.20        13.15         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       24.36        12.72         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       12.85        20.71        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       14.96        17.29         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        4.57         1.02         0.99        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        23.57        24.43        12.99        45.57        74.24 
TCGA-ZS-A9CG 
        8.22 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.20              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.00            108.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            11.80             14.96 
[1] "0.2 - 113.0 (11.8)" "0.0 - 108.8 (15.0)"
[1] "hr=" "2.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED         9        9         0          9          1          2
  3Q LOSS WILD-TYPE     137       63         2         43          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED          0         0         0
  3Q LOSS WILD-TYPE        2         1         2
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  9               137
  STAGE II                 9                63
  STAGE III                0                 2
  STAGE IIIA               9                43
  STAGE IIIB               1                 6
  STAGE IIIC               2                 5
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  3Q LOSS MUTATED      10  10  10   2
  3Q LOSS WILD-TYPE   145  68  54  10
D46V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1              10               145
  T2                 10                68
  T3                 10                54
  T4                  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"
D46V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    23   1
  3Q LOSS WILD-TYPE 199   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     23    1
  3Q LOSS WILD-TYPE  199    2
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              23               199
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    26   0   6
  3Q LOSS WILD-TYPE 212   4  63
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              26               212
  M1               0                 4
  MX               6                63
[1] 3 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
  3Q LOSS MUTATED    12  20
  3Q LOSS WILD-TYPE  88 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     12   20
  3Q LOSS WILD-TYPE   88  191
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              12                88
  MALE                20               191
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  3Q LOSS MUTATED                         1                       29
  3Q LOSS WILD-TYPE                       1                      274
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  3Q LOSS MUTATED                                  2
  3Q LOSS WILD-TYPE                                4
D46V8, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      29               274
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  3Q LOSS MUTATED    31   0   0   1
  3Q LOSS WILD-TYPE 243  14   1  15
D46V9, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              31               243
  R1               0                14
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  3Q LOSS MUTATED                                  0    15
  3Q LOSS WILD-TYPE                                1   126
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           0    17
  3Q LOSS WILD-TYPE                        15   128
D46V10, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15               126
  BLACK OR AFRICAN AMERICAN                      0                15
  WHITE                                         17               128
[1] 4 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
  3Q LOSS MUTATED     0  29
  3Q LOSS WILD-TYPE   8 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   29
  3Q LOSS WILD-TYPE    8  258
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              29               258
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    54  26
  4P LOSS WILD-TYPE 146  66
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               80               212 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               26                66 
$`4P LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       10.78         0.66        23.34         5.03        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-A3MC TCGA-DD-A113 
        9.50        14.60        13.45         0.66         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
       37.78         7.33         6.02        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-AAC8 
        5.62        30.61        26.83        30.51        29.56         0.53 
TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AACU 
       59.18        63.48        12.00        15.42        13.15        40.77 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADR 
       34.09        31.53        13.97        28.41        20.91        57.27 
TCGA-DD-AAE0 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK TCGA-DD-AAVQ 
        9.86        11.31        14.79        15.45        35.08        79.10 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7PZ 
       61.87        61.38        13.41        13.35         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 
        0.20         0.20        10.98         0.62        23.97         0.33 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A7M9 TCGA-G3-AAUZ 
       60.36         1.22        53.79        58.49         1.84        11.24 
TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.80         0.89         2.14        17.06        11.84        13.38 
TCGA-LG-A9QC TCGA-MI-A75G TCGA-PD-A5DF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB 
        5.92        18.38        21.01        15.52        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 
       14.40        15.98         7.04         4.01        13.55        24.43 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

$`4P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
        7.10        10.59        48.99        27.91        37.32        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z 
       46.78        27.52        27.52         2.99        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER 
       69.57        44.42         0.26        12.72         7.46         4.80 
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-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.07         0.10        83.57        53.33       113.00 
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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65         6.71        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       49.15        18.35        21.14        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-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72       100.96        13.48        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       55.40        12.53         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX 
        1.91        58.16        14.33        48.49        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        33.83        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       30.58        29.26         3.78        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        17.33         3.02         3.95         5.29         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         6.67         9.67         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE 
        8.52         4.64        12.56        12.69        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX 
       15.65        15.65        79.07        72.26        59.93        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       58.78        55.86        54.05        49.48        47.70        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E 
       15.85        13.91         0.23         0.20        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        0.20         0.20        18.74        19.99        11.74         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-A4ZQ TCGA-G3-A25T 
        8.12         6.38         0.13         0.03         0.39        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-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
        5.92        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV2 
       17.10         7.76        12.03         5.98         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD 
       20.75         4.01         2.14        24.36        12.72         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
       16.37         4.44         2.04        21.04        19.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       14.96         1.71         8.32         4.57         1.02         0.99 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57         8.22 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.73            113.00 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.50             14.55 
[1] "0.1 - 79.7 (14.5)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED        36       26         0         19          2          2
  4P LOSS WILD-TYPE     110       46         2         33          5          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED          2         1         1
  4P LOSS WILD-TYPE        0         0         1
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 36               110
  STAGE II                26                46
  STAGE III                0                 2
  STAGE IIIA              19                33
  STAGE IIIB               2                 5
  STAGE IIIC               2                 5
  STAGE IV                 2                 0
  STAGE IVA                1                 0
  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                T0+T1  T2  T3  T4
  4P LOSS MUTATED      38  28  22   4
  4P LOSS WILD-TYPE   117  50  42   8
D47V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              38               117
  T2                 28                50
  T3                 22                42
  T4                  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"
D47V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    62   2
  4P LOSS WILD-TYPE 160   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     62    2
  4P LOSS WILD-TYPE  160    1
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              62               160
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    71   3  18
  4P LOSS WILD-TYPE 167   1  51
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              71               167
  M1               3                 1
  MX              18                51
[1] 3 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
  4P LOSS MUTATED    25  67
  4P LOSS WILD-TYPE  75 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   67
  4P LOSS WILD-TYPE   75  144
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              25                75
  MALE                67               144
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4P LOSS MUTATED                         0                       90
  4P LOSS WILD-TYPE                       2                      213
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4P LOSS MUTATED                                  2
  4P LOSS WILD-TYPE                                4
D47V8, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      90               213
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  4P LOSS MUTATED    83   3   1   4
  4P LOSS WILD-TYPE 191  11   0  12
D47V9, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              83               191
  R1               3                11
  R2               1                 0
  RX               4                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
  4P LOSS MUTATED                                  0    47
  4P LOSS WILD-TYPE                                1    94
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           7    37
  4P LOSS WILD-TYPE                         8   108
D47V10, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         47                94
  BLACK OR AFRICAN AMERICAN                      7                 8
  WHITE                                         37               108
[1] 4 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
  4P LOSS MUTATED     3  86
  4P LOSS WILD-TYPE   5 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   86
  4P LOSS WILD-TYPE    5  201
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              86               201
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    79  34
  4Q LOSS WILD-TYPE 121  58
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              113               179 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                58 
$`4Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 
       10.78        10.59         0.66        27.52        23.34         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.66         0.10         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33         7.33         2.60        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NH 
       29.16        13.64        55.69         5.62        30.61        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AAC8 
       26.83        30.51        29.56        73.81         9.30         0.53 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACL 
       59.18        55.40        63.48        12.00        15.42         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACZ 
       58.16        13.15        48.49        40.77        38.04         5.62 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI 
       34.09        31.53        29.26        13.97        28.41        25.08 
TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE0 
       20.91         3.02         3.95        57.27         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEK 
        9.63         4.64        11.31        14.79        15.45        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAW0 TCGA-ED-A66X 
       79.10        59.93        61.87        61.38        54.05        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K 
        0.20         0.20         0.20        13.15         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-FV-A496 TCGA-FV-A4ZP 
       10.98         0.62        23.97         8.12         0.33        60.36 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A5SI TCGA-G3-A5SM 
        1.22        58.49        14.86        21.53        14.70        17.10 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-K7-A5RG 
        1.84        11.80         0.89         2.14         3.02        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75G TCGA-RC-A7SH 
       11.84        13.38        12.72         5.92        18.38        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        24.13        17.29        14.40        15.98         7.04 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        0.99         4.01        13.55        24.43        35.05 

$`4Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
        7.10        48.99        27.91        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        44.42 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       12.72         7.46         4.80         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        3.39         4.24         3.32         0.07        83.57       113.00 
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-A1EE TCGA-DD-A1EF TCGA-DD-A1EK TCGA-DD-A39V 
       19.79        75.65         6.71        12.95        18.35        21.14 
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-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78         0.36        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ 
       73.38        30.97        39.78        56.25       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72       100.96        13.48        11.41        65.75 
TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACQ 
       12.53         6.41        53.19        60.10         0.30        14.33 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.59         4.50        18.54        21.63        33.83        22.09 
TCGA-DD-AADA TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN 
       30.58         3.78        24.00        24.13         0.39        17.33 
TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAE3 
        5.29         7.10         8.28         6.67         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG 
        8.52        12.56        12.69        12.16        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       15.65        79.07        72.26        56.48        58.78        55.86 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        13.41        12.69        15.85        13.91 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
        0.23         0.20        13.41         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       19.10        27.88         6.38         0.13         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH 
       51.06        53.79        28.27        30.74        22.13        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC 
        5.92        19.53        19.23        11.97        20.42         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       12.03         5.98        11.24         8.55         9.70         9.17 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
        2.14        24.36         4.27         9.57        16.67        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MD TCGA-UB-AA0U 
        2.04        21.04        19.04        14.96         1.71         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.57         1.02         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
        0.69        12.99        45.57        74.24         8.22 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.73            113.00 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            14.40             14.96 
[1] "0.1 - 79.7 (14.4)"  "0.0 - 113.0 (15.0)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED        56       32         1         24          3          2
  4Q LOSS WILD-TYPE      90       40         1         28          4          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED          2         1         1
  4Q LOSS WILD-TYPE        0         0         1
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 56                90
  STAGE II                32                40
  STAGE III                1                 1
  STAGE IIIA              24                28
  STAGE IIIB               3                 4
  STAGE IIIC               2                 5
  STAGE IV                 2                 0
  STAGE IVA                1                 0
  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                T0+T1 T2 T3 T4
  4Q LOSS MUTATED      58 34 30  5
  4Q LOSS WILD-TYPE    97 44 34  7
D48V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              58                97
  T2                 34                44
  T3                 30                34
  T4                  5                 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"
D48V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    93   2
  4Q LOSS WILD-TYPE 129   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     93    2
  4Q LOSS WILD-TYPE  129    1
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              93               129
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED   105   3  19
  4Q LOSS WILD-TYPE 133   1  50
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0             105               133
  M1               3                 1
  MX              19                50
[1] 3 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
  4Q LOSS MUTATED    37  90
  4Q LOSS WILD-TYPE  63 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     37   90
  4Q LOSS WILD-TYPE   63  121
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              37                63
  MALE                90               121
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  4Q LOSS MUTATED                         0                      124
  4Q LOSS WILD-TYPE                       2                      179
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  4Q LOSS MUTATED                                  3
  4Q LOSS WILD-TYPE                                3
D48V8, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     124               179
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  4Q LOSS MUTATED   118   4   1   4
  4Q LOSS WILD-TYPE 156  10   0  12
D48V9, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             118               156
  R1               4                10
  R2               1                 0
  RX               4                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
  4Q LOSS MUTATED                                  0    72
  4Q LOSS WILD-TYPE                                1    69
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           8    47
  4Q LOSS WILD-TYPE                         7    98
D48V10, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         72                69
  BLACK OR AFRICAN AMERICAN                      8                 7
  WHITE                                         47                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"
D48V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 120
  4Q LOSS WILD-TYPE   5 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  120
  4Q LOSS WILD-TYPE    5  167
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             120               167
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    15   6
  5P LOSS WILD-TYPE 185  86
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21               271 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                86 
$`5P LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10S TCGA-CC-5258 TCGA-CC-A3M9 TCGA-DD-A11A TCGA-DD-A1EH 
        0.66        46.78         0.07         0.10         2.60        49.15 
TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI 
       29.16        32.52        48.49        29.26        28.41        25.08 
TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A496 TCGA-G3-A25S 
        6.67        79.10         0.20        22.85         0.33         1.22 
TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 
        1.84         2.14         3.02 

$`5P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        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-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         0.07         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-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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
        6.71        12.95        45.11         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-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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
        0.36        30.61        33.14        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        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 
      108.76        12.26         0.30        80.75        78.84        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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       40.77        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       13.97         3.78        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
        8.28         9.67         9.86         9.63         9.47         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA 
        8.52         4.64        12.56        11.31        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK 
       12.16        15.45        16.37        15.65        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       58.78        55.86        54.05        49.48        47.70        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-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        9.96        11.93        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP 
       27.88         8.12         6.38         0.13         0.03        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         5.98        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         0.89         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       18.38        12.85        20.71        10.85        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       15.98         7.04         8.32         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.07              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             79.1             113.0 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             6.67             14.60 
[1] "0.1 - 79.1 (6.7)"   "0.0 - 113.0 (14.6)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED        11        5         1          6          1          1
  5P LOSS WILD-TYPE     135       67         1         46          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5P LOSS MUTATED          0         0         0
  5P LOSS WILD-TYPE        2         1         2
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 11               135
  STAGE II                 5                67
  STAGE III                1                 1
  STAGE IIIA               6                46
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  5P LOSS MUTATED      12   5   9   0
  5P LOSS WILD-TYPE   143  73  55  12
D49V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1              12               143
  T2                  5                73
  T3                  9                55
  T4                  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"
D49V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    21   1
  5P LOSS WILD-TYPE 201   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     21    1
  5P LOSS WILD-TYPE  201    2
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              21               201
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED    23   0   3
  5P LOSS WILD-TYPE 215   4  66
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0              23               215
  M1               0                 4
  MX               3                66
[1] 3 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
  5P LOSS MUTATED     6  20
  5P LOSS WILD-TYPE  94 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   20
  5P LOSS WILD-TYPE   94  191
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               6                94
  MALE                20               191
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5P LOSS MUTATED                         1                       23
  5P LOSS WILD-TYPE                       1                      280
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5P LOSS MUTATED                                  2
  5P LOSS WILD-TYPE                                4
D49V8, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      23               280
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  5P LOSS MUTATED    24   1   0   1
  5P LOSS WILD-TYPE 250  13   1  15
D49V9, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              24               250
  R1               1                13
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  5P LOSS MUTATED                                  0    16
  5P LOSS WILD-TYPE                                1   125
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           1     9
  5P LOSS WILD-TYPE                        14   136
D49V10, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16               125
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          9               136
[1] 4 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
  5P LOSS MUTATED     0  26
  5P LOSS WILD-TYPE   8 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   26
  5P LOSS WILD-TYPE    8  261
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              26               261
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    20  11
  5Q LOSS WILD-TYPE 180  81
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31               261 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               11                81 
$`5Q LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A10S TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A11A 
        0.66        10.13        46.78         4.24         0.10         2.60 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A4NB TCGA-DD-AACS TCGA-DD-AAD8 
       12.95        49.15        29.16        32.52        48.49        31.53 
TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADW TCGA-DD-AAVQ TCGA-ED-A8O6 
       29.26        28.41        25.08         6.67        79.10         0.20 
TCGA-ED-A97K TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20        22.85        27.88         0.33        60.36         1.22 
TCGA-G3-A25X TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-UB-A7MB 
       58.49        12.03         1.84         2.14         3.02        17.29 
TCGA-UB-A7MF 
        7.04 

$`5Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT 
        0.66         0.07         2.86         0.39         3.39         3.32 
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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       33.14        73.38        30.97        30.15        26.83        30.51 
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       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        65.75        59.18        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        13.15        14.33        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADJ 
       34.09        22.09        30.58        13.97         3.78        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        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-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         8.12         6.38         0.13         0.03 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       14.70        11.97        20.42        17.10         7.76         5.98 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       20.71        10.85        58.88        16.37         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        2.04        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       14.96        14.40         1.71        15.98         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.02         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             79.1             113.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.95             14.60 
[1] "0.1 - 79.1 (12.9)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED        14        7         1         11          1          1
  5Q LOSS WILD-TYPE     132       65         1         41          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  5Q LOSS MUTATED          0         0         0
  5Q LOSS WILD-TYPE        2         1         2
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 14               132
  STAGE II                 7                65
  STAGE III                1                 1
  STAGE IIIA              11                41
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  5Q LOSS MUTATED      15   7  15   0
  5Q LOSS WILD-TYPE   140  71  49  12
D50V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1              15               140
  T2                  7                71
  T3                 15                49
  T4                  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"
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    26   1
  5Q LOSS WILD-TYPE 196   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     26    1
  5Q LOSS WILD-TYPE  196    2
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              26               196
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    30   0   7
  5Q LOSS WILD-TYPE 208   4  62
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              30               208
  M1               0                 4
  MX               7                62
[1] 3 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
  5Q LOSS MUTATED    12  25
  5Q LOSS WILD-TYPE  88 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     12   25
  5Q LOSS WILD-TYPE   88  186
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              12                88
  MALE                25               186
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  5Q LOSS MUTATED                         1                       33
  5Q LOSS WILD-TYPE                       1                      270
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  5Q LOSS MUTATED                                  3
  5Q LOSS WILD-TYPE                                3
D50V8, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        1                 1
  HEPATOCELLULAR CARCINOMA                      33               270
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  5Q LOSS MUTATED    34   2   0   1
  5Q LOSS WILD-TYPE 240  12   1  15
D50V9, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              34               240
  R1               2                12
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  5Q LOSS MUTATED                                  0    20
  5Q LOSS WILD-TYPE                                1   121
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           1    16
  5Q LOSS WILD-TYPE                        14   129
D50V10, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         20               121
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         16               129
[1] 4 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
  5Q LOSS MUTATED     0  37
  5Q LOSS WILD-TYPE   8 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   37
  5Q LOSS WILD-TYPE    8  250
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              37               250
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    14  10
  6P LOSS WILD-TYPE 186  82
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               268 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10                82 
$`6P LOSS MUTATED`
TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-A3M9 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        9.50        12.72         0.10       113.00         2.60        21.76 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ 
       90.71        19.79         6.71        12.95         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A39Z TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-AAEG TCGA-DD-AAVU 
       18.35        19.76        30.15        39.78        15.65        61.87 
TCGA-ED-A66Y TCGA-G3-AAV6 TCGA-UB-A7MB TCGA-UB-A7ME TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.23         2.14        17.29        15.98         0.69        35.05 

$`6P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A69H TCGA-BC-A8YO TCGA-BD-A3EP 
       13.84         0.26        22.36        14.60         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.78        83.57        53.33         7.33         0.46        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EL 
       79.40        66.31        75.65        45.11        49.15        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69         5.62        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-A4NI 
       30.61        33.14        32.52        73.38        30.97        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        65.75        59.18        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        1.91        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       33.83        34.09        22.09        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       13.97        28.41         3.78        25.08        24.00        24.13 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        17.33         3.02         3.95         5.29 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       57.27         7.10         8.28         6.67         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        13.41        12.69        15.85        13.91        13.35 
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        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        9.17         0.89         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        24.13        14.96        14.40         1.71 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55         4.67        25.71        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        74.24         8.22 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           113.00            108.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           16.635            14.365 
[1] "0.1 - 113.0 (16.6)" "0.0 - 108.8 (14.4)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED         9        5         0          6          1          1
  6P LOSS WILD-TYPE     137       67         2         46          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED          0         0         1
  6P LOSS WILD-TYPE        2         1         1
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  9               137
  STAGE II                 5                67
  STAGE III                0                 2
  STAGE IIIA               6                46
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  6P LOSS MUTATED      11   5   7   1
  6P LOSS WILD-TYPE   144  73  57  11
D51V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1              11               144
  T2                  5                73
  T3                  7                57
  T4                  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"
D51V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    17   1
  6P LOSS WILD-TYPE 205   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     17    1
  6P LOSS WILD-TYPE  205    2
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              17               205
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    19   1   4
  6P LOSS WILD-TYPE 219   3  65
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              19               219
  M1               1                 3
  MX               4                65
[1] 3 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
  6P LOSS MUTATED    13  11
  6P LOSS WILD-TYPE  87 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13   11
  6P LOSS WILD-TYPE   87  200
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              13                87
  MALE                11               200
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6P LOSS MUTATED                         0                       24
  6P LOSS WILD-TYPE                       2                      279
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6P LOSS MUTATED                                  0
  6P LOSS WILD-TYPE                                6
D51V8, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      24               279
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  6P LOSS MUTATED    22   1   0   1
  6P LOSS WILD-TYPE 252  13   1  15
D51V9, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              22               252
  R1               1                13
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  6P LOSS MUTATED                                  0     6
  6P LOSS WILD-TYPE                                1   135
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           1    16
  6P LOSS WILD-TYPE                        14   129
D51V10, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6               135
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                         16               129
[1] 4 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
  6P LOSS MUTATED     0  22
  6P LOSS WILD-TYPE   8 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   22
  6P LOSS WILD-TYPE    8  265
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              22               265
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    51  26
  6Q LOSS WILD-TYPE 149  66
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               77               215 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                66 
$`6Q LOSS MUTATED`
TCGA-4R-AA8I TCGA-BC-A10Q TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-CC-5260 
        7.10        37.32         0.26         9.50        12.72         2.86 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 
        0.10         0.07       113.00         2.60        21.76        90.71 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79         6.71        12.95         6.02        29.16        18.35 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4NH 
       55.69        19.76         7.66         0.36        33.14        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NS TCGA-DD-A73E TCGA-DD-AA3A TCGA-DD-AAC8 
       30.51        39.78        80.75         1.45        13.48         0.53 
TCGA-DD-AACE TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AAD3 
       63.48         6.41        53.19        13.15        40.77        33.83 
TCGA-DD-AAD8 TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADY TCGA-DD-AAE2 
       31.53        24.13        20.91         3.95         9.67         9.47 
TCGA-DD-AAE9 TCGA-DD-AAEG TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW3 
       12.69        15.65        59.93        61.87        58.78        47.70 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.23         0.20        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
       18.74        11.93        22.85        32.45        19.10        27.88 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A5SL TCGA-G3-A6UC 
        6.38        60.36        51.06        58.49        20.42         7.76 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-MI-A75E TCGA-MI-A75I 
        9.17         0.89         2.14        37.71        16.67        20.71 
TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       17.29        15.98         8.32         0.69        35.05 

$`6Q LOSS WILD-TYPE`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
       10.78        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        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-A3KG 
        1.12        69.57         5.03        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 
       14.60         7.46        13.45         4.80         0.66         0.07 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
       79.73        37.78        83.57        53.33         7.33         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EG TCGA-DD-A1EH 
       51.29        79.40        66.31        75.65        45.11        49.15 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       13.64        21.14         5.62        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       73.38        30.97        26.83        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
      108.76        12.26         0.30        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACA 
        7.56        10.98        27.72       100.96        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACJ 
       59.18        55.40        12.53        12.00        15.42        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW 
        0.30         1.91        58.16        14.33        48.49        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
        5.59         5.62         4.50        18.54        21.63        34.09 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       22.09        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ 
       25.08        24.00         0.39        17.33         3.02         5.29 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       57.27         7.10         8.28         6.67         9.86         9.63 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA 
        9.86         8.52         4.64        12.56        11.31        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       12.16        15.45        16.37        15.65        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 
       79.10        72.26        61.38        56.48        55.86        54.05 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A26S TCGA-EP-A2KA 
        0.20         0.20         0.20        13.15        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 
       10.98         0.62         9.96        14.40        23.97         8.12 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        0.13         0.03         0.33         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-A5SM 
        5.92        19.53        19.23        14.70        11.97        17.10 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       12.03         5.98         1.84        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF 
        9.70         3.02         1.02         2.20         2.66        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        18.38        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
       14.40         1.71         7.04         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        74.24         8.22 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           113.00            108.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            16.67             14.33 
[1] "0.1 - 113.0 (16.7)" "0.0 - 108.8 (14.3)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED        33       18         0         17          2          4
  6Q LOSS WILD-TYPE     113       54         2         35          5          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED          1         0         1
  6Q LOSS WILD-TYPE        1         1         1
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 33               113
  STAGE II                18                54
  STAGE III                0                 2
  STAGE IIIA              17                35
  STAGE IIIB               2                 5
  STAGE IIIC               4                 3
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  6Q LOSS MUTATED      35  22  19   3
  6Q LOSS WILD-TYPE   120  56  45   9
D52V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1              35               120
  T2                 22                56
  T3                 19                45
  T4                  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"
D52V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    56   2
  6Q LOSS WILD-TYPE 166   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     56    2
  6Q LOSS WILD-TYPE  166    1
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              56               166
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED    64   2  14
  6Q LOSS WILD-TYPE 174   2  55
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              64               174
  M1               2                 2
  MX              14                55
[1] 3 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
  6Q LOSS MUTATED    34  46
  6Q LOSS WILD-TYPE  66 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     34   46
  6Q LOSS WILD-TYPE   66  165
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              34                66
  MALE                46               165
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  6Q LOSS MUTATED                         0                       77
  6Q LOSS WILD-TYPE                       2                      226
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  6Q LOSS MUTATED                                  3
  6Q LOSS WILD-TYPE                                3
D52V8, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      77               226
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  6Q LOSS MUTATED    71   4   0   4
  6Q LOSS WILD-TYPE 203  10   1  12
D52V9, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              71               203
  R1               4                10
  R2               0                 1
  RX               4                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
  6Q LOSS MUTATED                                  0    33
  6Q LOSS WILD-TYPE                                1   108
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           3    41
  6Q LOSS WILD-TYPE                        12   104
D52V10, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         33               108
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                         41               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"
D52V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     2  73
  6Q LOSS WILD-TYPE   6 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   73
  6Q LOSS WILD-TYPE    6  214
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              73               214
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     8   5
  7P LOSS WILD-TYPE 192  87
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               13               279 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                87 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-CC-A3M9 TCGA-DD-A1EF TCGA-DD-A39X 
       13.84        22.36         0.39         0.10        12.95        55.69 
TCGA-DD-AACB TCGA-DD-AADB TCGA-DD-AADN TCGA-EP-A2KB TCGA-FV-A3I1 TCGA-K7-A5RG 
       59.18        29.26        17.33        10.98         8.12        17.06 
TCGA-RC-A7SK 
       15.52 

$`7P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KF TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         0.07         2.86         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        3.32         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-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.71        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14         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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       14.33        48.49        40.77        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       31.53        30.58        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       24.00        24.13        20.91         0.39         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         0.20         0.20 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        24.13        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       14.40         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        1.02         0.99         4.01        13.55         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.10              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            59.18            113.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            15.52             14.40 
[1] "0.1 - 59.2 (15.5)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.4"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P LOSS MUTATED         8        5         0          1          0          0
  7P LOSS WILD-TYPE     138       67         2         51          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED          0         0         0
  7P LOSS WILD-TYPE        2         1         2
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  8               138
  STAGE II                 5                67
  STAGE III                0                 2
  STAGE IIIA               1                51
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  7P LOSS MUTATED       8   5   1   0
  7P LOSS WILD-TYPE   147  73  63  12
D53V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               8               147
  T2                  5                73
  T3                  1                63
  T4                  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"
D53V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9   0
  7P LOSS WILD-TYPE 213   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9    0
  7P LOSS WILD-TYPE  213    3
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               9               213
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED    10   0   4
  7P LOSS WILD-TYPE 228   4  65
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0              10               228
  M1               0                 4
  MX               4                65
[1] 3 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
  7P LOSS MUTATED     7   7
  7P LOSS WILD-TYPE  93 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    7
  7P LOSS WILD-TYPE   93  204
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               7                93
  MALE                 7               204
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7P LOSS MUTATED                         0                       14
  7P LOSS WILD-TYPE                       2                      289
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                                6
D53V8, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      14               289
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  7P LOSS MUTATED    13   0   0   1
  7P LOSS WILD-TYPE 261  14   1  15
D53V9, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              13               261
  R1               0                14
  R2               0                 1
  RX               1                15
[1] 4 2
[1] 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
  7P LOSS MUTATED                                  0     7
  7P LOSS WILD-TYPE                                1   134
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1     6
  7P LOSS WILD-TYPE                        14   139
D53V10, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7               134
  BLACK OR AFRICAN AMERICAN                      1                14
  WHITE                                          6               139
[1] 4 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
  7P LOSS MUTATED     0  13
  7P LOSS WILD-TYPE   8 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   13
  7P LOSS WILD-TYPE    8  274
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              13               274
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     8   9
  7Q LOSS WILD-TYPE 192  83
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               275 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9                83 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5261 TCGA-DD-A1EF TCGA-DD-A1EL 
       48.99        13.84        22.36         0.39        12.95        13.64 
TCGA-DD-A39X TCGA-DD-AACB TCGA-DD-AACZ TCGA-DD-AADB TCGA-DD-AADF TCGA-ED-A7PX 
       55.69        59.18         5.62        29.26         3.78         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-G3-A25S TCGA-K7-A5RG TCGA-QA-A7B7 
        0.20        10.98         1.22        17.06         2.04 

$`7Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59         0.66        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         0.07         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-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65         6.71        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       18.35        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-A4NF 
        0.36        30.61        33.14        32.52        73.38        30.97 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        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       108.76        12.26         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC 
      100.96        13.48         0.53        11.41        65.75        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        63.48        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        33.83        34.09        22.09        31.53        30.58 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97        28.41        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        17.33         3.02         3.95         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
        7.10         8.28         6.67         9.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.47         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.23         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         0.20         0.20        18.74        19.99        11.74 
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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       12.72         5.92         4.27         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01        21.04        19.04        15.39        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.20              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            59.18            113.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            12.95             14.79 
[1] "0.2 - 59.2 (12.9)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "2.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q LOSS MUTATED         9        7         0          3          0          0
  7Q LOSS WILD-TYPE     137       65         2         49          7          7
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED          0         0         0
  7Q LOSS WILD-TYPE        2         1         2
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  9               137
  STAGE II                 7                65
  STAGE III                0                 2
  STAGE IIIA               3                49
  STAGE IIIB               0                 7
  STAGE IIIC               0                 7
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       9   7   3   0
  7Q LOSS WILD-TYPE   146  71  61  12
D54V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               9               146
  T2                  7                71
  T3                  3                61
  T4                  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"
D54V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13   0
  7Q LOSS WILD-TYPE 209   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13    0
  7Q LOSS WILD-TYPE  209    3
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              13               209
  1               0                 3
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED    16   0   3
  7Q LOSS WILD-TYPE 222   4  66
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              16               222
  M1               0                 4
  MX               3                66
[1] 3 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
  7Q LOSS MUTATED    11   8
  7Q LOSS WILD-TYPE  89 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11    8
  7Q LOSS WILD-TYPE   89  203
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11                89
  MALE                 8               203
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  7Q LOSS MUTATED                         0                       19
  7Q LOSS WILD-TYPE                       2                      284
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  7Q LOSS MUTATED                                  0
  7Q LOSS WILD-TYPE                                6
D54V8, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      19               284
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 6
[1] 3 2
[1] 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
  7Q LOSS MUTATED    15   2   0   2
  7Q LOSS WILD-TYPE 259  12   1  14
D54V9, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              15               259
  R1               2                12
  R2               0                 1
  RX               2                14
[1] 4 2
[1] 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
  7Q LOSS MUTATED                                  0     9
  7Q LOSS WILD-TYPE                                1   132
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3     7
  7Q LOSS WILD-TYPE                        12   138
D54V10, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9               132
  BLACK OR AFRICAN AMERICAN                      3                12
  WHITE                                          7               138
[1] 4 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
  7Q LOSS MUTATED     0  18
  7Q LOSS WILD-TYPE   8 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   18
  7Q LOSS WILD-TYPE    8  269
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              18               269
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   104  47
  8P LOSS WILD-TYPE  96  45
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              151               141 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               47                45 
$`8P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 
       37.32        10.13        27.52        27.52         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3EP 
       13.84         0.26        22.36        14.60        12.72        13.45 
TCGA-BW-A5NO TCGA-CC-5261 TCGA-CC-5262 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.66         0.39         3.39        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A1EL 
      113.00        21.76         6.71        45.11        29.16        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A3 
       21.14        55.69         5.62        19.76        25.81        17.59 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NH 
       13.78         0.36        30.61        33.14        73.38        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A 
       26.83        30.51        39.78         0.30        78.84        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-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACM 
       59.18        55.40        63.48        15.42         6.41        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AAD0 TCGA-DD-AAD3 
       13.15        14.33        48.49        40.77         4.50        33.83 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADK 
       31.53        30.58        29.26        13.97        25.08        24.13 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AAE0 
        0.39        17.33         3.02         3.95         5.29         9.86 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
        8.52         4.64        12.56        11.31        12.69        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       15.45        16.37        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW3 
       59.93        61.87        58.78        55.86        54.05        47.70 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       11.74         0.62        11.93        22.85        14.40        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A4ZP 
       19.10        27.88         8.12         6.38         0.03        60.36 
TCGA-G3-A25S TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A6UC 
        1.22        28.27        30.74        22.13        19.53         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 
       12.03         1.84         8.55         9.70         0.89         2.14 
TCGA-G3-AAV7 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E 
        3.02         2.66         4.01         5.92         9.57        16.67 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       20.71        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MD 
       19.04        15.39        15.52        24.13        17.29         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CV 
       15.98         7.04         8.32         1.02        13.55         4.67 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.21        23.57        24.43        12.99        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

$`8P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       46.78         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5263 
        9.50         7.46         4.80         0.07         2.86         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-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-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       18.35         7.66        70.06        20.12       102.74       107.11 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       32.52        30.97        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       12.26        80.75        13.48         0.53        11.41        65.75 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.53        12.00        53.19        60.10         0.30         1.91 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 
       38.04         5.59         5.62        18.54        21.63        34.09 
TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADR 
       22.09        28.41         3.78        24.00        20.91        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         8.28         6.67         9.67         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVW TCGA-DD-AAVX 
        9.86        14.79        15.65        35.08        61.38        56.48 
TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K 
        0.23         0.20        13.15        13.41         0.20         0.20 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A23B TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ 
       10.98         9.96        32.45         0.13         0.33         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        58.49        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        5.98        11.24        11.80         9.17         1.02         2.20 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       37.71        20.75        17.06         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75H TCGA-MR-A8JO 
       24.36        12.72         4.27        18.38        12.85        10.85 
TCGA-NI-A4U2 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       58.88        14.96        14.40         4.57         0.99         4.01 
TCGA-ZP-A9CY TCGA-ZP-A9D1 TCGA-ZS-A9CD 
       25.71         0.69        45.57 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           113.00            108.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            15.65             13.38 
[1] "0.0 - 113.0 (15.7)" "0.1 - 108.8 (13.4)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED        75       39         0         24          6          4
  8P LOSS WILD-TYPE      71       33         2         28          1          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED          1         1         1
  8P LOSS WILD-TYPE        1         0         1
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 75                71
  STAGE II                39                33
  STAGE III                0                 2
  STAGE IIIA              24                28
  STAGE IIIB               6                 1
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                1                 0
  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                T0+T1 T2 T3 T4
  8P LOSS MUTATED      81 45 31  5
  8P LOSS WILD-TYPE    74 33 33  7
D55V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              81                74
  T2                 45                33
  T3                 31                33
  T4                  5                 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"
D55V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   107   3
  8P LOSS WILD-TYPE 115   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    107    3
  8P LOSS WILD-TYPE  115    0
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             107               115
  1               3                 0
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED   119   2  41
  8P LOSS WILD-TYPE 119   2  28
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0             119               119
  M1               2                 2
  MX              41                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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    53 109
  8P LOSS WILD-TYPE  47 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     53  109
  8P LOSS WILD-TYPE   47  102
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              53                47
  MALE               109               102
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8P LOSS MUTATED                         0                      161
  8P LOSS WILD-TYPE                       2                      142
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8P LOSS MUTATED                                  1
  8P LOSS WILD-TYPE                                5
D55V8, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                     161               142
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   143   8   0   7
  8P LOSS WILD-TYPE 131   6   1   9
D55V9, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             143               131
  R1               8                 6
  R2               0                 1
  RX               7                 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
  8P LOSS MUTATED                                  1    69
  8P LOSS WILD-TYPE                                0    72
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          11    77
  8P LOSS WILD-TYPE                         4    68
D55V10, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         69                72
  BLACK OR AFRICAN AMERICAN                     11                 4
  WHITE                                         77                68
[1] 4 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
  8P LOSS MUTATED     5 149
  8P LOSS WILD-TYPE   3 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  149
  8P LOSS WILD-TYPE    3  138
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             149               138
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    23  10
  8Q LOSS WILD-TYPE 177  82
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               33               259 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                82 
$`8Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-BW-A5NO TCGA-CC-5261 TCGA-DD-A115 
       27.52        13.84        22.36         0.66         0.39        83.57 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NK TCGA-DD-A73C TCGA-DD-AACE 
       25.81        30.61        33.14        39.78         7.56        63.48 
TCGA-DD-AAD0 TCGA-DD-AAD8 TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AAE6 TCGA-DD-AAEB 
        4.50        31.53         3.95         6.67         4.64        12.16 
TCGA-DD-AAVU TCGA-ED-A7PY TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25V TCGA-G3-A7M9 
       61.87         0.20        27.88         0.03        28.27         1.84 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A7S9 
        9.70         0.89         2.14        16.37         2.04        21.04 
TCGA-UB-A7MF TCGA-WJ-A86L TCGA-ZS-A9CF 
        7.04         1.02        74.24 

$`8Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 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-A3KF 
       23.34         1.12        69.57         5.03        44.42         0.26 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.07         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-A116 
        0.07         0.10         0.13        79.73        37.78        53.33 
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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
        0.36        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         9.30        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG 
       65.75        59.18        55.40        12.53        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       30.58        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       24.00        24.13        20.91         0.39        17.33         3.02 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.63         9.47         9.86         8.52        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.69        14.79        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       35.08        79.07        79.10        72.26        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
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-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20         0.20         0.20        13.15        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K 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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A496 
       23.97        19.10         8.12         6.38         0.13         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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
        7.76        12.03         5.98        11.24         8.55        11.80 
TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.01        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V 
       17.29        14.40         1.71        15.98         8.32         4.57 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CG 
        8.22 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.03              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            83.57            113.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.16             14.70 
[1] "0.0 - 83.6 (12.2)"  "0.1 - 113.0 (14.7)"
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q LOSS MUTATED        14        9         0          9          1          1
  8Q LOSS WILD-TYPE     132       63         2         43          6          6
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED          0         0         1
  8Q LOSS WILD-TYPE        2         1         1
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 14               132
  STAGE II                 9                63
  STAGE III                0                 2
  STAGE IIIA               9                43
  STAGE IIIB               1                 6
  STAGE IIIC               1                 6
  STAGE IV                 0                 2
  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                T0+T1  T2  T3  T4
  8Q LOSS MUTATED      14  10  10   2
  8Q LOSS WILD-TYPE   141  68  54  10
D56V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1              14               141
  T2                 10                68
  T3                 10                54
  T4                  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"
D56V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    22   1
  8Q LOSS WILD-TYPE 200   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     22    1
  8Q LOSS WILD-TYPE  200    2
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              22               200
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    27   1   8
  8Q LOSS WILD-TYPE 211   3  61
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              27               211
  M1               1                 3
  MX               8                61
[1] 3 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
  8Q LOSS MUTATED    18  18
  8Q LOSS WILD-TYPE  82 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     18   18
  8Q LOSS WILD-TYPE   82  193
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              18                82
  MALE                18               193
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  8Q LOSS MUTATED                         0                       35
  8Q LOSS WILD-TYPE                       2                      268
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  8Q LOSS MUTATED                                  1
  8Q LOSS WILD-TYPE                                5
D56V8, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      35               268
  HEPATOCHOLANGIOCARCINOMA (MIXED)               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    32   1   0   3
  8Q LOSS WILD-TYPE 242  13   1  13
D56V9, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              32               242
  R1               1                13
  R2               0                 1
  RX               3                13
[1] 4 2
[1] 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
  8Q LOSS MUTATED                                  0    14
  8Q LOSS WILD-TYPE                                1   127
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    20
  8Q LOSS WILD-TYPE                        13   125
D56V10, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14               127
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         20               125
[1] 4 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
  8Q LOSS MUTATED     0  34
  8Q LOSS WILD-TYPE   8 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   34
  8Q LOSS WILD-TYPE    8  253
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              34               253
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    59  31
  9P LOSS WILD-TYPE 141  61
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               90               202 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               31                61 
$`9P LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       10.78        10.59        48.99        37.32        10.13        46.78 
TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 
       27.52         5.03        13.84         9.50        14.60         0.07 
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-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-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X 
       12.95        45.11         6.02        29.16        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A4NO 
        5.62        25.81        30.61        73.38        26.83        73.81 
TCGA-DD-AA3A TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACW 
       13.48        63.48        15.42        13.15        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADC TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO 
        5.62        33.83        13.97        24.13        20.91         3.02 
TCGA-DD-AADP TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED 
        3.95         9.63         9.86         4.64        11.31        15.45 
TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ 
       16.37        35.08        79.10        61.87        61.38        55.86 
TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A97K 
       54.05        13.41        13.35         0.20        13.15         0.20 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A25T 
        0.62        11.93        23.97         8.12         1.22        51.06 
TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75G 
       11.80         2.14         3.02         2.20        24.36        18.38 
TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       20.71        16.37        19.04        15.39        15.52        24.13 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       15.98         8.32         0.99         4.01        23.57        24.43 

$`9P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
        7.10         0.66        27.91        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42         0.26        22.36 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 
       12.72         7.46        13.45         4.80         0.66         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A11D 
        0.39         3.39         0.07        37.78       113.00        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       49.15        13.64        21.14        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-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       33.14        32.52        30.97        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       27.72       100.96         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       55.40        12.53        12.00         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACX 
        0.30         1.91        58.16        14.33        48.49         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        21.63        34.09        22.09        31.53 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        28.41         3.78        25.08        24.00 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39        17.33         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE7 
        6.67         9.67         9.86         9.47         8.52        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP 
       12.69        14.79        12.16        15.65        15.65        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 
       72.26        59.93        56.48        58.78        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       12.69        15.85        13.91         0.23         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S 
        0.20        13.41         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       11.74        10.98         9.96        22.85        14.40        32.45 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       19.10        27.88         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       60.36         0.39        53.79        28.27        30.74        58.49 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
       12.03         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        9.17         0.89         1.02         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-LG-A6GG 
       17.06         4.01         2.14        11.84        13.38        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
        5.92         4.27         9.57        16.67        12.85        10.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA 
       58.88         4.44        21.01         2.04        21.04        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L 
       17.29        14.40         1.71         7.04         4.57         1.02 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D4 
       13.55         4.67        25.71        23.21         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.57            113.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           14.995            14.400 
[1] "0.1 - 83.6 (15.0)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED        43       22         0         18          1          2
  9P LOSS WILD-TYPE     103       50         2         34          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED          1         1         2
  9P LOSS WILD-TYPE        1         0         0
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 43               103
  STAGE II                22                50
  STAGE III                0                 2
  STAGE IIIA              18                34
  STAGE IIIB               1                 6
  STAGE IIIC               2                 5
  STAGE IV                 1                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[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                T0+T1  T2  T3  T4
  9P LOSS MUTATED      46  26  23   4
  9P LOSS WILD-TYPE   109  52  41   8
D57V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              46               109
  T2                 26                52
  T3                 23                41
  T4                  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"
D57V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    72   2
  9P LOSS WILD-TYPE 150   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     72    2
  9P LOSS WILD-TYPE  150    1
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              72               150
  1               2                 1
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED    77   3  19
  9P LOSS WILD-TYPE 161   1  50
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              77               161
  M1               3                 1
  MX              19                50
[1] 3 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
  9P LOSS MUTATED    23  76
  9P LOSS WILD-TYPE  77 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     23   76
  9P LOSS WILD-TYPE   77  135
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              23                77
  MALE                76               135
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9P LOSS MUTATED                         0                       97
  9P LOSS WILD-TYPE                       2                      206
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9P LOSS MUTATED                                  2
  9P LOSS WILD-TYPE                                4
D57V8, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      97               206
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  9P LOSS MUTATED    85   6   1   5
  9P LOSS WILD-TYPE 189   8   0  11
D57V9, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              85               189
  R1               6                 8
  R2               1                 0
  RX               5                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
  9P LOSS MUTATED                                  0    53
  9P LOSS WILD-TYPE                                1    88
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                           5    40
  9P LOSS WILD-TYPE                        10   105
D57V10, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         53                88
  BLACK OR AFRICAN AMERICAN                      5                10
  WHITE                                         40               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"
D57V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  95
  9P LOSS WILD-TYPE   7 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   95
  9P LOSS WILD-TYPE    7  192
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              95               192
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    55  30
  9Q LOSS WILD-TYPE 145  62
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               85               207 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               30                62 
$`9Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       10.78        10.59        37.32        10.13        46.78        27.52 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5260 
        5.03        13.84         9.50        14.60         0.07         2.86 
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-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EF 
       53.33         7.33         2.60         0.46        21.76        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       45.11         6.02        29.16        18.35        55.69         5.62 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AA3A TCGA-DD-AACB 
       30.61        33.14        26.83        73.81        13.48        59.18 
TCGA-DD-AACE TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD8 
       63.48        13.15        40.77         5.62        33.83        31.53 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAED 
       24.13        20.91         3.02        11.31        14.79        15.45 
TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 
       35.08        79.10        61.87        61.38        55.86        54.05 
TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A2KC TCGA-EP-A3RK 
       13.41        13.35         0.20        13.15         0.62        11.93 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-G3-A25S 
       23.97        27.88         8.12         6.38         0.13         1.22 
TCGA-G3-A25T TCGA-G3-A3CH TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A9DB 
       51.06        25.64        11.80         2.14         3.02         2.20 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       18.38        20.71        16.37        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WQ-AB4B TCGA-ZP-A9D0 
       24.13        15.98         7.04         8.32         4.01        23.57 
TCGA-ZP-A9D2 
       24.43 

$`9Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10W 
        7.10         0.66        48.99        27.91        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       22.36        12.72         7.46        13.45         4.80         0.66 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.39         3.39         0.07        37.78        83.57       113.00 
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-A1EE TCGA-DD-A1EH TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 
        6.71        49.15        13.64        21.14        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-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       13.78         0.36        32.52        73.38        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        39.78        56.25        29.56       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 
       10.98         1.45        27.72       100.96         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       65.75        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       53.19        60.10         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       48.49        38.04         5.59         4.50        18.54        21.63 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       34.09        22.09        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
        3.78        25.08        24.00         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.56        12.69        12.16        16.37        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW2 
       79.07        72.26        59.93        56.48        58.78        49.48 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX 
       47.70        12.69        15.85        13.91         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS 
       18.74        19.99        11.74        10.98         9.96        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       14.40        32.45        19.10         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        0.39        53.79        28.27        30.74        58.49        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        22.13         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
        2.14        11.84        13.38        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO TCGA-NI-A4U2 
        4.27         9.57        16.67        12.85        10.85        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB 
        4.44        21.01         2.04        21.04        14.96        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-YA-A8S7 
       14.40         1.71         4.57         1.02         0.99        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        4.67        25.71        23.21         0.69        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            79.73            113.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            14.79             14.40 
[1] "0.1 - 79.7 (14.8)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.3"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED        38       21         0         15          1          4
  9Q LOSS WILD-TYPE     108       51         2         37          6          3
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED          1         1         2
  9Q LOSS WILD-TYPE        1         0         0
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 38               108
  STAGE II                21                51
  STAGE III                0                 2
  STAGE IIIA              15                37
  STAGE IIIB               1                 6
  STAGE IIIC               4                 3
  STAGE IV                 1                 1
  STAGE IVA                1                 0
  STAGE IVB                2                 0
[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                T0+T1  T2  T3  T4
  9Q LOSS MUTATED      41  26  19   5
  9Q LOSS WILD-TYPE   114  52  45   7
D58V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1              41               114
  T2                 26                52
  T3                 19                45
  T4                  5                 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"
D58V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    61   3
  9Q LOSS WILD-TYPE 161   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     61    3
  9Q LOSS WILD-TYPE  161    0
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              61               161
  1               3                 0
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED    66   3  22
  9Q LOSS WILD-TYPE 172   1  47
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              66               172
  M1               3                 1
  MX              22                47
[1] 3 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
  9Q LOSS MUTATED    23  68
  9Q LOSS WILD-TYPE  77 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     23   68
  9Q LOSS WILD-TYPE   77  143
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              23                77
  MALE                68               143
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  9Q LOSS MUTATED                         0                       89
  9Q LOSS WILD-TYPE                       2                      214
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  9Q LOSS MUTATED                                  2
  9Q LOSS WILD-TYPE                                4
D58V8, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      89               214
  HEPATOCHOLANGIOCARCINOMA (MIXED)               2                 4
[1] 3 2
[1] 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
  9Q LOSS MUTATED    77   5   1   6
  9Q LOSS WILD-TYPE 197   9   0  10
D58V9, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              77               197
  R1               5                 9
  R2               1                 0
  RX               6                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
  9Q LOSS MUTATED                                  0    46
  9Q LOSS WILD-TYPE                                1    95
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           5    40
  9Q LOSS WILD-TYPE                        10   105
D58V10, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         46                95
  BLACK OR AFRICAN AMERICAN                      5                10
  WHITE                                         40               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
  9Q LOSS MUTATED     1  89
  9Q LOSS WILD-TYPE   7 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   89
  9Q LOSS WILD-TYPE    7  198
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              89               198
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    29   8
  10P LOSS WILD-TYPE 171  84
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                37                255 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 84 
$`10P LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO 
        5.03        13.84         9.50         7.46        13.45         0.66 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A11C TCGA-DD-A39Y TCGA-DD-A4NI 
        0.10         0.07         0.13        21.76         5.62        26.83 
TCGA-DD-A4NQ TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADR 
       12.26        15.42        40.77        31.53        30.58        57.27 
TCGA-DD-AAVU TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 
       61.87         0.20         0.20         0.20        23.97        27.88 
TCGA-G3-A25X TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
       58.49        11.80         0.89        17.06        11.84        13.38 
TCGA-NI-A4U2 TCGA-QA-A7B7 TCGA-RG-A7D4 TCGA-WQ-A9G7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       58.88         2.04        24.13         0.99         0.69        35.05 
TCGA-ZS-A9CF 
       74.24 

$`10P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5260 
       22.36        14.60        12.72         4.80         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A113 
        0.39         3.39         4.24         3.32         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
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-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      100.96        13.48         0.53        11.41        65.75        59.18 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        63.48        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        33.83        34.09        22.09        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       28.41         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS 
        0.39        17.33         3.02         3.95         5.29         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       35.08        79.07        79.10        72.26        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
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-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20         0.20        13.15        13.41         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-A3I1 
       11.93        22.85        14.40        32.45        19.10         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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14         3.02         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       20.75         4.01         2.14        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF 
       10.85        16.37         4.44        21.01        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04         8.32         4.57         1.02         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55         4.67        25.71        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57         8.22 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             74.24             113.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.38              14.79 
[1] "0.1 - 74.2 (13.4)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED        12       13         0          9          0
  10P LOSS WILD-TYPE     134       59         2         43          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED            2        0         1         0
  10P LOSS WILD-TYPE          5        2         0         2
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  12                134
  STAGE II                 13                 59
  STAGE III                 0                  2
  STAGE IIIA                9                 43
  STAGE IIIB                0                  7
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  10P LOSS MUTATED      14  13  11   2
  10P LOSS WILD-TYPE   141  65  53  10
D59V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1               14                141
  T2                  13                 65
  T3                  11                 53
  T4                   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"
D59V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    22   1
  10P LOSS WILD-TYPE 200   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     22    1
  10P LOSS WILD-TYPE  200    2
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               22                200
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    29   0  11
  10P LOSS WILD-TYPE 209   4  58
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               29                209
  M1                0                  4
  MX               11                 58
[1] 3 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
  10P LOSS MUTATED    12  28
  10P LOSS WILD-TYPE  88 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     12   28
  10P LOSS WILD-TYPE   88  183
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               12                 88
  MALE                 28                183
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10P LOSS MUTATED                         0                       37
  10P LOSS WILD-TYPE                       2                      266
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10P LOSS MUTATED                                  3
  10P LOSS WILD-TYPE                                3
D59V8, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       37                266
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  10P LOSS MUTATED    35   1   0   4
  10P LOSS WILD-TYPE 239  13   1  12
D59V9, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               35                239
  R1                1                 13
  R2                0                  1
  RX                4                 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
  10P LOSS MUTATED                                  0    17
  10P LOSS WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    18
  10P LOSS WILD-TYPE                        10   127
D59V10, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                124
  BLACK OR AFRICAN AMERICAN                       5                 10
  WHITE                                          18                127
[1] 4 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
  10P LOSS MUTATED     1  36
  10P LOSS WILD-TYPE   7 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   36
  10P LOSS WILD-TYPE    7  251
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               36                251
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    42  18
  10Q LOSS WILD-TYPE 158  74
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                60                232 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                 74 
$`10Q LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
        0.66        37.32        10.13         2.99         5.03        13.84 
TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-A1HT 
        9.50         7.46        13.45         0.66         2.86         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A11C 
        0.10         0.07         0.13        37.78         2.60        21.76 
TCGA-DD-A1EG TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NQ TCGA-DD-AACG 
       45.11        13.64         5.62        26.83        12.26        15.42 
TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 
       14.33        40.77         5.62        33.83        34.09        31.53 
TCGA-DD-AADA TCGA-DD-AADL TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE8 TCGA-ED-A459 
       30.58        20.91        57.27         9.67        11.31        13.41 
TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A8O6 TCGA-ED-A97K TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.20         0.20         0.20         0.20        23.97        27.88 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV4 
        0.33        53.79        58.49        11.97        11.80         0.89 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-QA-A7B7 
       17.06        11.84        13.38        10.85        58.88         2.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-WQ-A9G7 TCGA-ZP-A9D1 TCGA-ZS-A9CE 
       15.52        24.13         1.71         0.99         0.69        35.05 

$`10Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S 
        7.10        10.78        10.59        48.99        27.91        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52        27.52        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BD-A3ER 
       44.42         0.26        22.36        14.60        12.72         4.80 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A113 
        0.07         0.39         3.39         4.24         0.10        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       83.57        53.33       113.00         7.33         0.46        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V 
       12.95        49.15         6.02        29.16        18.35        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       33.14        32.52        73.38        30.97        30.15        30.51 
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       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       13.15        48.49        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       21.63        22.09        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       25.08        24.00        24.13         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 
        3.95         5.29         7.10         8.28         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        47.70        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.23         0.20         0.20        13.15        13.41         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-A3I1 
       11.93        22.85        14.40        32.45        19.10         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-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-A5SL 
       25.64         5.92        19.53        19.23        14.70        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ 
       17.10         7.76        12.03         5.98         1.84        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        8.55         9.70         9.17         2.14         3.02         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.20         2.66        37.71        20.75         4.01         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        12.85        20.71        16.37         4.44        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       21.04        19.04        15.39        14.96        17.29        14.40 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B 
       15.98         7.04         8.32         4.57         1.02         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55         4.67        25.71        23.21        23.57        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        74.24         8.22 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             58.88             113.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            11.905             15.650 
[1] "0.1 - 58.9 (11.9)"  "0.0 - 113.0 (15.7)"
[1] "hr=" "1.4"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED        26       16         0         13          1
  10Q LOSS WILD-TYPE     120       56         2         39          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED            3        0         1         0
  10Q LOSS WILD-TYPE          4        2         0         2
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  26                120
  STAGE II                 16                 56
  STAGE III                 0                  2
  STAGE IIIA               13                 39
  STAGE IIIB                1                  6
  STAGE IIIC                3                  4
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED      28  17  16   5
  10Q LOSS WILD-TYPE   127  61  48   7
D60V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1               28                127
  T2                  17                 61
  T3                  16                 48
  T4                   5                  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"
D60V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    43   1
  10Q LOSS WILD-TYPE 179   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     43    1
  10Q LOSS WILD-TYPE  179    2
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               43                179
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED    51   0  15
  10Q LOSS WILD-TYPE 187   4  54
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               51                187
  M1                0                  4
  MX               15                 54
[1] 3 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
  10Q LOSS MUTATED    20  46
  10Q LOSS WILD-TYPE  80 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     20   46
  10Q LOSS WILD-TYPE   80  165
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               20                 80
  MALE                 46                165
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  10Q LOSS MUTATED                         1                       61
  10Q LOSS WILD-TYPE                       1                      242
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  10Q LOSS MUTATED                                  4
  10Q LOSS WILD-TYPE                                2
D60V8, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       61                242
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  2
[1] 3 2
[1] 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
  10Q LOSS MUTATED    55   3   0   7
  10Q LOSS WILD-TYPE 219  11   1   9
D60V9, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               55                219
  R1                3                 11
  R2                0                  1
  RX                7                  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
  10Q LOSS MUTATED                                  0    34
  10Q LOSS WILD-TYPE                                1   107
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           9    23
  10Q LOSS WILD-TYPE                         6   122
D60V10, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          34                107
  BLACK OR AFRICAN AMERICAN                       9                  6
  WHITE                                          23                122
[1] 4 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
  10Q LOSS MUTATED     1  61
  10Q LOSS WILD-TYPE   7 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   61
  10Q LOSS WILD-TYPE    7  226
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               61                226
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    32  15
  11P LOSS WILD-TYPE 168  77
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                47                245 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                 77 
$`11P LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 TCGA-BC-A217 
       10.78         0.66        37.32        46.78         5.03        13.84 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1E9 
        0.10         0.07         0.13        79.73        83.57        90.71 
TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NI 
       12.95        29.16        55.69        32.52        73.38        26.83 
TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADD TCGA-DD-AADN 
       59.18        13.15        34.09        22.09        28.41        17.33 
TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O6 
        3.02         9.86        35.08         0.20         0.20         0.20 
TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A5SJ 
        0.62        23.97         0.33        60.36         1.22        11.97 
TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K2 TCGA-KR-A7K7 
        1.84        11.80         2.14         3.02        11.84        13.38 
TCGA-MI-A75G TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-YA-A8S7 
       18.38        24.13        14.96        14.40        13.55 

$`11P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T 
        7.10        10.59        48.99        27.91        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       44.42         0.26        22.36         9.50        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A114 
        0.39         3.39         4.24         3.32         0.10        37.78 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       33.14        30.97        30.15        30.51        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        63.48        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
       53.19        60.10         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       48.49        40.77        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       18.54        21.63        33.83        31.53        30.58        29.26 
TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       13.97         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.63         9.47         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        16.37        15.65        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41         0.20         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       11.74        10.98         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-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.03         0.39        51.06        53.79        28.27        30.74 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.53        19.23        14.70        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
       12.03         5.98        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        0.89         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       17.06         4.01         2.14        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        4.27         9.57        16.67        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.39        15.52        17.29         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             90.71             113.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             13.55              14.79 
[1] "0.1 - 90.7 (13.6)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED        17       13         0         15          1
  11P LOSS WILD-TYPE     129       59         2         37          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED            2        1         1         0
  11P LOSS WILD-TYPE          5        1         0         2
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  17                129
  STAGE II                 13                 59
  STAGE III                 0                  2
  STAGE IIIA               15                 37
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      19  15  18   1
  11P LOSS WILD-TYPE   136  63  46  11
D61V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               19                136
  T2                  15                 63
  T3                  18                 46
  T4                   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"
D61V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    38   2
  11P LOSS WILD-TYPE 184   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     38    2
  11P LOSS WILD-TYPE  184    1
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               38                184
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED    43   1   9
  11P LOSS WILD-TYPE 195   3  60
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               43                195
  M1                1                  3
  MX                9                 60
[1] 3 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
  11P LOSS MUTATED    15  38
  11P LOSS WILD-TYPE  85 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     15   38
  11P LOSS WILD-TYPE   85  173
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               15                 85
  MALE                 38                173
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11P LOSS MUTATED                         1                       49
  11P LOSS WILD-TYPE                       1                      254
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11P LOSS MUTATED                                  3
  11P LOSS WILD-TYPE                                3
D61V8, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       49                254
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  11P LOSS MUTATED    47   4   0   2
  11P LOSS WILD-TYPE 227  10   1  14
D61V9, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               47                227
  R1                4                 10
  R2                0                  1
  RX                2                 14
[1] 4 2
[1] 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
  11P LOSS MUTATED                                  0    23
  11P LOSS WILD-TYPE                                1   118
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           2    28
  11P LOSS WILD-TYPE                        13   117
D61V10, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          23                118
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          28                117
[1] 4 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
  11P LOSS MUTATED     2  47
  11P LOSS WILD-TYPE   6 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   47
  11P LOSS WILD-TYPE    6  240
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               47                240
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    37  17
  11Q LOSS WILD-TYPE 163  75
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                54                238 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                 75 
$`11Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A112 
       10.78         0.66        27.91        37.32        46.78         5.03 
TCGA-BC-A217 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
       13.84         4.24         0.10         0.13        79.73        83.57 
TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A4NB 
        2.60        90.71        12.95        29.16        55.69        32.52 
TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-A73B TCGA-DD-AACB TCGA-DD-AACP TCGA-DD-AAD5 
       73.38        26.83         9.30        59.18        13.15        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADD TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADY 
       22.09        31.53        28.41         3.02         3.95         9.67 
TCGA-DD-AAE3 TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEK TCGA-ED-A7PZ TCGA-ED-A7XO 
        9.86         4.64        15.45        35.08         0.20         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KC TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
        0.20         0.62        23.97         0.33        60.36         1.22 
TCGA-G3-A5SJ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-KR-A7K7 
       11.97        11.80         9.70         2.14        11.84        13.38 
TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 
       19.04        24.13        14.96        14.40         7.04        13.55 

$`11Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        7.10        10.59        48.99        10.13        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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45         4.80         0.66         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A116 
        3.39         3.32         0.07         0.10        37.78        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA 
      113.00         7.33         0.46        21.76        51.29        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
        6.02        18.35        13.64        21.14         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-A4NF 
      107.11        13.78         0.36        30.61        33.14        30.97 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        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 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        7.56        10.98         1.45        27.72       100.96        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        65.75        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        13.97         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADR 
       24.13        20.91         0.39        17.33         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        7.10         8.28         6.67         9.86         9.63         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        8.52        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       16.37        15.65        15.65        79.07        79.10        72.26 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       54.05        49.48        47.70        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         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-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV3 TCGA-G3-AAV4 
        5.98         1.84        11.24         8.55         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC 
       17.06         4.01         2.14        24.36        12.72         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
        4.27         9.57        16.67        18.38        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-A7ME 
       21.04        15.39        15.52        17.29         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV 
        8.32         4.57         1.02         0.99         4.01         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             90.71             113.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.265             15.125 
[1] "0.1 - 90.7 (13.3)"  "0.0 - 113.0 (15.1)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED        25       11         0         17          0
  11Q LOSS WILD-TYPE     121       61         2         35          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED            2        1         1         0
  11Q LOSS WILD-TYPE          5        1         0         2
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  25                121
  STAGE II                 11                 61
  STAGE III                 0                  2
  STAGE IIIA               17                 35
  STAGE IIIB                0                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      27  13  19   1
  11Q LOSS WILD-TYPE   128  65  45  11
D62V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               27                128
  T2                  13                 65
  T3                  19                 45
  T4                   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"
D62V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    46   2
  11Q LOSS WILD-TYPE 176   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     46    2
  11Q LOSS WILD-TYPE  176    1
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               46                176
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED    50   1   9
  11Q LOSS WILD-TYPE 188   3  60
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               50                188
  M1                1                  3
  MX                9                 60
[1] 3 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
  11Q LOSS MUTATED    19  41
  11Q LOSS WILD-TYPE  81 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     19   41
  11Q LOSS WILD-TYPE   81  170
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               19                 81
  MALE                 41                170
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  11Q LOSS MUTATED                         1                       56
  11Q LOSS WILD-TYPE                       1                      247
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  11Q LOSS MUTATED                                  3
  11Q LOSS WILD-TYPE                                3
D62V8, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       56                247
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  11Q LOSS MUTATED    52   5   0   3
  11Q LOSS WILD-TYPE 222   9   1  13
D62V9, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               52                222
  R1                5                  9
  R2                0                  1
  RX                3                 13
[1] 4 2
[1] 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
  11Q LOSS MUTATED                                  0    27
  11Q LOSS WILD-TYPE                                1   114
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           3    30
  11Q LOSS WILD-TYPE                        12   115
D62V10, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          27                114
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          30                115
[1] 4 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
  11Q LOSS MUTATED     3  53
  11Q LOSS WILD-TYPE   5 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   53
  11Q LOSS WILD-TYPE    5  234
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               53                234
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  16
  12P LOSS WILD-TYPE 170  76
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                46                246 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                16                 76 
$`12P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG 
       13.84         9.50         3.32         0.13         7.33        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 
       49.15        29.16        13.64        55.69         5.62         7.66 
TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A73F 
       33.14        30.15        26.83        30.51        73.81        27.72 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADM 
       63.48        15.42        40.77        34.09        31.53         0.39 
TCGA-DD-AADO TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU 
        3.02         9.86        16.37        35.08        79.07        61.87 
TCGA-ED-A7XP TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A496 
       13.15         0.20         0.62         8.12         6.38         0.33 
TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A7M6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-MI-A75G 
        1.22        21.53        12.03         3.02         1.02        18.38 
TCGA-MI-A75I TCGA-RC-A7SK TCGA-UB-AA0U TCGA-ZP-A9D1 
       20.71        15.52         8.32         0.69 

$`12P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
        0.26        22.36        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.10         0.07         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z 
        6.71        12.95         6.02        18.35        21.14        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
       25.81        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF 
       13.78         0.36        30.61        32.52        73.38        30.97 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       59.18        55.40        12.53        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        38.04         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       21.63        33.83        22.09        30.58        29.26        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       28.41         3.78        25.08        24.00        24.13        20.91 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       17.33         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.63         9.47         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.45        15.65        15.65        79.10        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        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        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 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-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
       19.10        27.88         0.13         0.03        60.36         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 
       11.97        20.42        17.10         7.76         5.98         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       11.24         8.55        11.80         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        2.14         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MR-A8JO 
        5.92         4.27         9.57        16.67        12.85        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         7.04         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        4.01        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       24.43        12.99        45.57        35.05        74.24         8.22 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             79.07             113.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             14.63              14.50 
[1] "0.1 - 79.1 (14.6)"  "0.0 - 113.0 (14.5)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED        20       15         1          8          2
  12P LOSS WILD-TYPE     126       57         1         44          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12P LOSS MUTATED            2        2         0         0
  12P LOSS WILD-TYPE          5        0         1         2
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  20                126
  STAGE II                 15                 57
  STAGE III                 1                  1
  STAGE IIIA                8                 44
  STAGE IIIB                2                  5
  STAGE IIIC                2                  5
  STAGE IV                  2                  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                 T0+T1  T2  T3  T4
  12P LOSS MUTATED      22  18  11   1
  12P LOSS WILD-TYPE   133  60  53  11
D63V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1               22                133
  T2                  18                 60
  T3                  11                 53
  T4                   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"
D63V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    37   2
  12P LOSS WILD-TYPE 185   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     37    2
  12P LOSS WILD-TYPE  185    1
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               37                185
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    42   2   8
  12P LOSS WILD-TYPE 196   2  61
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               42                196
  M1                2                  2
  MX                8                 61
[1] 3 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
  12P LOSS MUTATED    17  35
  12P LOSS WILD-TYPE  83 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     17   35
  12P LOSS WILD-TYPE   83  176
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               17                 83
  MALE                 35                176
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12P LOSS MUTATED                         0                       51
  12P LOSS WILD-TYPE                       2                      252
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12P LOSS MUTATED                                  1
  12P LOSS WILD-TYPE                                5
D63V8, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       51                252
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    45   3   1   2
  12P LOSS WILD-TYPE 229  11   0  14
D63V9, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               45                229
  R1                3                 11
  R2                1                  0
  RX                2                 14
[1] 4 2
[1] 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
  12P LOSS MUTATED                                  0    26
  12P LOSS WILD-TYPE                                1   115
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           3    22
  12P LOSS WILD-TYPE                        12   123
D63V10, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          26                115
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          22                123
[1] 4 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
  12P LOSS MUTATED     2  48
  12P LOSS WILD-TYPE   6 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   48
  12P LOSS WILD-TYPE    6  239
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               48                239
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    16   9
  12Q LOSS WILD-TYPE 184  83
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                267 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 83 
$`12Q LOSS MUTATED`
TCGA-BC-A217 TCGA-CC-A1HT TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EH 
       13.84         3.32         0.13         7.33        45.11        49.15 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-AACE 
       13.64        55.69         5.62        26.83        73.81        63.48 
TCGA-DD-AACG TCGA-DD-AACU TCGA-DD-AAD8 TCGA-DD-AAE3 TCGA-DD-AAEK TCGA-DD-AAVU 
       15.42        40.77        31.53         9.86        35.08        61.87 
TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25Z TCGA-MI-A75G 
        0.20         0.62         8.12         0.33        21.53        18.38 
TCGA-ZP-A9D1 
        0.69 

$`12Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO 
        0.26        22.36         9.50        14.60        12.72         7.46 
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.45         4.80         0.66         0.07         2.86         0.39 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 
        3.39         4.24         0.10         0.07         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65         6.71        12.95         6.02        29.16        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       33.14        32.52        73.38        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH 
       65.75        59.18        55.40        12.53        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP 
       53.19        60.10         0.30         1.91        58.16        13.15 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
       14.33        48.49        38.04         5.59         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       18.54        21.63        33.83        34.09        22.09        30.58 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       29.26        13.97        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.13        20.91         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.86         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       11.31        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        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        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         0.20         0.20        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
       10.98         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         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-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       30.74        58.49        14.86        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27         9.57        16.67        12.85        20.71 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        4.57         1.02         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.05        74.24         8.22 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.13               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             73.81             113.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             15.42              14.40 
[1] "0.1 - 73.8 (15.4)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED        11        9         1          5          1
  12Q LOSS WILD-TYPE     135       63         1         47          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED            0        2         0         0
  12Q LOSS WILD-TYPE          7        0         1         2
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  11                135
  STAGE II                  9                 63
  STAGE III                 1                  1
  STAGE IIIA                5                 47
  STAGE IIIB                1                  6
  STAGE IIIC                0                  7
  STAGE IV                  2                  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                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED      12  10   7   1
  12Q LOSS WILD-TYPE   143  68  57  11
D64V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1               12                143
  T2                  10                 68
  T3                   7                 57
  T4                   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"
D64V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    23   0
  12Q LOSS WILD-TYPE 199   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     23    0
  12Q LOSS WILD-TYPE  199    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               23                199
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED    25   2   3
  12Q LOSS WILD-TYPE 213   2  66
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0               25                213
  M1                2                  2
  MX                3                 66
[1] 3 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
  12Q LOSS MUTATED     9  21
  12Q LOSS WILD-TYPE  91 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9   21
  12Q LOSS WILD-TYPE   91  190
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                9                 91
  MALE                 21                190
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  12Q LOSS MUTATED                         0                       29
  12Q LOSS WILD-TYPE                       2                      274
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  12Q LOSS MUTATED                                  1
  12Q LOSS WILD-TYPE                                5
D64V8, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       29                274
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    27   0   1   1
  12Q LOSS WILD-TYPE 247  14   0  15
D64V9, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               27                247
  R1                0                 14
  R2                1                  0
  RX                1                 15
[1] 4 2
[1] 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
  12Q LOSS MUTATED                                  0    17
  12Q LOSS WILD-TYPE                                1   124
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           2    11
  12Q LOSS WILD-TYPE                        13   134
D64V10, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                124
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          11                134
[1] 4 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
  12Q LOSS MUTATED     1  28
  12Q LOSS WILD-TYPE   7 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   28
  12Q LOSS WILD-TYPE    7  259
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               28                259
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    66  31
  13Q LOSS WILD-TYPE 134  61
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                97                195 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                31                 61 
$`13Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W 
       10.78        10.59        37.32        10.13        27.52         2.99 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO 
        5.03        13.84        22.36         9.50        14.60         7.46 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        0.66         0.07         2.86         0.39         3.39         0.10 
TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.07        79.73        83.57        53.33       113.00         2.60 
TCGA-DD-A11C TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Y 
       21.76        12.95         6.02        18.35        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A5 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NH TCGA-DD-A4NN 
       25.81       102.74        30.61        33.14        30.15        29.56 
TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AACG 
       73.81        12.26        27.72       100.96        13.48        15.42 
TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AAD1 
       53.19         1.91        58.16        13.15        48.49        18.54 
TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADK 
       31.53        13.97        28.41         3.78        25.08        24.13 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AAE0 TCGA-DD-AAE8 TCGA-DD-AAED 
        0.39         3.02        57.27         9.86        11.31        15.45 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-ED-A4XI TCGA-ED-A7PX TCGA-ED-A7PZ 
       15.65        35.08        79.10        12.69         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A3RK TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S 
        0.20        13.15        11.93        27.88         6.38         1.22 
TCGA-G3-A25T TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-AAV4 
       51.06        58.49        25.64        17.10        12.03         0.89 
TCGA-G3-AAV7 TCGA-GJ-A9DB TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-MI-A75G TCGA-MI-A75I 
        3.02         2.20        17.06        11.84        18.38        20.71 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
       10.85        16.37        21.01        19.04        15.39        15.52 
TCGA-UB-A7MA TCGA-UB-AA0U TCGA-WJ-A86L TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZS-A9CE 
       14.96         8.32         1.02        13.55        25.71        35.05 
TCGA-ZS-A9CG 
        8.22 

$`13Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        7.10         0.66        48.99        27.91        46.78        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        44.42         0.26 
TCGA-BC-A69I TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB 
       12.72        13.45         4.80         4.24         3.32         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
        0.13        37.78         7.33         0.46        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65         6.71        45.11 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 
       49.15        29.16        13.64        21.14        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59        20.12       107.11        13.78         0.36 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        73.38        30.97        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       56.25       108.76         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AAC9 
        9.30         7.56        10.98         1.45         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        6.41        60.10         0.30        14.33        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         5.62         4.50        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADN 
       22.09        30.58        29.26        24.00        20.91        17.33 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        3.95         5.29         7.10         8.28         6.67         9.67 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.63         9.47         9.86         8.52         4.64        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP 
       12.69        14.79        12.16        16.37        15.65        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG 
       55.86        54.05        49.48        47.70        13.41        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 
       13.91        13.35         0.23         0.20        13.41         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K 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-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        0.62         9.96        22.85        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42         7.76         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       11.80         9.70         9.17         2.14         1.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-KR-A7K8 
       37.71        20.75         4.01         2.14        13.38        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RG-A7D4 TCGA-UB-A7MB 
       58.88         4.44         2.04        21.04        24.13        17.29 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0V TCGA-WQ-A9G7 
       14.40         1.71        15.98         7.04         4.57         0.99 
TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.01         4.67        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       12.99        45.57        74.24 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            113.00             108.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.96              14.40 
[1] "0.1 - 113.0 (15.0)" "0.0 - 108.8 (14.4)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED        42       31         1         17          3
  13Q LOSS WILD-TYPE     104       41         1         35          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED            4        0         0         2
  13Q LOSS WILD-TYPE          3        2         1         0
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  42                104
  STAGE II                 31                 41
  STAGE III                 1                  1
  STAGE IIIA               17                 35
  STAGE IIIB                3                  4
  STAGE IIIC                4                  3
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 2                  0
[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                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      43  34  21   9
  13Q LOSS WILD-TYPE   112  44  43   3
D65V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               43                112
  T2                  34                 44
  T3                  21                 43
  T4                   9                  3
[1] 4 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
  13Q LOSS MUTATED    77   1
  13Q LOSS WILD-TYPE 145   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     77    1
  13Q LOSS WILD-TYPE  145    2
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               77                145
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    82   2  23
  13Q LOSS WILD-TYPE 156   2  46
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               82                156
  M1                2                  2
  MX               23                 46
[1] 3 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
  13Q LOSS MUTATED    40  67
  13Q LOSS WILD-TYPE  60 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     40   67
  13Q LOSS WILD-TYPE   60  144
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               40                 60
  MALE                 67                144
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  13Q LOSS MUTATED                         1                      102
  13Q LOSS WILD-TYPE                       1                      201
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  13Q LOSS MUTATED                                  4
  13Q LOSS WILD-TYPE                                2
D65V8, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      102                201
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  2
[1] 3 2
[1] 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
  13Q LOSS MUTATED    88   8   0   8
  13Q LOSS WILD-TYPE 186   6   1   8
D65V9, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               88                186
  R1                8                  6
  R2                0                  1
  RX                8                  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
  13Q LOSS MUTATED                                  0    52
  13Q LOSS WILD-TYPE                                1    89
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                           4    51
  13Q LOSS WILD-TYPE                        11    94
D65V10, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          52                 89
  BLACK OR AFRICAN AMERICAN                       4                 11
  WHITE                                          51                 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"
D65V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3 100
  13Q LOSS WILD-TYPE   5 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3  100
  13Q LOSS WILD-TYPE    5  187
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              100                187
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    56  28
  14Q LOSS WILD-TYPE 144  64
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                84                208 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                28                 64 
$`14Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 
       10.78         0.66        37.32        10.13        27.52         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 
       13.84         0.26        22.36         0.07         2.86         0.39 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 
        3.32         0.07         0.10         0.13        79.73        83.57 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EG TCGA-DD-A1EJ 
      113.00         2.60        21.76        90.71        45.11        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 
       13.64        55.69         5.62         7.66        13.78        30.61 
TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AA3A 
       32.52        30.15        26.83        73.81        12.26        13.48 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 
       63.48        15.42        48.49        40.77         5.62        34.09 
TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADM 
       22.09        29.26        28.41         3.78        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAEE 
       17.33         3.02        57.27         6.67         9.86        16.37 
TCGA-DD-AAEG TCGA-DD-AAVU TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       15.65        61.87        47.70        13.41         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KB TCGA-EP-A3RK TCGA-FV-A4ZP 
       13.41         0.20         0.20        10.98        11.93        60.36 
TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 
        1.22        58.49        25.64        17.10         1.84        11.80 
TCGA-G3-AAV7 TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SH 
        3.02        17.06        13.38        16.37        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D2 
       15.52        24.13        14.40         0.99         4.01        24.43 

$`14Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U 
        7.10        10.59        48.99        27.91        46.78        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-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A116 
        0.66         3.39         4.24         0.10        37.78        53.33 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         0.46        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       21.14        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF 
      102.74       107.11         0.36        33.14        73.38        30.97 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        39.78        56.25        29.56       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        27.72       100.96         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       59.18        55.40        12.53        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       60.10         0.30         1.91        58.16        13.15        14.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       38.04         5.59         4.50        18.54        21.63        33.83 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       31.53        30.58        13.97        25.08        24.00        24.13 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 
        3.95         5.29         7.10         8.28         9.67         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.47         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEK 
       12.69        14.79        12.16        15.45        15.65        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX 
       79.07        79.10        72.26        59.93        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-ED-A4XI TCGA-ED-A5KG 
       58.78        55.86        54.05        49.48        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20        13.15 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74         0.62         9.96 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         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-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 
       20.42         7.76        12.03         5.98        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         2.14         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.66        37.71        20.75         4.01         2.14        11.84 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V 
       18.38        12.85        20.71        10.85        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
       21.01         2.04        21.04        14.96        17.29         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-YA-A8S7 
       15.98         7.04         8.32         4.57         1.02        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57         0.69        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            113.00             108.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            14.895             14.500 
[1] "0.1 - 113.0 (14.9)" "0.0 - 108.8 (14.5)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED        33       27         0         22          4
  14Q LOSS WILD-TYPE     113       45         2         30          3
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED            3        1         0         1
  14Q LOSS WILD-TYPE          4        1         1         1
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  33                113
  STAGE II                 27                 45
  STAGE III                 0                  2
  STAGE IIIA               22                 30
  STAGE IIIB                4                  3
  STAGE IIIC                3                  4
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED      34  30  28   5
  14Q LOSS WILD-TYPE   121  48  36   7
D66V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1               34                121
  T2                  30                 48
  T3                  28                 36
  T4                   5                  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"
D66V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    73   1
  14Q LOSS WILD-TYPE 149   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     73    1
  14Q LOSS WILD-TYPE  149    2
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               73                149
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED    81   2  14
  14Q LOSS WILD-TYPE 157   2  55
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               81                157
  M1                2                  2
  MX               14                 55
[1] 3 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
  14Q LOSS MUTATED    27  70
  14Q LOSS WILD-TYPE  73 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     27   70
  14Q LOSS WILD-TYPE   73  141
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               27                 73
  MALE                 70                141
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  14Q LOSS MUTATED                         1                       93
  14Q LOSS WILD-TYPE                       1                      210
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  14Q LOSS MUTATED                                  3
  14Q LOSS WILD-TYPE                                3
D66V8, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       93                210
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  14Q LOSS MUTATED    84   4   0   7
  14Q LOSS WILD-TYPE 190  10   1   9
D66V9, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               84                190
  R1                4                 10
  R2                0                  1
  RX                7                  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
  14Q LOSS MUTATED                                  0    54
  14Q LOSS WILD-TYPE                                1    87
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           4    37
  14Q LOSS WILD-TYPE                        11   108
D66V10, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          54                 87
  BLACK OR AFRICAN AMERICAN                       4                 11
  WHITE                                          37                108
[1] 4 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
  14Q LOSS MUTATED     2  89
  14Q LOSS WILD-TYPE   6 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   89
  14Q LOSS WILD-TYPE    6  198
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               89                198
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    29  21
  15Q LOSS WILD-TYPE 171  71
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                50                242 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 71 
$`15Q LOSS MUTATED`
TCGA-5C-A9VH TCGA-BC-A112 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3MA 
       10.59         5.03         9.50        14.60         0.07         0.07 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EI 
       79.73        37.78        83.57         2.60        90.71         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NQ 
       29.16        13.64         5.62       102.74        33.14        12.26 
TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AADB TCGA-DD-AADK 
        9.30         0.53        15.42         1.91        29.26        24.13 
TCGA-DD-AADO TCGA-DD-AAE1 TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX 
        3.02         9.63        79.10        13.41         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-EP-A2KB TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25Z 
        0.20        13.41        10.98         0.33        60.36        21.53 
TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       17.10         1.84        11.80         0.89         2.14         3.02 
TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-WQ-A9G7 
       17.06        11.84        13.38        24.13        14.96         0.99 
TCGA-YA-A8S7 TCGA-ZS-A9CF 
       13.55        74.24 

$`15Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       22.36        12.72         7.46        13.45         4.80         0.66 
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-A3MB TCGA-CC-A3MC TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.10         0.13        53.33       113.00         7.33         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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A39V 
        6.71        12.95        45.11        49.15        18.35        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-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       107.11        13.78         0.36        30.61        32.52 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       73.38        30.97        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        10.98         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      100.96        13.48        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        63.48        12.00         6.41        53.19        60.10 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
        0.30        58.16        13.15        14.33        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       38.04         5.59         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC 
       33.83        34.09        22.09        31.53        30.58        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADM 
       28.41         3.78        25.08        24.00        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       17.33         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        6.67         9.67         9.86         9.47         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
       15.45        16.37        15.65        15.65        35.08        79.07 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       55.86        54.05        49.48        47.70        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 
       13.91        13.35         0.20         0.20        13.15         0.20 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        0.20         0.20        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        32.45        23.97 
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-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-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       58.49        14.86        22.13        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       19.23        14.70        11.97        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-GJ-A6C0 
        5.98        11.24         8.55         9.70         9.17         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.20         2.66        37.71        20.75         4.01         2.14 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       24.36        12.72         5.92         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       18.38        12.85        20.71        10.85        58.88        16.37 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH 
        4.44        21.01         2.04        21.04        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       15.52        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
        8.32         4.57         1.02         4.01         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CG 
       35.05         8.22 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            102.74             113.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            12.050             15.585 
[1] "0.1 - 102.7 (12.1)" "0.0 - 113.0 (15.6)"
[1] "hr=" "1.6"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED        19       20         1         13          1
  15Q LOSS WILD-TYPE     127       52         1         39          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED            3        0         0         0
  15Q LOSS WILD-TYPE          4        2         1         2
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  19                127
  STAGE II                 20                 52
  STAGE III                 1                  1
  STAGE IIIA               13                 39
  STAGE IIIB                1                  6
  STAGE IIIC                3                  4
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED      20  21  17   1
  15Q LOSS WILD-TYPE   135  57  47  11
D67V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1               20                135
  T2                  21                 57
  T3                  17                 47
  T4                   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"
D67V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    41   2
  15Q LOSS WILD-TYPE 181   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     41    2
  15Q LOSS WILD-TYPE  181    1
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               41                181
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED    52   0   7
  15Q LOSS WILD-TYPE 186   4  62
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               52                186
  M1                0                  4
  MX                7                 62
[1] 3 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
  15Q LOSS MUTATED    19  40
  15Q LOSS WILD-TYPE  81 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   40
  15Q LOSS WILD-TYPE   81  171
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                 81
  MALE                 40                171
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  15Q LOSS MUTATED                         0                       57
  15Q LOSS WILD-TYPE                       2                      246
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  15Q LOSS MUTATED                                  2
  15Q LOSS WILD-TYPE                                4
D67V8, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       57                246
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  15Q LOSS MUTATED    53   3   0   3
  15Q LOSS WILD-TYPE 221  11   1  13
D67V9, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               53                221
  R1                3                 11
  R2                0                  1
  RX                3                 13
[1] 4 2
[1] 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
  15Q LOSS MUTATED                                  0    28
  15Q LOSS WILD-TYPE                                1   113
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           5    26
  15Q LOSS WILD-TYPE                        10   119
D67V10, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          28                113
  BLACK OR AFRICAN AMERICAN                       5                 10
  WHITE                                          26                119
[1] 4 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
  15Q LOSS MUTATED     3  53
  15Q LOSS WILD-TYPE   5 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   53
  15Q LOSS WILD-TYPE    5  234
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               53                234
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    59  28
  16P LOSS WILD-TYPE 141  64
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                87                205 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                28                 64 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       13.84         9.50        14.60        13.45         0.66         0.07 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        2.86         0.39         3.39         0.10         0.10         0.13 
TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       37.78         0.46        12.95        49.15         6.02        29.16 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NH 
        5.62        19.76         0.36        30.61        73.38        30.15 
TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-AACC 
       26.83        29.56        73.81        12.26         9.30        55.40 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU 
       15.42         1.91        58.16        13.15        48.49        40.77 
TCGA-DD-AACW TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI 
       38.04         5.62        33.83        30.58        29.26        25.08 
TCGA-DD-AADJ TCGA-DD-AADL TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADW 
       24.00        20.91         3.02         3.95        57.27         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE8 TCGA-DD-AAED 
        9.67         9.86         9.63         4.64        11.31        15.45 
TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVZ TCGA-ED-A5KG TCGA-ED-A66X 
       35.08        59.93        61.87        55.86        15.85        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-ES-A2HS 
        0.23         0.20         0.20         0.20        10.98        22.85 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25X TCGA-G3-A25Y 
       32.45        23.97        27.88         6.38        58.49        14.86 
TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
        1.84         2.14         3.02        13.38        18.38        20.71 
TCGA-QA-A7B7 TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MF TCGA-WQ-A9G7 
        2.04        15.39        24.13        14.96         7.04         0.99 
TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZS-A9CG 
       13.55         0.69         8.22 

$`16P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A3KF TCGA-BC-A3KG TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-CC-5263 
        0.26        22.36        12.72         7.46         4.80         4.24 
TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        3.32         0.07        79.73        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK 
       66.31        19.79        75.65         6.71        45.11        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       13.64        21.14        55.69        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP 
       32.52        30.97        30.51        39.78        56.25       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D 
        0.30        80.75        78.84        10.98         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       65.75        59.18        12.53        63.48        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACX TCGA-DD-AAD0 
       53.19        60.10         0.30        14.33         5.59         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC 
       18.54        21.63        34.09        22.09        31.53        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADQ 
       28.41         3.78        24.13         0.39        17.33         5.29 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 
        7.10         8.28         9.47         9.86         8.52        12.56 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       12.69        14.79        12.16        16.37        15.65        15.65 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       79.07        79.10        72.26        61.38        56.48        58.78 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 
       54.05        49.48        47.70        13.41        12.69        13.91 
TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K 
        0.20         0.20         0.20        13.15        13.41         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-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       14.40        19.10         8.12         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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       19.23        14.70        11.97        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       12.03         5.98        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         0.89         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 
       10.85        58.88        16.37         4.44        21.01        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.52        17.29        14.40         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY 
        8.32         4.57         1.02         4.01         4.67        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.21        23.57        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF 
       74.24 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             73.81             113.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.45              15.52 
[1] "0.1 - 73.8 (13.4)"  "0.0 - 113.0 (15.5)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED        39       28         1         19          3
  16P LOSS WILD-TYPE     107       44         1         33          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED            3        1         1         1
  16P LOSS WILD-TYPE          4        1         0         1
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  39                107
  STAGE II                 28                 44
  STAGE III                 1                  1
  STAGE IIIA               19                 33
  STAGE IIIB                3                  4
  STAGE IIIC                3                  4
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  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                 T0+T1  T2  T3  T4
  16P LOSS MUTATED      42  30  23   4
  16P LOSS WILD-TYPE   113  48  41   8
D68V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1               42                113
  T2                  30                 48
  T3                  23                 41
  T4                   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"
D68V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    75   2
  16P LOSS WILD-TYPE 147   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     75    2
  16P LOSS WILD-TYPE  147    1
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               75                147
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED    83   2  14
  16P LOSS WILD-TYPE 155   2  55
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               83                155
  M1                2                  2
  MX               14                 55
[1] 3 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
  16P LOSS MUTATED    36  63
  16P LOSS WILD-TYPE  64 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     36   63
  16P LOSS WILD-TYPE   64  148
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               36                 64
  MALE                 63                148
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16P LOSS MUTATED                         0                       97
  16P LOSS WILD-TYPE                       2                      206
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16P LOSS MUTATED                                  2
  16P LOSS WILD-TYPE                                4
D68V8, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       97                206
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  16P LOSS MUTATED    87   2   0   9
  16P LOSS WILD-TYPE 187  12   1   7
D68V9, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               87                187
  R1                2                 12
  R2                0                  1
  RX                9                  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    58
  16P LOSS WILD-TYPE                                1    83
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           6    34
  16P LOSS WILD-TYPE                         9   111
D68V10, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          58                 83
  BLACK OR AFRICAN AMERICAN                       6                  9
  WHITE                                          34                111
[1] 4 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
  16P LOSS MUTATED     4  92
  16P LOSS WILD-TYPE   4 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   92
  16P LOSS WILD-TYPE    4  195
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               92                195
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    82  34
  16Q LOSS WILD-TYPE 118  58
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               116                176 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                34                 58 
$`16Q LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        0.66        46.78         2.99        44.42        13.84        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       14.60         7.46        13.45         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.39         4.24         0.10         0.13        79.73        37.78 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       53.33         2.60         0.46        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4ND 
       29.16         5.62        19.76         0.36        30.61        73.38 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73B 
       30.15        26.83        29.56        73.81        12.26         9.30 
TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL 
       55.40        12.00        15.42         6.41        53.19         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADI 
        5.62        18.54        33.83        30.58        29.26        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP 
       24.00        24.13        20.91         0.39         3.02         3.95 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE6 
       57.27         6.67         9.67         9.86         9.63         4.64 
TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       11.31        15.45        15.65        35.08        79.10        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A5KG 
       61.87        61.38        55.86        54.05        13.41        15.85 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB 
       13.35         0.23         0.20         0.20         0.20        10.98 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-G3-A25S 
       22.85        32.45        23.97        27.88         6.38         1.22 
TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M9 
       53.79        58.49        14.86        25.64        14.70         1.84 
TCGA-G3-AAUZ TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I 
       11.24         2.14         3.02        13.38        18.38        20.71 
TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA 
        4.44         2.04        19.04        15.39        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MF TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CZ 
       17.29         7.04         8.32         1.02         0.99        23.21 
TCGA-ZP-A9D1 TCGA-ZS-A9CG 
        0.69         8.22 

$`16Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       10.13        27.52        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-BC-A5W4 TCGA-BC-A69I TCGA-BD-A3ER 
       69.57         5.03         0.26         9.50        12.72         4.80 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A115 TCGA-DD-A118 
        3.39         3.32         0.10         0.07        83.57       113.00 
TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        7.33        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL 
       19.79        75.65         6.71        45.11        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        55.69        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NR 
       30.97        30.51        39.78        56.25       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        10.98         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACX 
       59.18        12.53        63.48        60.10         0.30         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC 
        4.50        21.63        34.09        22.09        31.53        13.97 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADN TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
       28.41         3.78        17.33         5.29         7.10         8.28 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
        9.47         9.86         8.52        12.56        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVX 
       12.16        16.37        15.65        79.07        72.26        56.48 
TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7PX 
       58.78        49.48        47.70        12.69        13.91         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A12J 
        0.20         0.20        13.15        13.41         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        11.74         0.62         9.96        11.93        14.40 
TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       19.10         8.12         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        0.39        51.06        28.27        30.74        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
        5.92        19.53        19.23        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        7.76        12.03         5.98         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        9.17         0.89         1.02         2.20         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 
       20.75        17.06         4.01         2.14        11.84        24.36 
TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       12.72         5.92         4.27         9.57        16.67        12.85 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SK 
       10.85        58.88        16.37        21.01        21.04        15.52 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0V TCGA-WQ-AB4B TCGA-YA-A8S7 
       14.40         1.71        15.98         4.57         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
        4.67        25.71        23.57        24.43        12.99        45.57 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             79.73             113.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             14.65              14.40 
[1] "0.1 - 79.7 (14.6)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED        52       40         1         21          3
  16Q LOSS WILD-TYPE      94       32         1         31          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED            3        1         1         1
  16Q LOSS WILD-TYPE          4        1         0         1
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  52                 94
  STAGE II                 40                 32
  STAGE III                 1                  1
  STAGE IIIA               21                 31
  STAGE IIIB                3                  4
  STAGE IIIC                3                  4
  STAGE IV                  1                  1
  STAGE IVA                 1                  0
  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                 T0+T1 T2 T3 T4
  16Q LOSS MUTATED      56 42 26  5
  16Q LOSS WILD-TYPE    99 36 38  7
D69V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1               56                 99
  T2                  42                 36
  T3                  26                 38
  T4                   5                  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"
D69V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    98   2
  16Q LOSS WILD-TYPE 124   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     98    2
  16Q LOSS WILD-TYPE  124    1
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               98                124
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED   107   2  20
  16Q LOSS WILD-TYPE 131   2  49
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0              107                131
  M1                2                  2
  MX               20                 49
[1] 3 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
  16Q LOSS MUTATED    45  84
  16Q LOSS WILD-TYPE  55 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     45   84
  16Q LOSS WILD-TYPE   55  127
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               45                 55
  MALE                 84                127
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  16Q LOSS MUTATED                         0                      126
  16Q LOSS WILD-TYPE                       2                      177
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  16Q LOSS MUTATED                                  3
  16Q LOSS WILD-TYPE                                3
D69V8, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                      126                177
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  16Q LOSS MUTATED   113   6   0  10
  16Q LOSS WILD-TYPE 161   8   1   6
D69V9, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              113                161
  R1                6                  8
  R2                0                  1
  RX               10                  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"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0    78
  16Q LOSS WILD-TYPE                                1    63
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           7    41
  16Q LOSS WILD-TYPE                         8   104
D69V10, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          78                 63
  BLACK OR AFRICAN AMERICAN                       7                  8
  WHITE                                          41                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"
D69V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     6 119
  16Q LOSS WILD-TYPE   2 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6  119
  16Q LOSS WILD-TYPE    2  168
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              119                168
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    90  49
  17P LOSS WILD-TYPE 110  43
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               139                153 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                49                 43 
$`17P LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Y 
        0.66        48.99        27.91        10.13        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
        1.12        69.57         5.03        13.84         0.26        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5260 
        9.50        14.60         7.46        13.45         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-CC-A3MC 
        0.39         3.39         4.24         3.32         0.10         0.13 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       51.29        79.40        66.31        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A3 
       29.16        18.35        13.64         5.62        25.81        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI 
       20.12       102.74        33.14        32.52        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NQ TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-AACA TCGA-DD-AACC 
       30.51        12.26         9.30         1.45        65.75        55.40 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       63.48        15.42         6.41        60.10         1.91        58.16 
TCGA-DD-AACQ TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 
       14.33         5.59         5.62        18.54        33.83        22.09 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADN 
       31.53        29.26        13.97         3.78        20.91        17.33 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE4 
       57.27         6.67         9.67         9.86         9.47         8.52 
TCGA-DD-AAE6 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP 
        4.64        14.79        12.16        16.37        35.08        79.07 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ 
       79.10        72.26        61.87        13.41         0.20         0.20 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KC TCGA-FV-A23B TCGA-FV-A2QQ 
       13.41         0.20         0.20         0.62        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       19.10        27.88         0.03         1.22        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       14.86        21.53        25.64        20.42        17.10        12.03 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 
        1.84        11.24        11.80         0.89         3.02         1.02 
TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G 
       37.71         2.14        11.84        12.72        16.67        18.38 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-RG-A7D4 
       20.71        58.88         4.44         2.04        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WJ-A86L 
       17.29        14.40         1.71        15.98         7.04         1.02 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CE 
        4.01        13.55         0.69        24.43        12.99        35.05 
TCGA-ZS-A9CF 
       74.24 

$`17P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T 
        7.10        10.78        10.59        37.32        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A216 TCGA-BC-A69I TCGA-BD-A3ER TCGA-BW-A5NO 
        2.99        25.32        44.42        12.72         4.80         0.66 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 
        0.10         0.07        79.73        37.78         0.46        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A39V TCGA-DD-A39X 
       19.79        75.65         6.71        12.95        21.14        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       19.76         7.66        70.06       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.61        73.38        30.97        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       108.76         0.30        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
        7.56        10.98        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACI TCGA-DD-AACK 
       11.41        59.18        12.53        12.00        53.19         0.30 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD2 
       13.15        48.49        40.77        38.04         4.50        21.63 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       34.09        30.58        28.41        25.08        24.00        24.13 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU 
        0.39         3.02         3.95         5.29         7.10         8.28 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAED 
        9.63         9.86        12.56        11.31        12.69        15.45 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       15.65        15.65        59.93        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       55.86        54.05        49.48        47.70        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP 
       13.91        13.35         0.23         0.20         0.20        13.15 
TCGA-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        0.20        18.74        19.99        11.74        10.98         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       11.93        22.85        14.40         8.12         6.38         0.13 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X 
        0.33        60.36         0.39        51.06        30.74        58.49 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       22.13         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV6 
        7.76         5.98         8.55         9.70         9.17         2.14 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K7 
        2.20         2.66        20.75        17.06         4.01        13.38 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MR-A8JO 
       24.36         5.92         4.27         9.57        12.85        10.85 
TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MA 
       16.37        21.01        21.04        19.04        15.39        14.96 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        8.32         4.57         0.99         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       23.57        45.57         8.22 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            113.00             108.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             14.79              13.91 
[1] "0.0 - 113.0 (14.8)" "0.1 - 108.8 (13.9)"
[1] "hr=" "1.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED        59       39         2         29          3
  17P LOSS WILD-TYPE      87       33         0         23          4
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED            7        2         1         1
  17P LOSS WILD-TYPE          0        0         0         1
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  59                 87
  STAGE II                 39                 33
  STAGE III                 2                  0
  STAGE IIIA               29                 23
  STAGE IIIB                3                  4
  STAGE IIIC                7                  0
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  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                 T0+T1 T2 T3 T4
  17P LOSS MUTATED      64 44 36  8
  17P LOSS WILD-TYPE    91 34 28  4
D70V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1               64                 91
  T2                  44                 34
  T3                  36                 28
  T4                   8                  4
[1] 4 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
  17P LOSS MUTATED   109   3
  17P LOSS WILD-TYPE 113   0
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    109    3
  17P LOSS WILD-TYPE  113    0
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              109                113
  1                3                  0
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED   119   3  31
  17P LOSS WILD-TYPE 119   1  38
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0              119                119
  M1                3                  1
  MX               31                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    50 103
  17P LOSS WILD-TYPE  50 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     50  103
  17P LOSS WILD-TYPE   50  108
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               50                 50
  MALE                103                108
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17P LOSS MUTATED                         1                      148
  17P LOSS WILD-TYPE                       1                      155
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17P LOSS MUTATED                                  4
  17P LOSS WILD-TYPE                                2
D70V8, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                      148                155
  HEPATOCHOLANGIOCARCINOMA (MIXED)                4                  2
[1] 3 2
[1] 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
  17P LOSS MUTATED   132   7   1  11
  17P LOSS WILD-TYPE 142   7   0   5
D70V9, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              132                142
  R1                7                  7
  R2                1                  0
  RX               11                  5
[1] 4 2
[1] 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
  17P LOSS MUTATED                                  0    76
  17P LOSS WILD-TYPE                                1    65
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    64
  17P LOSS WILD-TYPE                         6    81
D70V10, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          76                 65
  BLACK OR AFRICAN AMERICAN                       9                  6
  WHITE                                          64                 81
[1] 4 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
  17P LOSS MUTATED     6 140
  17P LOSS WILD-TYPE   2 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6  140
  17P LOSS WILD-TYPE    2  147
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              140                147
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    18  12
  17Q LOSS WILD-TYPE 182  80
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                262 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 80 
$`17Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A5W4 TCGA-BD-A3EP TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EJ 
       10.13         9.50        13.45        66.31        45.11        29.16 
TCGA-DD-A3A0 TCGA-DD-A4NB TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-AACH 
       25.81        32.52        30.15        26.83        30.51         6.41 
TCGA-DD-AACZ TCGA-DD-AAE0 TCGA-DD-AAEK TCGA-ED-A82E TCGA-ED-A97K TCGA-FV-A2QQ 
        5.62         9.86        35.08        13.41         0.20        23.97 
TCGA-FV-A3I0 TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-KR-A7K0 
       27.88        20.42        17.10         1.84        11.80         2.14 
TCGA-KR-A7K2 TCGA-RG-A7D4 TCGA-UB-A7MF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9D1 
       11.84        24.13         7.04         4.01        13.55         0.69 

$`17Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        46.78        27.52        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-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER 
        0.26        22.36        14.60        12.72         7.46         4.80 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         0.07         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-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        12.95        49.15         6.02        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-A4ND TCGA-DD-A4NF TCGA-DD-A4NK 
        0.36        30.61        33.14        73.38        30.97        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       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42        53.19        60.10         0.30         1.91        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX 
       13.15        14.33        48.49        40.77        38.04         5.59 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        3.02         3.95         5.29        57.27         7.10         8.28 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        6.67         9.67         9.63         9.47         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
        4.64        12.56        11.31        12.69        14.79        12.16 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ 
       15.45        16.37        15.65        15.65        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
        0.20         0.20        13.15         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-A3I1 TCGA-FV-A3R2 
       22.85        14.40        32.45        19.10         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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       14.70        11.97         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
        4.01        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         8.32         4.57         1.02         0.99 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
        4.67        25.71        23.21        23.57        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.31             113.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             13.50              14.65 
[1] "0.2 - 66.3 (13.5)"  "0.0 - 113.0 (14.6)"
[1] "hr=" "1.6"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED         8        9         0          9          2
  17Q LOSS WILD-TYPE     138       63         2         43          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  17Q LOSS MUTATED            2        1         1         0
  17Q LOSS WILD-TYPE          5        1         0         2
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   8                138
  STAGE II                  9                 63
  STAGE III                 0                  2
  STAGE IIIA                9                 43
  STAGE IIIB                2                  5
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED      11  10  12   1
  17Q LOSS WILD-TYPE   144  68  52  11
D71V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1               11                144
  T2                  10                 68
  T3                  12                 52
  T4                   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"
D71V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    21   2
  17Q LOSS WILD-TYPE 201   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     21    2
  17Q LOSS WILD-TYPE  201    1
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               21                201
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED    27   1   6
  17Q LOSS WILD-TYPE 211   3  63
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               27                211
  M1                1                  3
  MX                6                 63
[1] 3 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
  17Q LOSS MUTATED    13  21
  17Q LOSS WILD-TYPE  87 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     13   21
  17Q LOSS WILD-TYPE   87  190
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               13                 87
  MALE                 21                190
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  17Q LOSS MUTATED                         1                       30
  17Q LOSS WILD-TYPE                       1                      273
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  17Q LOSS MUTATED                                  3
  17Q LOSS WILD-TYPE                                3
D71V8, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       30                273
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  17Q LOSS MUTATED    32   1   0   1
  17Q LOSS WILD-TYPE 242  13   1  15
D71V9, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               32                242
  R1                1                 13
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  17Q LOSS MUTATED                                  0    10
  17Q LOSS WILD-TYPE                                1   131
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           2    21
  17Q LOSS WILD-TYPE                        13   124
D71V10, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          10                131
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          21                124
[1] 4 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
  17Q LOSS MUTATED     2  29
  17Q LOSS WILD-TYPE   6 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   29
  17Q LOSS WILD-TYPE    6  258
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               29                258
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    40  18
  18P LOSS WILD-TYPE 160  74
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                234 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 74 
$`18P LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 
        0.66        10.13         5.03        13.84         0.10       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39X 
        2.60         0.46        12.95        29.16        13.64        55.69 
TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-A4NI TCGA-DD-A4NO TCGA-DD-A73E 
        5.62        20.12        32.52        26.83        73.81         1.45 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
      100.96         0.53        59.18        55.40        12.53        63.48 
TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADA 
       53.19        13.15         5.62        34.09        22.09        30.58 
TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AAE2 TCGA-DD-AAEG TCGA-DD-AAEK TCGA-ED-A459 
       25.08         3.02         9.47        15.65        35.08        13.41 
TCGA-ED-A7PX TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 
        0.20        13.15        13.41         0.20        22.85        27.88 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G 
        0.33         1.22        11.80         2.14        13.38        18.38 
TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
       10.85        16.37        19.04        15.52        14.96        17.29 
TCGA-UB-A7MC TCGA-YA-A8S7 TCGA-ZS-A9CE TCGA-ZS-A9CG 
       14.40        13.55        35.05         8.22 

$`18P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57        44.42         0.26        22.36         9.50 
TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO 
       14.60        12.72         7.46        13.45         4.80         0.66 
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-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.10         0.07         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.33         7.33        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65         6.71        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
        6.02        18.35        21.14        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
       70.06        17.59       102.74       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ 
       30.61        33.14        73.38        30.97        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       39.78        56.25        29.56       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACF TCGA-DD-AACG 
       27.72        13.48        11.41        65.75        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ 
        6.41        60.10         0.30         1.91        58.16        14.33 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 
       48.49        40.77        38.04         5.59         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       21.63        33.83        31.53        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
        3.78        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.67         9.86         9.63         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       16.37        15.65        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        47.70        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 
        0.23         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-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
       11.93        14.40        32.45        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        6.38         0.13         0.03        60.36         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       11.97        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
        1.84        11.24         8.55         9.70         9.17         0.89 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        3.02         1.02         2.20         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01         2.14        11.84        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I 
        5.92         4.27         9.57        16.67        12.85        20.71 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH 
       58.88         4.44        21.01         2.04        21.04        15.39 
TCGA-RG-A7D4 TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V 
       24.13         1.71        15.98         7.04         8.32         4.57 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        1.02         0.99         4.01         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.57         0.69        24.43        12.99        45.57        74.24 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.10               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            113.00             108.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            13.740             14.745 
[1] "0.1 - 113.0 (13.7)" "0.0 - 108.8 (14.7)"
[1] "hr=" "1"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED        30       18         0          9          0
  18P LOSS WILD-TYPE     116       54         2         43          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED            2        1         0         0
  18P LOSS WILD-TYPE          5        1         1         2
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  30                116
  STAGE II                 18                 54
  STAGE III                 0                  2
  STAGE IIIA                9                 43
  STAGE IIIB                0                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  18P LOSS MUTATED      31  19  11   1
  18P LOSS WILD-TYPE   124  59  53  11
D72V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1               31                124
  T2                  19                 59
  T3                  11                 53
  T4                   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"
D72V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    46   1
  18P LOSS WILD-TYPE 176   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46    1
  18P LOSS WILD-TYPE  176    2
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               46                176
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    50   1  11
  18P LOSS WILD-TYPE 188   3  58
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               50                188
  M1                1                  3
  MX               11                 58
[1] 3 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
  18P LOSS MUTATED    24  38
  18P LOSS WILD-TYPE  76 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     24   38
  18P LOSS WILD-TYPE   76  173
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               24                 76
  MALE                 38                173
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18P LOSS MUTATED                         2                       57
  18P LOSS WILD-TYPE                       0                      246
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18P LOSS MUTATED                                  3
  18P LOSS WILD-TYPE                                3
D72V8, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       57                246
  HEPATOCHOLANGIOCARCINOMA (MIXED)                3                  3
[1] 3 2
[1] 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
  18P LOSS MUTATED    56   2   0   4
  18P LOSS WILD-TYPE 218  12   1  12
D72V9, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               56                218
  R1                2                 12
  R2                0                  1
  RX                4                 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
  18P LOSS MUTATED                                  0    29
  18P LOSS WILD-TYPE                                1   112
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                           2    31
  18P LOSS WILD-TYPE                        13   114
D72V10, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          29                112
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          31                114
[1] 4 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
  18P LOSS MUTATED     2  57
  18P LOSS WILD-TYPE   6 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   57
  18P LOSS WILD-TYPE    6  230
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               57                230
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    43  18
  18Q LOSS WILD-TYPE 157  74
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                61                231 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 74 
$`18Q LOSS MUTATED`
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       10.59         0.66        10.13         5.03        44.42        13.84 
TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EF TCGA-DD-A1EJ 
        0.10       113.00         2.60         0.46        12.95        29.16 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NI 
       13.64        55.69         5.62        30.61        32.52        26.83 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACB 
       73.81         9.30         1.45       100.96         0.53        59.18 
TCGA-DD-AACE TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD6 
       63.48        53.19        13.15         5.59         5.62        22.09 
TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AAE2 TCGA-DD-AAEG 
       30.58        25.08         3.02         6.67         9.47        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-ED-A459 TCGA-ED-A66X TCGA-ED-A7XP TCGA-ED-A82E 
       35.08        79.07        13.41        13.35        13.15        13.41 
TCGA-ED-A8O6 TCGA-ES-A2HS TCGA-FV-A3I0 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-AAV1 
        0.20        22.85        27.88         0.33         1.22        11.80 
TCGA-G3-AAV6 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A8LF TCGA-RC-A7SF 
        2.14        13.38        18.38        10.85        16.37        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZS-A9CE 
       15.52        24.13        14.40         7.04        13.55        35.05 
TCGA-ZS-A9CG 
        8.22 

$`18Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S 
        7.10        10.78        48.99        27.91        37.32        46.78 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       27.52        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
       69.57         0.26        22.36         9.50        14.60        12.72 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         0.07         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-A116 TCGA-DD-A119 
        0.13        79.73        37.78        83.57        53.33         7.33 
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-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK 
       75.65         6.71        45.11        49.15         6.02        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        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-A4NA 
       20.12       102.74       107.11        13.78         0.36        33.14 
TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC9 
       10.98         7.56        10.98        27.72        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       65.75        55.40        12.53        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS 
       60.10         0.30         1.91        58.16        14.33        48.49 
TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       40.77        38.04         4.50        18.54        21.63        33.83 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       34.09        31.53        29.26        13.97        28.41         3.78 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP 
       24.00        24.13        20.91         0.39        17.33         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 
        5.29        57.27         7.10         8.28         9.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 
        9.63         9.86         8.52         4.64        12.56        11.31 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
       12.69        14.79        12.16        15.45        16.37        15.65 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
       79.10        72.26        59.93        61.87        61.38        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI 
       58.78        55.86        54.05        49.48        47.70        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       15.85        13.91         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-ED-A97K 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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10         8.12         6.38         0.13         0.03 
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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.70         9.17         0.89         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.84        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        12.85        20.71        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MD 
        2.04        21.04        15.39        14.96        17.29         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.98         8.32         4.57         1.02         0.99         4.01 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       12.99        45.57        74.24 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.10               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            113.00             108.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.41              14.96 
[1] "0.1 - 113.0 (13.4)" "0.0 - 108.8 (15.0)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED        32       17         0         11          0
  18Q LOSS WILD-TYPE     114       55         2         41          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED            2        1         0         1
  18Q LOSS WILD-TYPE          5        1         1         1
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  32                114
  STAGE II                 17                 55
  STAGE III                 0                  2
  STAGE IIIA               11                 41
  STAGE IIIB                0                  7
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  18Q LOSS MUTATED      33  18  13   2
  18Q LOSS WILD-TYPE   122  60  51  10
D73V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               33                122
  T2                  18                 60
  T3                  13                 51
  T4                   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"
D73V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    49   1
  18Q LOSS WILD-TYPE 173   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     49    1
  18Q LOSS WILD-TYPE  173    2
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               49                173
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    52   2  12
  18Q LOSS WILD-TYPE 186   2  57
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               52                186
  M1                2                  2
  MX               12                 57
[1] 3 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
  18Q LOSS MUTATED    25  41
  18Q LOSS WILD-TYPE  75 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     25   41
  18Q LOSS WILD-TYPE   75  170
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               25                 75
  MALE                 41                170
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  18Q LOSS MUTATED                         2                       62
  18Q LOSS WILD-TYPE                       0                      241
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  18Q LOSS MUTATED                                  2
  18Q LOSS WILD-TYPE                                4
D73V8, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       62                241
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  18Q LOSS MUTATED    61   1   0   4
  18Q LOSS WILD-TYPE 213  13   1  12
D73V9, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               61                213
  R1                1                 13
  R2                0                  1
  RX                4                 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
  18Q LOSS MUTATED                                  0    30
  18Q LOSS WILD-TYPE                                1   111
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                           3    33
  18Q LOSS WILD-TYPE                        12   112
D73V10, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          30                111
  BLACK OR AFRICAN AMERICAN                       3                 12
  WHITE                                          33                112
[1] 4 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
  18Q LOSS MUTATED     3  59
  18Q LOSS WILD-TYPE   5 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   59
  18Q LOSS WILD-TYPE    5  228
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               59                228
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    22  13
  19P LOSS WILD-TYPE 178  79
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                35                257 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                 79 
$`19P LOSS MUTATED`
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
        2.99         5.03         0.26         0.07         4.24         3.32 
TCGA-DD-A11A TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NJ 
        2.60        45.11         6.02        29.16         5.62        30.51 
TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACZ 
       63.48        15.42        13.15        48.49        40.77         5.62 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AAE8 TCGA-DD-AAVR TCGA-ED-A8O6 
       13.97        28.41        20.91        11.31        72.26         0.20 
TCGA-ED-A97K TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A3CH TCGA-G3-A7M6 
        0.20         0.33        60.36         1.22        25.64        12.03 
TCGA-G3-AAV1 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-ZP-A9CV 
       11.80        15.52        24.13        14.96         4.67 

$`19P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       37.32        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       23.34         1.12        69.57        44.42        13.84        22.36 
TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER 
        9.50        14.60        12.72         7.46        13.45         4.80 
TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 TCGA-CC-A3MA 
        0.66         2.86         0.39         3.39         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-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        12.95 
TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z 
       49.15        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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       73.38        30.97        30.15        26.83        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       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       27.72       100.96        13.48         0.53        11.41        65.75 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACI 
       59.18        55.40        12.53        12.00         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACW 
       60.10         0.30         1.91        58.16        14.33        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI 
       22.09        31.53        30.58        29.26         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.00        24.13         0.39        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       12.56        12.69        14.79        12.16        15.45        16.37 
TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS 
       15.65        15.65        35.08        79.07        79.10        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        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-ED-A8O5 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.13         0.03         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       30.74        58.49        14.86        21.53        22.13         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 
        7.76         5.98         1.84        11.24         8.55         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO 
        9.57        16.67        18.38        12.85        20.71        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       58.88        16.37         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       19.04        15.39        17.29        14.40         1.71        15.98 
TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        7.04         8.32         4.57         1.02         0.99         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
       13.55        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             72.26             113.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.03              14.79 
[1] "0.1 - 72.3 (12.0)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.6"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED        20        6         0         10          1
  19P LOSS WILD-TYPE     126       66         2         42          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED            2        0         0         0
  19P LOSS WILD-TYPE          5        2         1         2
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  20                126
  STAGE II                  6                 66
  STAGE III                 0                  2
  STAGE IIIA               10                 42
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  19P LOSS MUTATED      22   6  11   3
  19P LOSS WILD-TYPE   133  72  53   9
D74V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1               22                133
  T2                   6                 72
  T3                  11                 53
  T4                   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"
D74V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    32   1
  19P LOSS WILD-TYPE 190   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     32    1
  19P LOSS WILD-TYPE  190    2
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               32                190
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    37   0   5
  19P LOSS WILD-TYPE 201   4  64
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               37                201
  M1                0                  4
  MX                5                 64
[1] 3 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
  19P LOSS MUTATED     9  33
  19P LOSS WILD-TYPE  91 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   33
  19P LOSS WILD-TYPE   91  178
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                9                 91
  MALE                 33                178
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19P LOSS MUTATED                         0                       40
  19P LOSS WILD-TYPE                       2                      263
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19P LOSS MUTATED                                  2
  19P LOSS WILD-TYPE                                4
D74V8, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       40                263
  HEPATOCHOLANGIOCARCINOMA (MIXED)                2                  4
[1] 3 2
[1] 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
  19P LOSS MUTATED    34   4   0   3
  19P LOSS WILD-TYPE 240  10   1  13
D74V9, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               34                240
  R1                4                 10
  R2                0                  1
  RX                3                 13
[1] 4 2
[1] 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
  19P LOSS MUTATED                                  0    28
  19P LOSS WILD-TYPE                                1   113
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           2    12
  19P LOSS WILD-TYPE                        13   133
D74V10, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          28                113
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                          12                133
[1] 4 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
  19P LOSS MUTATED     0  41
  19P LOSS WILD-TYPE   8 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   41
  19P LOSS WILD-TYPE    8  246
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               41                246
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    16   7
  19Q LOSS WILD-TYPE 184  85
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                269 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 85 
$`19Q LOSS MUTATED`
TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A11A 
        5.03         0.26         0.07         4.24         3.32         2.60 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A4NJ TCGA-DD-AACE TCGA-DD-AACS 
        6.02        29.16         5.62        30.51        63.48        48.49 
TCGA-DD-AACU TCGA-DD-AADL TCGA-DD-AAE8 TCGA-DD-AAVR TCGA-DD-AAVW TCGA-ED-A8O6 
       40.77        20.91        11.31        72.26        61.38         0.20 
TCGA-FV-A4ZP TCGA-G3-AAV1 TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       60.36        11.80        15.52        24.13        14.96 

$`19Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3M9 
        4.80         0.66         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-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-A1EE 
       90.71        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11        49.15        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-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-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
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       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACF 
       11.41        65.75        59.18        55.40        12.53        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ 
       58.16        13.15        14.33        38.04         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        33.83        34.09        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF 
       31.53        30.58        29.26        13.97        28.41         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       25.08        24.00        24.13         0.39        17.33         3.02 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
        3.95         5.29        57.27         7.10         8.28         6.67 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
        9.67         9.86         9.63         9.47         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
        4.64        12.56        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       59.93        61.87        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       49.48        47.70        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-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV3 
        5.98         1.84        11.24         8.55         9.70         9.17 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        0.89         2.14         3.02         1.02         2.20         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       13.38        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        18.38        12.85        20.71        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       15.39        17.29        14.40         1.71        15.98         7.04 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
        8.32         4.57         1.02         0.99         4.01        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
        4.67        25.71        23.21        23.57         0.69        24.43 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        35.05        74.24         8.22 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             72.26             113.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             14.96              14.40 
[1] "0.1 - 72.3 (15.0)"  "0.0 - 113.0 (14.4)"
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED        13        5         0          8          1
  19Q LOSS WILD-TYPE     133       67         2         44          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED            2        0         0         0
  19Q LOSS WILD-TYPE          5        2         1         2
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  13                133
  STAGE II                  5                 67
  STAGE III                 0                  2
  STAGE IIIA                8                 44
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED      14   5   9   2
  19Q LOSS WILD-TYPE   141  73  55  10
D75V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1               14                141
  T2                   5                 73
  T3                   9                 55
  T4                   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"
D75V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    24   1
  19Q LOSS WILD-TYPE 198   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     24    1
  19Q LOSS WILD-TYPE  198    2
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               24                198
  1                1                  2
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    28   0   2
  19Q LOSS WILD-TYPE 210   4  67
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               28                210
  M1                0                  4
  MX                2                 67
[1] 3 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
  19Q LOSS MUTATED     6  24
  19Q LOSS WILD-TYPE  94 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6   24
  19Q LOSS WILD-TYPE   94  187
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 94
  MALE                 24                187
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  19Q LOSS MUTATED                         0                       29
  19Q LOSS WILD-TYPE                       2                      274
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  19Q LOSS MUTATED                                  1
  19Q LOSS WILD-TYPE                                5
D75V8, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  2
  HEPATOCELLULAR CARCINOMA                       29                274
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    24   2   0   3
  19Q LOSS WILD-TYPE 250  12   1  13
D75V9, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               24                250
  R1                2                 12
  R2                0                  1
  RX                3                 13
[1] 4 2
[1] 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
  19Q LOSS MUTATED                                  0    21
  19Q LOSS WILD-TYPE                                1   120
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           2     7
  19Q LOSS WILD-TYPE                        13   138
D75V10, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                120
  BLACK OR AFRICAN AMERICAN                       2                 13
  WHITE                                           7                138
[1] 4 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
  19Q LOSS MUTATED     0  29
  19Q LOSS WILD-TYPE   8 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   29
  19Q LOSS WILD-TYPE    8  258
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               29                258
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    11   7
  20P LOSS WILD-TYPE 189  85
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                274 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 85 
$`20P LOSS MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Z TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A1EK TCGA-DD-A39Y 
       10.78         1.12         0.13        79.73        18.35         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AACS TCGA-DD-AACX 
       17.59       102.74        73.81        12.26        48.49         5.59 
TCGA-DD-AAD5 TCGA-DD-AADA TCGA-DD-AADM TCGA-ED-A8O5 TCGA-ED-A97K TCGA-MR-A8JO 
       34.09        30.58         0.39         0.20         0.20        10.85 

$`20P LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.59         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       10.13        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP 
       22.36         9.50        14.60        12.72         7.46        13.45 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        4.80         0.66         0.07         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 
        4.24         3.32         0.10         0.07         0.10        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-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65         6.71        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        13.64        21.14        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
        7.66        70.06        20.12       107.11        13.78         0.36 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        30.97        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP 
       26.83        30.51        39.78        56.25        29.56       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       10.98         1.45        27.72       100.96        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        65.75        59.18        55.40        12.53        63.48 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACU TCGA-DD-AACW 
        1.91        58.16        13.15        14.33        40.77        38.04 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        33.83        22.09 
TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
       31.53        29.26        13.97        28.41         3.78        25.08 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       24.00        24.13        20.91        17.33         3.02         3.95 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        5.29        57.27         7.10         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
        9.86         9.63         9.47         9.86         8.52         4.64 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED 
       12.56        11.31        12.69        14.79        12.16        15.45 
TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       16.37        15.65        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       72.26        59.93        61.87        61.38        56.48        58.78 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       55.86        54.05        49.48        47.70        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-ED-A8O6 TCGA-EP-A12J 
        0.20         0.20        13.15        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        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-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       58.49        14.86        21.53        22.13        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        14.70        11.97        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
        7.76        12.03         5.98         1.84        11.24         8.55 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80         9.70         9.17         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.02         2.20         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
        5.92         4.27         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71        58.88        16.37         4.44        21.01         2.04 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.04        15.39        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       17.29        14.40         1.71        15.98         7.04         8.32 
TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        4.57         1.02         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       25.71        23.21        23.57         0.69        24.43        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        35.05        74.24         8.22 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            102.74             113.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            11.555             14.650 
[1] "0.1 - 102.7 (11.6)" "0.0 - 113.0 (14.6)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED         8        6         1          4          0
  20P LOSS WILD-TYPE     138       66         1         48          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED            0        0         0         1
  20P LOSS WILD-TYPE          7        2         1         1
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   8                138
  STAGE II                  6                 66
  STAGE III                 1                  1
  STAGE IIIA                4                 48
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       8   6   5   1
  20P LOSS WILD-TYPE   147  72  59  11
D76V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                8                147
  T2                   6                 72
  T3                   5                 59
  T4                   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"
D76V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    19   0
  20P LOSS WILD-TYPE 203   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     19    0
  20P LOSS WILD-TYPE  203    3
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               19                203
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED    17   1   2
  20P LOSS WILD-TYPE 221   3  67
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0               17                221
  M1                1                  3
  MX                2                 67
[1] 3 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
  20P LOSS MUTATED     6  14
  20P LOSS WILD-TYPE  94 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6   14
  20P LOSS WILD-TYPE   94  197
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                6                 94
  MALE                 14                197
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20P LOSS MUTATED                         1                       18
  20P LOSS WILD-TYPE                       1                      285
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20P LOSS MUTATED                                  1
  20P LOSS WILD-TYPE                                5
D76V8, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                       18                285
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    19   0   0   1
  20P LOSS WILD-TYPE 255  14   1  15
D76V9, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               19                255
  R1                0                 14
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  20P LOSS MUTATED                                  0    12
  20P LOSS WILD-TYPE                                1   129
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0     8
  20P LOSS WILD-TYPE                        15   137
D76V10, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                129
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           8                137
[1] 4 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
  20P LOSS MUTATED     1  18
  20P LOSS WILD-TYPE   7 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   18
  20P LOSS WILD-TYPE    7  269
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               18                269
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     5   3
  20Q LOSS WILD-TYPE 195  89
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                284 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 89 
$`20Q LOSS MUTATED`
TCGA-DD-A113 TCGA-DD-A39Y TCGA-DD-A3A5 TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-AAD5 
       79.73         5.62       102.74        73.81        12.26        34.09 
TCGA-ED-A8O5 TCGA-MR-A8JO 
        0.20        10.85 

$`20Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
        7.10        10.78        10.59         0.66        48.99        27.91 
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-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         0.07         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-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        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-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        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-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       33.14        32.52        73.38        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NR 
       30.51        39.78        56.25        29.56       108.76         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        27.72       100.96        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59         5.62         4.50        18.54        21.63        33.83 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        25.08        24.00        24.13        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       17.33         3.02         3.95         5.29        57.27         7.10 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
        8.28         6.67         9.67         9.86         9.63         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 
        9.86         8.52         4.64        12.56        11.31        12.69 
TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH 
       14.79        12.16        15.45        16.37        15.65        15.65 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        79.07        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 
       61.38        56.48        58.78        55.86        54.05        49.48 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       47.70        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        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
        5.98         1.84        11.24         8.55        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        9.17         0.89         2.14         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD 
       11.84        13.38        24.36        12.72         5.92         4.27 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       16.37         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        0.99         4.01        13.55         4.67        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE 
       23.57         0.69        24.43        12.99        45.57        35.05 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       74.24         8.22 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.20               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            102.74             113.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            23.175             14.500 
[1] "0.2 - 102.7 (23.2)" "0.0 - 113.0 (14.5)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  20Q LOSS MUTATED         4        3         1          1          0
  20Q LOSS WILD-TYPE     142       69         1         51          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  20Q LOSS MUTATED            0        0         0         0
  20Q LOSS WILD-TYPE          7        2         1         2
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   4                142
  STAGE II                  3                 69
  STAGE III                 1                  1
  STAGE IIIA                1                 51
  STAGE IIIB                0                  7
  STAGE IIIC                0                  7
  STAGE IV                  0                  2
  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                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       4   3   2   0
  20Q LOSS WILD-TYPE   151  75  62  12
D77V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                4                151
  T2                   3                 75
  T3                   2                 62
  T4                   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"
D77V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 214   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      8    0
  20Q LOSS WILD-TYPE  214    3
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                8                214
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     8   0   1
  20Q LOSS WILD-TYPE 230   4  68
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                8                230
  M1                0                  4
  MX                1                 68
[1] 3 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
  20Q LOSS MUTATED     3   6
  20Q LOSS WILD-TYPE  97 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    6
  20Q LOSS WILD-TYPE   97  205
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                 97
  MALE                  6                205
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  20Q LOSS MUTATED                         1                        8
  20Q LOSS WILD-TYPE                       1                      295
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  20Q LOSS MUTATED                                  0
  20Q LOSS WILD-TYPE                                6
D77V8, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         1                  1
  HEPATOCELLULAR CARCINOMA                        8                295
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  6
[1] 3 2
[1] 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
  20Q LOSS MUTATED     8   0   0   1
  20Q LOSS WILD-TYPE 266  14   1  15
D77V9, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                8                266
  R1                0                 14
  R2                0                  1
  RX                1                 15
[1] 4 2
[1] 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
  20Q LOSS MUTATED                                  0     4
  20Q LOSS WILD-TYPE                                1   137
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     5
  20Q LOSS WILD-TYPE                        15   140
D77V10, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                137
  BLACK OR AFRICAN AMERICAN                       0                 15
  WHITE                                           5                140
[1] 4 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
  20Q LOSS MUTATED     1   7
  20Q LOSS WILD-TYPE   7 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    7
  20Q LOSS WILD-TYPE    7  280
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                7                280
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    52  35
  21Q LOSS WILD-TYPE 148  57
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                87                205 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                35                 57 
$`21Q LOSS MUTATED`
TCGA-5C-A9VH TCGA-BC-A10U TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A69H TCGA-BD-A3EP 
       10.59        27.52         5.03        44.42        14.60        13.45 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3MB TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 
        3.39         3.32         0.10         7.33         2.60        90.71 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       12.95        45.11        49.15        29.16        13.64        21.14 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
        5.62        25.81         7.66        13.78        30.61        32.52 
TCGA-DD-A4NI TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE 
       26.83       100.96        13.48         0.53        12.53        63.48 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ 
       15.42        53.19         0.30        13.15        40.77         5.62 
TCGA-DD-AAD2 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL 
       21.63        22.09        31.53        13.97        28.41        20.91 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE3 
       17.33         3.95         5.29        57.27         9.67         9.86 
TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAVS TCGA-DD-AAW2 TCGA-DD-AAW3 
       11.31        16.37        15.65        59.93        49.48        47.70 
TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-EP-A2KC TCGA-EP-A3JL 
       13.41         0.23         0.20         0.20         0.62         9.96 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25S 
       11.93        32.45        23.97         0.33        60.36         1.22 
TCGA-G3-A25Z TCGA-G3-A7M9 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       21.53         1.84        11.80         9.70         9.17         0.89 
TCGA-G3-AAV6 TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG 
        2.14        37.71        17.06         2.14        13.38        12.72 
TCGA-MI-A75E TCGA-MR-A8JO TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MF TCGA-WQ-AB4B 
       16.67        10.85        19.04        24.13         7.04         4.01 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D1 
       13.55         4.67         0.69 

$`21Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78         0.66        48.99        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        69.57        13.84         0.26        22.36         9.50 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
       12.72         7.46         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        0.39         4.24         0.10         0.07         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       37.78        83.57        53.33       113.00         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       51.29        79.40        66.31        19.79        75.65         6.71 
TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 
        6.02        18.35        55.69        19.76        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NA TCGA-DD-A4ND 
       20.12       102.74       107.11         0.36        33.14        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        30.15        30.51        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       108.76        12.26         0.30        80.75        78.84 
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-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACF TCGA-DD-AACH 
       11.41        65.75        59.18        55.40        12.00         6.41 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACW 
       60.10         1.91        58.16        14.33        48.49        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AADA 
        5.59         4.50        18.54        33.83        34.09        30.58 
TCGA-DD-AADB TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
       29.26         3.78        25.08        24.00        24.13         0.39 
TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
        3.02         7.10         8.28         6.67         9.86         9.63 
TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA 
        9.47         8.52         4.64        12.56        12.69        14.79 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       12.16        15.45        15.65        35.08        79.07        79.10 
TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.26        61.87        61.38        56.48        58.78        55.86 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PY 
       54.05        12.69        15.85        13.91        13.35         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        13.15        13.41         0.20         0.20         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HS TCGA-ES-A2HT 
       18.74        19.99        11.74        10.98        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-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.39        51.06        53.79        28.27        30.74        58.49 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        22.13        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-GJ-A9DB 
        5.98        11.24         8.55         3.02         1.02         2.20 
TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
        2.66        20.75         4.01        11.84        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        4.27         9.57        18.38        12.85        20.71        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SH 
       16.37         4.44        21.01         2.04        21.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        14.96        17.29        14.40         1.71        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9CY TCGA-ZP-A9CZ 
        8.32         4.57         1.02         0.99        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
       23.57        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.10               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            100.96             113.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             13.45              15.45 
[1] "0.1 - 101.0 (13.4)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1.8"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED        45       18         1         15          2
  21Q LOSS WILD-TYPE     101       54         1         37          5
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED            4        2         1         1
  21Q LOSS WILD-TYPE          3        0         0         1
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  45                101
  STAGE II                 18                 54
  STAGE III                 1                  1
  STAGE IIIA               15                 37
  STAGE IIIB                2                  5
  STAGE IIIC                4                  3
  STAGE IV                  2                  0
  STAGE IVA                 1                  0
  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                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      49  20  20   4
  21Q LOSS WILD-TYPE   106  58  44   8
D78V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               49                106
  T2                  20                 58
  T3                  20                 44
  T4                   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"
D78V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    68   2
  21Q LOSS WILD-TYPE 154   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     68    2
  21Q LOSS WILD-TYPE  154    1
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               68                154
  1                2                  1
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    76   3  15
  21Q LOSS WILD-TYPE 162   1  54
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               76                162
  M1                3                  1
  MX               15                 54
[1] 3 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
  21Q LOSS MUTATED    25  69
  21Q LOSS WILD-TYPE  75 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     25   69
  21Q LOSS WILD-TYPE   75  142
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               25                 75
  MALE                 69                142
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  21Q LOSS MUTATED                         2                       91
  21Q LOSS WILD-TYPE                       0                      212
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  21Q LOSS MUTATED                                  1
  21Q LOSS WILD-TYPE                                5
D78V8, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       91                212
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    83   3   1   3
  21Q LOSS WILD-TYPE 191  11   0  13
D78V9, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               83                191
  R1                3                 11
  R2                1                  0
  RX                3                 13
[1] 4 2
[1] 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
  21Q LOSS MUTATED                                  0    45
  21Q LOSS WILD-TYPE                                1    96
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           6    40
  21Q LOSS WILD-TYPE                         9   105
D78V10, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          45                 96
  BLACK OR AFRICAN AMERICAN                       6                  9
  WHITE                                          40                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"
D78V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2  85
  21Q LOSS WILD-TYPE   6 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   85
  21Q LOSS WILD-TYPE    6  202
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               85                202
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    32  19
  22Q LOSS WILD-TYPE 168  73
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                51                241 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                19                 73 
$`22Q LOSS MUTATED`
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A5W4 
       10.78        37.32        27.52        13.84         0.26         9.50 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-CC-5260 TCGA-CC-A1HT TCGA-DD-A113 TCGA-DD-A114 
        7.46        13.45         2.86         3.32        79.73        37.78 
TCGA-DD-A11A TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A4NB TCGA-DD-A4NI 
        2.60        55.69         5.62       107.11        32.52        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A73B TCGA-DD-AAC8 TCGA-DD-AACZ 
       30.51        73.81       108.76         9.30         0.53         5.62 
TCGA-DD-AADF TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AAE3 TCGA-DD-AAEE TCGA-ED-A459 
        3.78         5.29         7.10         9.86        16.37        13.41 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-EP-A2KB TCGA-FV-A4ZP 
        0.23         0.20         0.20        13.15        10.98        60.36 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A5SI TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-K7-A5RG 
        1.22        51.06        14.70         1.84         9.17        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-QA-A7B7 
       11.84        13.38        18.38        20.71        10.85         2.04 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-WQ-AB4B 
       24.13        14.40         4.01 

$`22Q LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R 
        7.10        10.59         0.66        48.99        27.91        10.13 
TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
       46.78        27.52         2.99        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A69I 
       69.57         5.03        44.42        22.36        14.60        12.72 
TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.80         0.66         0.07         0.39         3.39         4.24 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.07         0.10         0.13        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-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65         6.71        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-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        19.76        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-A4ND TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       73.38        30.97        30.15        39.78        56.25        29.56 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73C 
       12.26         0.30        80.75        78.84        10.98         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 
       10.98         1.45        27.72       100.96        13.48        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       65.75        59.18        55.40        12.53        63.48        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        60.10         0.30         1.91 
TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW 
       58.16        13.15        14.33        48.49        40.77        38.04 
TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.59         4.50        18.54        21.63        33.83        34.09 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        31.53        30.58        29.26        13.97        28.41 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       25.08        24.00        24.13        20.91         0.39        17.33 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
        3.02         3.95        57.27         8.28         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE7 
        9.86         9.63         9.47         8.52         4.64        12.56 
TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
       11.31        12.69        14.79        12.16        15.45        15.65 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       15.65        35.08        79.07        79.10        72.26        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       61.87        61.38        56.48        58.78        55.86        54.05 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       49.48        47.70        12.69        15.85        13.91        13.35 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20         0.20        13.41         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-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
        8.12         6.38         0.13         0.03         0.33         0.39 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       53.79        28.27        30.74        58.49        14.86        21.53 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       22.13        25.64         5.92        19.53        19.23        11.97 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ 
       20.42        17.10         7.76        12.03         5.98        11.24 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
        8.55        11.80         9.70         0.89         2.14         3.02 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 
        1.02         2.20         2.66        37.71        20.75         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        2.14        24.36        12.72         5.92         4.27         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        12.85        58.88        16.37         4.44        21.01 
TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
       21.04        19.04        15.39        15.52        14.96        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L 
        1.71        15.98         7.04         8.32         4.57         1.02 
TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
        0.99        13.55         4.67        25.71        23.21        23.57 
TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        24.43        12.99        45.57        35.05        74.24 
TCGA-ZS-A9CG 
        8.22 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.20               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            108.76             113.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             11.84              15.45 
[1] "0.2 - 108.8 (11.8)" "0.0 - 113.0 (15.4)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED        22       19         0         10          1
  22Q LOSS WILD-TYPE     124       53         2         42          6
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED            2        1         0         0
  22Q LOSS WILD-TYPE          5        1         1         2
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  22                124
  STAGE II                 19                 53
  STAGE III                 0                  2
  STAGE IIIA               10                 42
  STAGE IIIB                1                  6
  STAGE IIIC                2                  5
  STAGE IV                  1                  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                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED      22  22  11   3
  22Q LOSS WILD-TYPE   133  56  53   9
D79V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1               22                133
  T2                  22                 56
  T3                  11                 53
  T4                   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"
D79V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    39   0
  22Q LOSS WILD-TYPE 183   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     39    0
  22Q LOSS WILD-TYPE  183    3
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               39                183
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    46   1  11
  22Q LOSS WILD-TYPE 192   3  58
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               46                192
  M1                1                  3
  MX               11                 58
[1] 3 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
  22Q LOSS MUTATED    23  35
  22Q LOSS WILD-TYPE  77 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     23   35
  22Q LOSS WILD-TYPE   77  176
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               23                 77
  MALE                 35                176
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  22Q LOSS MUTATED                         2                       55
  22Q LOSS WILD-TYPE                       0                      248
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  22Q LOSS MUTATED                                  1
  22Q LOSS WILD-TYPE                                5
D79V8, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         2                  0
  HEPATOCELLULAR CARCINOMA                       55                248
  HEPATOCHOLANGIOCARCINOMA (MIXED)                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    46   5   0   6
  22Q LOSS WILD-TYPE 228   9   1  10
D79V9, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               46                228
  R1                5                  9
  R2                0                  1
  RX                6                 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
  22Q LOSS MUTATED                                  0    21
  22Q LOSS WILD-TYPE                                1   120
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           7    30
  22Q LOSS WILD-TYPE                         8   115
D79V10, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          21                120
  BLACK OR AFRICAN AMERICAN                       7                  8
  WHITE                                          30                115
[1] 4 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
  22Q LOSS MUTATED     2  51
  22Q LOSS WILD-TYPE   6 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   51
  22Q LOSS WILD-TYPE    6  236
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               51                236
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    41  14
  XQ LOSS WILD-TYPE 159  78
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               237 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                78 
$`XQ LOSS MUTATED`
TCGA-5C-AAPD TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A5W4 TCGA-BC-A69I 
        0.66        10.13         5.03        13.84         9.50        12.72 
TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11B TCGA-DD-A4NA 
        0.07        37.78        83.57        53.33         0.46        33.14 
TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACU TCGA-DD-AACW 
       73.81         9.30        15.42        53.19        40.77        38.04 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADC TCGA-DD-AADL TCGA-DD-AADP TCGA-DD-AADW 
       34.09        31.53        13.97        20.91         3.95         6.67 
TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE8 TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP 
        9.67         9.47        11.31        15.45        15.65        79.07 
TCGA-DD-AAVU TCGA-ED-A459 TCGA-ED-A7PX TCGA-ED-A7PZ TCGA-ED-A97K TCGA-FV-A2QR 
       61.87        13.41         0.20         0.20         0.20        19.10 
TCGA-FV-A3I0 TCGA-G3-A6UC TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV7 
       27.88         7.76         8.55         9.70         0.89         3.02 
TCGA-HP-A5N0 TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-MI-A75E TCGA-QA-A7B7 TCGA-RC-A7SH 
       37.71        13.38         5.92        16.67         2.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MC TCGA-UB-A7MF TCGA-ZP-A9CV TCGA-ZP-A9D2 TCGA-ZS-A9CE 
       15.52        14.40         7.04         4.67        24.43        35.05 
TCGA-ZS-A9CF 
       74.24 

$`XQ LOSS WILD-TYPE`
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q 
        7.10        10.78        10.59        48.99        27.91        37.32 
TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       46.78        27.52        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        69.57        44.42         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 
        7.46        13.45         4.80         0.66         0.07         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        0.39         3.39         4.24         3.32         0.10         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
        0.13        79.73       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-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
        6.71        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-A4NB TCGA-DD-A4ND 
      107.11        13.78         0.36        30.61        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        30.15        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         7.56        10.98         1.45        27.72       100.96 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        65.75        59.18        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       12.53        63.48        12.00         6.41        60.10         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACX 
        1.91        58.16        13.15        14.33        48.49         5.59 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        33.83        22.09 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ 
       30.58        29.26        28.41         3.78        25.08        24.00 
TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       24.13         0.39        17.33         3.02         5.29        57.27 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 
        7.10         8.28         9.86         9.63         9.86         8.52 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAEE 
        4.64        12.56        12.69        14.79        12.16        16.37 
TCGA-DD-AAEG TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       15.65        35.08        79.10        72.26        59.93        61.38 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        58.78        55.86        54.05        49.48        47.70 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A12J 
        0.20        13.15        13.41         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-A2QQ TCGA-FV-A3I1 TCGA-FV-A3R2 
       22.85        14.40        32.45        23.97         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-A25X TCGA-G3-A25Y 
       51.06        53.79        28.27        30.74        58.49        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-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 
       14.70        11.97        20.42        17.10        12.03         5.98 
TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV3 TCGA-G3-AAV6 TCGA-GJ-A6C0 
        1.84        11.24        11.80         9.17         2.14         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.20         2.66        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75G 
       11.84        24.36        12.72         4.27         9.57        18.38 
TCGA-MI-A75H TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       12.85        20.71        10.85        58.88        16.37         4.44 
TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       21.01        21.04        19.04        24.13        14.96        17.29 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 
        1.71        15.98         8.32         4.57         1.02         0.99 
TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 
        4.01        13.55        25.71        23.21        23.57         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CG 
       12.99        45.57         8.22 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            83.57            113.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.84             14.79 
[1] "0.1 - 83.6 (13.8)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED        25       17         0          8          1          2
  XQ LOSS WILD-TYPE     121       55         2         44          6          5
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED          1         0         0
  XQ LOSS WILD-TYPE        1         1         2
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 25               121
  STAGE II                17                55
  STAGE III                0                 2
  STAGE IIIA               8                44
  STAGE IIIB               1                 6
  STAGE IIIC               2                 5
  STAGE IV                 1                 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                T0+T1  T2  T3  T4
  XQ LOSS MUTATED      26  20  11   1
  XQ LOSS WILD-TYPE   129  58  53  11
D80V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              26               129
  T2                 20                58
  T3                 11                53
  T4                  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"
D80V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    41   1
  XQ LOSS WILD-TYPE 181   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     41    1
  XQ LOSS WILD-TYPE  181    2
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              41               181
  1               1                 2
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    48   1  10
  XQ LOSS WILD-TYPE 190   3  59
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              48               190
  M1               1                 3
  MX              10                59
[1] 3 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
  XQ LOSS MUTATED    13  46
  XQ LOSS WILD-TYPE  87 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   46
  XQ LOSS WILD-TYPE   87  165
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              13                87
  MALE                46               165
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  XQ LOSS MUTATED                         0                       56
  XQ LOSS WILD-TYPE                       2                      247
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  XQ LOSS MUTATED                                  3
  XQ LOSS WILD-TYPE                                3
D80V8, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 2
  HEPATOCELLULAR CARCINOMA                      56               247
  HEPATOCHOLANGIOCARCINOMA (MIXED)               3                 3
[1] 3 2
[1] 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
  XQ LOSS MUTATED    54   1   0   4
  XQ LOSS WILD-TYPE 220  13   1  12
D80V9, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              54               220
  R1               1                13
  R2               0                 1
  RX               4                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
  XQ LOSS MUTATED                                  0    31
  XQ LOSS WILD-TYPE                                1   110
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           2    25
  XQ LOSS WILD-TYPE                        13   120
D80V10, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         31               110
  BLACK OR AFRICAN AMERICAN                      2                13
  WHITE                                         25               120
[1] 4 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
  XQ LOSS MUTATED     2  52
  XQ LOSS WILD-TYPE   6 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   52
  XQ LOSS WILD-TYPE    6  235
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              52               235
[1] 2 2
[1] FALSE
